Bio-Formats Documentation
The following documentation is split into four parts. About Bio-Formats explains the goal of the software, discusses how it processes metadata, and provides other useful information such as version history and how to report bugs. User Information focuses on how to use Bio-Formats as a plugin for ImageJ and Fiji, and also gives details of other software packages which can use Bio-Formats to read and write microscopy formats. Developer Documentation covers more indepth information on using Bio-Formats as a Java library and how to interface from non-Java codes. Finally, Formats is a guide to all the file formats currently supported by Bio-Formats.
Bio-Formats 7.3.0 requires Java 8 or above and uses the June 2016 release of the OME Model.
Bio-Formats is a community project and we welcome your input. You can find guidance on Reporting a bug and contact us via the forums. Further information about how the OME team works and how you can contribute to our projects is in the Contributing Developer Documentation.
About Bio-Formats
Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats.
The primary goal of Bio-Formats is to facilitate the exchange of microscopy data between different software packages and organizations. It achieves this by converting proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format.
We believe the standardization of microscopy metadata to a common structure is of vital importance to the community. You may find LOCI’s article on open source software in science of interest.
License, copyright, and citation
Licensing information for Bio-Formats is described on the OME licensing page. Unless otherwise noted, the current copyright statement is:
- Copyright (C) 2005 - 2018 Open Microscopy Environment:
Board of Regents of the University of Wisconsin-Madison
Glencoe Software, Inc.
University of Dundee
Bio-Formats can be cited in publications as follows:
Melissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology 189(5), 777-782. doi: 10.1083/jcb.201004104
Additional citation information can be found on the main OME citation page.
Help
There is a guide for reporting bugs here.
For help relating to opening images in ImageJ or FIJI or when using the command line tools, refer to the users documentation. You can also find tips on common issues with specific formats on the pages linked from the supported formats table.
Please contact us if you have any questions or problems with Bio-Formats not addressed by referring to the documentation.
Other places where questions are commonly asked and/or bugs are reported include:
ome-devel mailing list (searchable using google with ‘site:lists.openmicroscopy.org.uk’)
ome-users mailing list (searchable using google with ‘site:lists.openmicroscopy.org.uk’)
Bio-Formats versions
Since Bio-Formats 5.1.3, Bio-Formats is decoupled from OMERO with its own release schedule rather than being updated whenever a new version of OMERO is released. This change allows for more frequent releases to get fixes out to the community faster. See the version history for a list of changes in each release.
Versioning policy
The following set of rules describe the current versioning policy using RFC 2119.
The Bio-Formats API follows strict semantic versioning since Bio-Formats 5.4.0 i.e.:
The version number MUST take the form X.Y.Z where X, Y, and Z are non-negative integers, and MUST NOT contain leading zeroes. X is the major version, Y is the minor version and Z is the patch version.
The patch version Z MUST be incremented if only backwards-compatible bug fixes are introduced. A bug fix is defined as an internal change that fixes incorrect behavior.
The minor version Y MUST be incremented if new, backwards-compatible functionality is introduced to the public API.
The major version X MUST be incremented when backwards-incompatible changes are introduced to the public API.
Either the minor version or the major version MUST be incremented if the version of a non-OME/external dependency is updated.
Serialization functionality was implemented as a ReaderWrapper called Memoizer in Bio-Formats 5.0.0 and is exposed to the community via a public API. Since Bio-Format 5.4.0,:
The minor version Y MUST be incremented if changes are introduced that are not backwards compatible with regard to serialization.
Serialized memo files written with a previous minor version MAY not be readable by later versions and MAY need to be rewritten.
Consumers with code relying on Bio-Formats caching stability SHOULD not upgrade the minor version of Bio-Formats version for now.
For format reader fixes and additions, the policy should read as follows:
The minor version Y MUST be incremented when a new file format reader is introduced.
The minor version Y MUST be incremented when a non backwards-compatible format bug fix is introduced, e.g. a fix that modifies the core metadata of existing files.
The patch version Z MUST be incremented if only backwards-compatible format bug fixes are introduced.
See this GitHub issue for further details.
Why Java?
From a practical perspective, Bio-Formats is written in Java because it is cross-platform and widely used, with a vast array of libraries for handling common programming tasks. Java is one of the easiest languages from which to deploy cross-platform software. In contrast to C++, which has a large number of complex platform issues to consider, and Python, which leans heavily on C and C++ for many of its components (e.g., NumPy and SciPy), Java code is compiled one time into platform-independent byte code, which can be deployed as is to all supported platforms. And despite this enormous flexibility, Java manages to provide time performance nearly equal to C++, often better in the case of I/O operations (see further discussion on the comparative speed of Java on the LOCI site).
There are also historical reasons associated with the fact that the project grew out of work on the VisAD Java component library. You can read more about the origins of Bio-Formats on the LOCI Bio-Formats homepage.
Bio-Formats metadata processing
Pixels in microscopy are almost always very straightforward, stored on evenly spaced rectangular grids. It is the metadata (details about the acquisition, experiment, user, and other information) that can be complex. Using the OME data model enables applications to support a single metadata format, rather than the multitude of proprietary formats available today.
Every file format has a distinct set of metadata, stored differently. Bio-Formats processes and converts each format’s metadata structures into a standard form called the OME data model, according to the OME-XML specification. We have defined an open exchange format called OME-TIFF that stores its metadata as OME-XML. Any software package that supports OME-TIFF is also compatible with the dozens of formats listed on the Bio-Formats page, because Bio-Formats can convert your files to OME-TIFF format.
To facilitate support of OME-XML, we have created a library in Java for reading and writing OME-XML metadata.
There are three types of metadata in Bio-Formats, which we call core metadata, original metadata, and OME metadata.
Core metadata only includes things necessary to understand the basic structure of the pixels: image resolution; number of focal planes, time points, channels, and other dimensional axes; byte order; dimension order; color arrangement (RGB, indexed color or separate channels); and thumbnail resolution.
Original metadata is information specific to a particular file format. These fields are key/value pairs in the original format, with no guarantee of cross-format naming consistency or compatibility. Nomenclature often differs between formats, as each vendor is free to use their own terminology.
OME metadata is information from #1 and #2 converted by Bio-Formats into the OME data model. Performing this conversion is the primary purpose of Bio-Formats. Bio-Formats uses its ability to convert proprietary metadata into OME-XML as part of its integration with the OME and OMERO servers— essentially, they are able to populate their databases in a structured way because Bio-Formats sorts the metadata into the proper places. This conversion is nowhere near complete or bug free, but we are constantly working to improve it. We would greatly appreciate any and all input from users concerning missing or improperly converted metadata fields.
User Information
Using Bio-Formats with ImageJ and Fiji
The following sections explain the features of Bio-Formats and how to use it within ImageJ and Fiji:
ImageJ overview
ImageJ is an image processing and analysis application written in Java, widely used in the life sciences fields, with an extensible plugin infrastructure. You can use Bio-Formats as a plugin for ImageJ to read and write images in the formats it supports.
Installation
Download bioformats_package.jar and drop it into your ImageJ/plugins folder. Next time you run ImageJ, a new Bio-Formats submenu with several plugins will appear in the Plugins menu, including the Bio-Formats Importer and Bio-Formats Exporter.
Usage
The Bio-Formats Importer plugin can display image stacks in several ways:
In a standard ImageJ window (including as a hyperstack)
With Joachim Walter’s Image5D plugin (if installed)
With Rainer Heintzmann’s View5D plugin (if installed)
ImageJ v1.37 and later automatically (via HandleExtraFileTypes) calls
the Bio-Formats logic, if installed, as needed when a file is opened
within ImageJ, i.e. when using instead of
explicitly choosing
from the
menu.
For a more detailed description of each plugin, see the Bio-Formats page of the ImageJ wiki.
Upgrading
To upgrade, just overwrite the old bioformats_package.jar with the latest one.
You can also upgrade the Bio-Formats plugin directly from ImageJ. Select from the ImageJ menu, then select which release you would like to use. You will then need to restart ImageJ to complete the upgrade process.
Macros and plugins
Bio-Formats is fully scriptable in a macro, and callable from a plugin. To use in a macro, use the Macro Recorder to record a call to the Bio-Formats Importer with the desired options. You can also perform more targeted metadata queries using the Bio-Formats macro extensions.
Here are some example ImageJ macros and plugins that use Bio-Formats to get you started:
basicMetadata.txt - A macro that uses the Bio-Formats macro extensions to print the chosen file’s basic dimensional parameters to the Log.
planeTimings.txt - A macro that uses the Bio-Formats macro extensions to print the chosen file’s plane timings to the Log.
recursiveTiffConvert.txt - A macro for recursively converting files to TIFF using Bio-Formats.
bfOpenAsHyperstack.txt - This macro from Wayne Rasband opens a file as a hyperstack using only the Bio-Formats macro extensions (without calling the Bio-Formats Importer plugin).
zvi2HyperStack.txt - This macro from Sebastien Huart reads in a ZVI file using Bio-Formats, synthesizes the LUT using emission wavelength metadata, and displays the result as a hyperstack.
dvSplitTimePoints.txt - This macro from Sebastien Huart splits timepoints/channels on all DV files in a folder.
batchTiffConvert.txt - This macro converts all files in a directory to TIFF using the Bio-Formats macro extensions.
Read_Image - A simple plugin that demonstrates how to use Bio-Formats to read files into ImageJ.
Mass_Importer - A simple plugin that demonstrates how to open all image files in a directory using Bio-Formats, grouping files with similar names to avoiding opening the same dataset more than once.
Usage tips
“How do I make the options window go away?” is a common question. There are a few ways to do this:
To disable the options window only for files in a specific format, select , then pick the format from the list and make sure the “Windowless” option is checked.
To avoid the options window entirely, use the menu item to import files.
Open files by calling the Bio-Formats importer plugin from a macro.
A common cause of problems having multiple copies of
bioformats_package.jarin you ImageJ plugins folder, or a copy ofbioformats_package.jarand a copy offormats-gpl.jar. It is often difficult to determine for sure that this is the problem - the only error message that pretty much guarantees it is aNoSuchMethodException. If you downloaded the latest version and whatever error message or odd behavior you are seeing has been reported as fixed, it is worth removing all copies ofbioformats_package.jar(or any other Bio-Formats jars) and download a fresh version.The Bio-Formats Exporter plugin’s file chooser will automatically add the first listed file extension to the file name if a specific file format is selected in the
Files of Typebox (e.g..ome.tiffor OME-TIFF). This can prevent BigTIFF and OME BigTIFF files from being created, as the.btfor.ome.btffile extension will be overwritten. To ensure that the desired extension is used, select or in theFiles of typebox, as an extension will not be automatically added in those cases.Saving an open image using Bio-Formats must be done via or the corresponding macro code. and do not use Bio-Formats. In particular, using to save a TIFF will result in an ImageJ-specific TIFF being written. While Bio-Formats can read ImageJ TIFFs, other software may not; see TIFF (Tagged Image File Format) for additional information.
Fiji overview
Fiji is an image processing package. It can be described as a distribution of ImageJ together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
Fiji works with Bio-Formats out of the box, because it comes bundled with the Bio-Formats ImageJ plugins.
The Fiji documentation has been combined with the ImageJ wiki; for further details on Bio-Formats in Fiji, see the Bio-Formats ImageJ page.
Upgrading
Upgrading Bio-Formats within Fiji is as simple as invoking the “Update Fiji” command from the Help menu. By default, Fiji even automatically checks for updates every time it is launched, so you will always be notified when new versions of Bio-Formats (or any other bundled plugin) are available.
Manual upgrade
Manually updating your Fiji installation should not be necessary but if you need to do so, the steps are detailed below. Note that although we assume you will be upgrading to the latest release version, all previous versions of Bio-Formats are available from http://downloads.openmicroscopy.org/bio-formats/ so you can revert to an earlier version using this guide if you need to.
Fiji must first be fully updated
Close Fiji
Open the Fiji installation folder (typically named ‘Fiji.app’)
Remove bio-formats_plugins.jar from the ‘plugins’ sub-folder
Remove all of the .jars from the ‘jars/bio-formats’ sub-folder:
ome-jai.jar
formats-gpl.jar
ome-common.jar
turbojpeg.jar
ome-xml.jar
formats-bsd.jar
ome-poi.jar
specification.jar
mdbtools-java.jar
metakit.jar
formats-api.jar
Download bio-formats_plugins.jar (from the latest release http://downloads.openmicroscopy.org/bio-formats/) and place it in the ‘plugins’ sub-folder
Download each of the following (from the latest release http://downloads.openmicroscopy.org/bio-formats/) and place them in the ‘jars/bio-formats’ sub-folder:
ome-jai.jar
formats-gpl.jar
ome-common.jar
turbojpeg.jar
ome-xml.jar
formats-bsd.jar
ome-poi.jar
specification.jar
mdbtools-java.jar
metakit.jar
formats-api.jar
To Check Version of Bio-Formats Check that the version of Bio-Formats matches the freshly downloaded version.
Start Fiji and open any Image file using
Note
It is vital to perform all of those steps in order; omitting even one will cause a problem. In particular, make sure that the old files are fully removed; it is not sufficient to add the new files to any sub-directory without removing the old files first.
Bio-Formats features in ImageJ and Fiji
When you select Bio-Formats under the Plugin menu, you will see the following features:
The Bio-Formats Importer is a plugin for loading images into ImageJ or Fiji. It can read over 140 proprietary life sciences formats and standardizes their acquisition metadata into the common OME data model. It will also extract and set basic metadata values such as spatial calibration if they are available in the file.
The Bio-Formats Exporter is a plugin for exporting data to disk. It can save to the open OME-TIFF file format, as well as several movie formats (e.g. QuickTime, AVI) and graphics formats (e.g. PNG, JPEG).
The Bio-Formats Remote Importer is a plugin for importing data from a remote URL. It is likely to be less robust than working with files on disk, so we recommend downloading your data to disk and using the regular Bio-Formats Importer whenever possible.
The Bio-Formats Windowless Importer is a version of the Bio-Formats Importer plugin that runs with the last used settings to avoid any additional dialogs beyond the file chooser. If you always use the same import settings, you may wish to use the windowless importer to save time (Learn more here).
The Bio-Formats Macro Extensions plugin prints out the set of commands that can be used to create macro extensions. The commands and the instructions for using them are printed to the ImageJ log window.
The Stack Slicer plugin is a helper plugin used by the Bio-Formats Importer. It can also be used to split a stack across channels, focal planes or time points.
The Bio-Formats Plugins Configuration dialog is a useful way to configure the behavior of the Bio-Formats plugin or each file format. The general tab allows you to configure features of the Bio-Formats plugin such as the display of the slice label (see Bio-Formats plugin configuration options). The Formats tab lists supported file formats and toggles each format on or off, which is useful if your file is detected as the wrong format. It also toggles whether each format bypasses the importer options dialog through the “Windowless” checkbox. You can also configure any specific option for each format (see Additional reader and writer options). The Libraries tab provides a list of available helper libraries used by Bio-Formats.
The Bio-Formats Plugins Shortcut Window opens a small window with a quick-launch button for each plugin. Dragging and dropping files onto the shortcut window opens them quickly using the Bio-Formats Importer plugin.
The Update Bio-Formats Plugins command will check for updates to the plugins. We recommend you update to the newest Trunk build as soon as you think you may have discovered a bug.
Installing Bio-Formats in ImageJ
Note
Since FIJI is essentially ImageJ with plugins like Bio-Formats already built in, people who install Fiji can skip this section.
If you are also using the OMERO plugin for ImageJ, you may find the set-up guide on the new user help site useful for getting you started with both plugins at the same time.
Once you download and install ImageJ, you can install the Bio-Formats plugin by going to the Bio-Formats download page and saving the bioformats_package.jar to the Plugins directory within ImageJ.
Plugin Directory for ImageJ: Where in ImageJ’s file structure you should place the file once you downloaded it.
You may have to quit and restart ImageJ. Once you restart it, you will find Bio-Formats in the Bio-Formats option under the Plugins menu:
You are now ready to start using Bio-Formats.
Using Bio-Formats to load images into ImageJ
This section will explain how to use Bio-Formats to import files into ImageJ and how to use the settings on the Bio-Formats Import Options screen.
Opening files
There are three ways you can open a file using Bio-Formats:
Select the Bio-Formats Importer under the Bio-Formats plugins menu.
Drag and drop it onto the Bio-Formats Plugins Shortcut window.
Use the Open command in the File menu.
Unless you used the Bio-Formats Plugins Configuration dialog to open the file type windowlessly, you know you used Bio-Formats to open a file when you see a screen like this:
If you used the File > Open command and did not see the Bio-Formats Import Options screen, ImageJ/Fiji probably used another plugin instead of Bio-Formats to open the file. If this happens and you want to open a file using Bio-Formats, use one of the other two methods instead.
Opening files windowlessly
When you open a file with Bio-Formats, the Import Options Screen automatically recalls the settings you last used to open a file with that specific format (e.g. JPG, TIF, LSM, etc.). If you always choose the same options whenever you open files in a specific file format, you can save yourself time by bypassing the Bio-Formats Import Options screen. You can accomplish this two ways:
1. You can select the Bio-Formats Windowless Importer, located in the Bio-Formats menu under ImageJ’s Plugin menu. When you select this option, Bio-Formats will import the file using the same settings you used the last time you imported a file with the same format.
2. If you invariably use the same settings when you open files in a specific format, you can always bypass the Import Options Screen by changing the settings in the Bio-Formats Plugins Configuration option, which is also located in the Bio-Formats menu under ImageJ’s Plugin menu.
Once you select this option, select the file format you are interested in from the list on the left side of the screen. Check both the Enabled and Windowless boxes. Once you do this, whenever you open a file using the Bio-Formats Windowless Importer,the Bio-Formats Importer, or the drag-and-drop method described in the previous section, the file will always open the same way using the last setting used.
Please note that if you want to change any of the import settings once you enable this windowless option, you will have to go back to the Bio-Formats Plugins Configuration screen, unselect the windowless option, open a file using the regular Bio-Formats Importer, select your settings, and re-select the windowless option.
Group files with similar names
Note
The functionality described below is also available outside ImageJ, by using a pattern file to tell Bio-Formats how to group the files. See Grouping files using a pattern file for more information.
One of the most important features of Bio-Formats is to combine multiple files from a data set into one coherent, multi-dimensional image.
To demonstrate how to use the Group files with similar names feature, you can use the dub data set available under LOCI’s Sample Data page. You will notice that it is a large dataset: each of the 85 files shows the specimen at 33 optical sections along the z-plane at a specific time.
If you open just one file in ImageJ/Fiji using the Bio-Formats Importer, you will get an image incorporating three dimensions (x, y, z). However, if you select Group files with similar names from the Bio-Formats Import Options screen, you will be able to create a 4-D image (x, y, z, and t) incorporating the 85 files.
After clicking OK, you will see a screen like this:
This screen allows you to select which files within the 85-file cluster to use to create that 4-D image. Some information will be pre-populated in the fields. Unless you want to change the settings in that field, there is no need to change or delete it. If you click OK at this point, you will load all 85 files.
However, you can specify which files you want to open by adjusting the “axis information”, the file “name contains”, or the “pattern” sections. Even though there are three options, you only need to need to make changes to one of them. Since Bio-Format’s precedence for processing data is from top to bottom, only the uppermost section that you made changes to will be used. If you change multiple boxes, any information you enter into lower boxes will be ignored.
To return to the example involving the dub data set, suppose you want to open the first image and only every fifth image afterwards (i.e. dub01, dub06, dub11 … dub81). This would give you 17 images. There are different ways to accomplish this:
You can use the Axis Settings only when your files are numbered in sequential order and you want to open only a subset of the files that have similar names. Since the dub data set is numbered sequentially, you can use this feature.
Axis 1 number of images refers to the total number of images you want to open. Since you want to view 17 images, enter 17. Axis 1 axis first image specifies which image in the set you want to be the first. Since you want to start with dub01, enter 1 in that box. You also want to view only every fifth image, so enter 5 in the Axis 1 axis increment box.
The File name contains box should be used if all of the files that you want to open have common text. This is especially useful when the files are not numbered. For example, if you have “Image_Red.tif”, “Image_Green.tif”, and “Image_Blue.tif” you could enter “Image_” in the box to group them all.
To continue the example involving the dub data set, you cannot use the file name contains box to open every fifth image. However, if you only wanted to open dub10 thorough dub19, you could enter “dub1” in the file name contains box.
The pattern box can be used to do either of the options listed above or much more. This box can accept a single file name like “dub01.pic”. It can also contain a pattern that use “<” and “>” to specify what numbers or text the file names contain.
There are three basic forms to the “< >” blocks:
Text enumeration - “Image_<Red,Green,Blue>.tif” is the pattern for Image_Red.tif, Image_Green.tif, Image_Blue.tif. (Note that the order you in which you enter the file names is the order in which they will be loaded.)
Number range - “dub<1-85>.pic” is the pattern for “dub1.pic”, “dub2.pic”, “dub3.pic” … “dub85.pic”.
Number range with step - “dub<1-85:5>.pic” is the pattern for “dub1.pic”, “dub6.pic”, “dub11.pic”, “dub11.pic” … “dub85.pic”.
It can also accept a Java regular expression.
Autoscale
Autoscale helps increase the brightness and contrast of an image by adjusting the range of light intensity within an image to match the range of possible display values. Note that Autoscale does not change your data. It just changes how it is displayed.
Each pixel in an image has a numerical value ascribed to it to describe its intensity. The bit depth—the number of possible values– depends on the number of bits used in the image. Eight bits, for example, gives 256 values to express intensity where 0 is completely black, 255 is completely white, and 1 through 254 display increasingly lighter shades of grey.
ImageJ can collect the intensity information about each pixel from an image or stack and create a histogram (you can see it by selecting Histogram under the Analyze menu). Here is the histogram of a one particular image:
Notice that the histogram heavily skews left. Even though there are 256 possible values, only 0 thorough 125 are being used.
Autoscale adjusts the image so the smallest and largest number in that image or stack’s histogram become the darkest and brightest settings. For this image, pixels with the intensity of 125 will be displayed in pure white. The other values will be adjusted too to help show contrast between values that were too insignificant to see before.
Here is one image Bio-Formats imported with and without using Autoscale:
Autoscale readjusts the image based on the highest value in the entire data set. This means if the highest value in your dataset is close to maximum display value, Autoscale’s adjusting may be undetectable to the eye.
ImageJ/Fiji also has its own tools for adjusting the image, which are available by selecting Brightness/Contrast, which is under the Adjust option in the Image menu.
Managing memory in ImageJ/Fiji using Bio-Formats
When dealing with a large stack of images, you may receive a warning like this:
This means the allotted memory is less than what Bio-Formats needs to load all the images. If you have a very large data set, you may have to:
Crop the view area
Open only a subset of images
Use Virtual Stack
Increase ImageJ/Fiji’s memory.
If your files contain JPEG or JPEG-2000 images, you may see this memory warning even if your file size is smaller than the amount of allocated memory. This is because compressed images like JPEG need to be decompressed into memory before being displayed and require more memory than their file size suggests. If you are having this issue, try utilizing one of the memory management tools below.
Cropping the view area
Crop on Import is useful if your images are very large and you are only interested in one specific section of the stack you are importing. If you select this feature, you will see a screen where you can enter the height and width (in pixels) of the part of image you want to see. Note that these measurements are from the top left corner of the image.
Opening only a subset of images
The Specify Range for Each Series option is useful for viewing a portion of a data set where all the plane images are encapsulated into one file (e.g. the Zeiss LSM format). If your file has a large quantity of images, you can specify which channels, Z-planes, and times you want to load.
Use Virtual Stack
Virtual Stack conserves memory by not loading specific images until necessary. Virtual Stack does not contain a buffer and may produce choppy animations.
Increasing ImageJ/Fiji’s memory
Finally, you can also increase the amount of the computer memory devoted to ImageJ/Fiji by selecting Memory & Threads under the Edit menu.
Generally, allocating more than 75% of the computer’s total memory will cause ImageJ/Fiji to become slow and unstable.
Please note that, unlike the other two features, ImageJ/Fiji itself provides this feature and not Bio-Formats. You can find out more about this feature by looking at ImageJ’s documentation.
Bio-Formats plugin configuration options
The Bio-Formats plugin can be configured by opening the Bio-Formats Plugins Configuration dialog from the Plugin menu. The General tab allows for configuration of features for the plugin such as upgrade checking or modifying the slice label pattern.
Configuring the slice label pattern
The slice label is the text displayed at the top of the image window in ImageJ. The values displayed here can be modified by configuring the slice label pattern.
- The list of available parameters for configuration is as follows::
- %s:
series index
- %n:
series name
- %c:
channel index
- %w:
channel name
- %z:
Z index
- %t:
T index
- %A:
acquisition timestamp
Each index value will be 1-based rather than 0-based. The index will be displayed
along with the total dimension count and with a prefix for the particular dimension.
For example using %c for channel index will result in the display c:1/3.
See also
Command line tools
The Bio-Formats Command line tools (bftools.zip) provide a complete package for carrying out a variety of tasks:
Command line tools
There are several scripts for using Bio-Formats on the command line.
Displaying images and metadata
The showinf command line tool can be used to show the images and metadata contained in a file.
If no options are specified, showinf displays a summary of available options.
To simply display images:
showinf /path/to/file
All of the images in the first ‘series’ (or 5 dimensional stack) will be opened and displayed in a simple image viewer. The number of series, image dimensions, and other basic metadata will be printed to the console.
- -noflat
Do not flatten resolutions into individual series:
showinf -noflat /path/to/file
- -series SERIES
Displays a different series, for example the second one:
showinf -series 1 /path/to/file
Note that series numbers begin with 0.
- -omexml
Displays the OME-XML metadata for a file on the console:
showinf -omexml /path/to/file
- -nopix
Image reading can be suppressed if only the metadata is needed:
showinf -nopix /path/to/file
- -option KEY VALUE
Passes options expressed as key/value pairs:
showinf -option key value /path/to/file
e.g. additional reader options, see Additional reader and writer options:
showinf -option leicalif.old_physical_size true /path/to/file
Added in version 5.3.0.
- -range START END
A subset of images can also be opened instead of the entire stack, by specifying the start and end plane indices (inclusive):
showinf -range 0 0 /path/to/file
That opens only the first image in first series in the file.
- -crop X,Y,WIDTH,HEIGHT
For very large images, it may also be useful to open a small tile from the image instead of reading everything into memory. To open the upper-left-most 512×512 tile from the images:
showinf -crop 0,0,512,512 /path/to/file
The parameter to
-cropis of the formatx,y,width,height. The (x, y) coordinate (0, 0) is the upper-left corner of the image;x + widthmust be less than or equal to the image width andy + heightmust be less than or equal to the image height.
- -no-upgrade
By default, showinf will check for a new version of Bio-Formats. This can take several seconds (especially on a slow internet connection); to save time, the update check can be disabled:
showinf -no-upgrade /path/to/file
- -novalid
Similarly, if OME-XML is displayed then it will automatically be validated. On slow or missing internet connections, this can take some time, and so can be disabled:
showinf -novalid /path/to/file
- -nocore
Most output can be suppressed:
showinf -nocore /path/to/file
- -omexml-only
Displays the OME-XML alone:
showinf -omexml-only /path/to/file
This is particularly helpful when there are hundreds or thousands of series.
- -debug
Enables debugging output if more information is needed:
showinf -debug /path/to/file
- -fast
Displays an image as quickly as possible. This is achieved by converting the raw data into a 8 bit RGB image:
showinf -fast /path/to/file
Note
Due to the data conversion to a RGB image, using this option results in a loss of precision.
- -autoscale
Adjusts the display range to the minimum and maximum pixel values:
showinf -autoscale /path/to/file
Note
This option automatically sets the
-fastoption and suffers from the same limitations.
- -cache
Caches the reader under the same directory as the input file after initialization:
showinf -cache /path/to/file
- -cache-dir DIR
Specifies the base directory under which the reader should be cached:
showinf -cache-dir /tmp/cachedir /path/to/file
- -swap DIMENSIONORDER
Overrides the default input dimension order:
showinf -swap XYZTC /path/to/file
- -format FORMAT
Specifies the reader to be used for opening the specified file. The utility will look for a reader named
loci.formats.in.<FORMAT>Reader. If the reader does not exist or no-formatoption is passed, the file will be opened withloci.formats.in.ImageReader:showinf -format APNG test.png
- -fill UNSIGNED_BYTE
Sets the fill value to use for undefined pixels. Valid values are 0-255, with 0 representing a black pixel and 255 representing a white pixel. The value set here will be applied to all bytes in an undefined pixel, e.g. setting to 128 (0x80) on a uint16 image will result in a pixel value of 32896 (0x8080). The default fill value is typically 0, but some readers may have different defaults.
Added in version 6.13.0.
Converting a file to different format
The bfconvert command line tool can be used to convert files between supported formats.
bfconvert with no options displays a summary of available options.
To convert a file to single output file (e.g. TIFF):
bfconvert /path/to/input output.tiff
The output file format is determined by the extension of the output file, e.g. .tiff for TIFF files, .ome.tiff for OME-TIFF, .png for PNG.
- -option KEY VALUE
Passes options expressed as key/value pairs:
bfconvert -option key value /path/to/input /path/to/output
e.g. additional writer options, see Additional reader and writer options:
bfconvert -option ometiff.companion converted.companion.ome input.fake converted.ome.tiff
Added in version 5.4.0.
- -noflat
Do not flatten resolutions into individual series. This option is mandatory to read images with pyramidal levels using the sub-resolution API and generate an output image with sub-resolutions. As of Bio-Formats 6.0.0, only the OME-TIFF output format properly supports this option:
bfconvert -noflat /path/to/input output-first-series.ome.tiff
Added in version 6.0.0.
- -series SERIES
All images in the input file are converted by default. To convert only one series:
bfconvert -series 0 /path/to/input output-first-series.tiff
- -timepoint TIMEPOINT
To convert only one timepoint:
bfconvert -timepoint 0 /path/to/input output-first-timepoint.tiff
- -channel CHANNEL
To convert only one channel:
bfconvert -channel 0 /path/to/input output-first-channel.tiff
- -z Z
To convert only one Z section:
bfconvert -z 0 /path/to/input output-first-z.tiff
- -range START END
To convert images between certain indices (inclusive):
bfconvert -range 0 2 /path/to/input output-first-3-images.tiff
- -tilex TILEX, -tiley TILEY
All images larger than 4096×4096 will be saved as a set of tiles if the output format supports doing so. The default tile size is determined by the input format, and can be overridden like this:
bfconvert -tilex 512 -tiley 512 /path/to/input output-512x512-tiles.tiff
-tilexis the width in pixels of each tile;-tileyis the height in pixels of each tile. The last row and column of tiles may be slightly smaller if the image width and height are not multiples of the specified tile width and height. Note that specifying-tilexand-tileywill cause tiles to be written even if the image is smaller than 4096×4096.Also note that the specified tile size will affect performance. If large amounts of data are being processed, it is a good idea to try converting a single tile with a few different tile sizes using the
-cropoption. This gives an idea of what the most performant size will be.
- -crop X,Y,WIDTH,HEIGHT
For very large images, it may also be useful to convert a small tile from the image instead of reading everything into memory. To convert the upper-left-most 512×512 tile from the images:
bfconvert -crop 0,0,512,512 /path/to/file output-512x512-crop.tiff
The parameter to
-cropis of the formatx,y,width,height. The (x, y) coordinate (0, 0) is the upper-left corner of the image;x + widthmust be less than or equal to the image width andy + heightmust be less than or equal to the image height.
Images can also be written to multiple files by specifying a pattern string in the output file. For example, to write one series, timepoint, channel, and Z section per file:
bfconvert /path/to/input output_series_%s_Z%z_C%c_T%t.tiff
%s is the series index, %z is the Z section index, %c is the
channel index, and %t is the timepoint index (all indices begin at 0).
For large images in particular, it can also be useful to write each tile to a separate file:
bfconvert -tilex 512 -tiley 512 /path/to/input output_tile_%x_%y_%m.jpg
%x is the row index of the tile, %y is the column
index of the tile, and %m is the overall tile index. As above, all
indices begin at 0. Note that if %x or %y is included in the file
name pattern, then the other must be included too. The only exception is if
%m was also included in the pattern.
Note for Windows Users: The command interpreter for batch files needs the %
characters to be doubled in order to process the sequencing variables
correctly. So in Windows, the above example would read:
bfconvert /path/to/input output_series_%%s_Z%%z_C%%c_T%%t.tif
- -compression COMPRESSION
By default, all images will be written uncompressed. Supported compression modes vary based upon the output format, but when multiple modes are available the compression can be changed using the
-compressionoption. For example, to use LZW compression in a TIFF file:bfconvert -compression LZW /path/to/input output-lzw.tiff
- -quality QUALITY
Specify the compression quality to be used. The interpretation of this value depends upon the
-compressionoption used.For uncompressed output,
-qualityhas no effect.When used with
-compression JPEG,-qualitymust take a value between0.25(25%, extremely lossy) and1.0(100%, nearly lossless). The default is0.75.When used with
-compression JPEG-2000,-qualitymust take a positive integer value. This is interpreted as an encoding rate in bits per pixel, with higher values representing less lossy compression. The default is10.Added in version 7.3.0.
- -overwrite
If the specified output file already exists, bfconvert will prompt to overwrite the file. When running bfconvert non-interactively, it may be useful to always allow bfconvert to overwrite the output file:
bfconvert -overwrite /path/to/input /path/to/output
- -nooverwrite
To always exit without overwriting:
bfconvert -nooverwrite /path/to/input /path/to/output
- -nolookup
To disable the conversion of lookup tables, leaving the output file without any lookup tables:
bfconvert -nolookup /path/to/input /path/to/output
Added in version 5.2.1.
- -bigtiff
This option forces the writing of a BigTiff file:
bfconvert -bigtiff /path/to/input output.ome.tiff
Added in version 5.1.2.
The
-bigtiffoption is not necessary if a BigTiff extension is used for the output file, e.g.:bfconvert /path/to/input output.ome.btf
- -nobigtiff
This option disables the automatic switching to BigTiff based upon the number of pixel bytes (TIFF files larger than 4GB):
bfconvert -nobigtiff /path/to/input output.ome.tiff
Added in version 6.4.0.
Using the
-nobigtiffwill disable writing BigTiff when the output format is less than 4GB. It will not be able to write standard Tiff files greater than 4GB. An example of when it might be used would be when converting using a compression codec that reduces the size of the output file, e.g.:bfconvert -nobigtiff -compression LZW /path/to/input output.ome.btf
- -padded
This option is used alongside a pattern string when writing an image to multiple files. When set this will enforce zero padding on the filename indexes set in the provided pattern string:
bfconvert /path/to/input output_xy%sz%zc%ct%t.ome.tif -padded
Added in version 5.2.2.
- -pyramid-resolutions RESOLUTIONS
- -pyramid-scale SCALE
When using
-noflatby default, each series of the converted file will contain the same number of resolutions as in the input file. The-pyramid-resolutionsoption allows to set the number of expected resolutions in the output file for each series. If the target number of resolutions is greater than the actual number of sub-resolutions present in the input file, additional pyramidal levels will be calculated using the downsampling factor specified by the-pyramid-scaleoption:bfconvert -noflat -pyramid-resolutions 4 -pyramid-scale 2 /path/to/input out.ome.tiff
Added in version 6.0.0.
- -cache
This option will cache the initialized reader under the same directory as the input file after initialization:
bfconvert -cache /path/to/input output.ome.tiff
Added in version 6.2.0.
- -cache-dir DIRECTORY
This option is to be used in conjunction with
-cache. When used it specifies the directory to store the cached initialized reader. If unspecified, the cached reader will be stored under the same folder as the image file:bfconvert -cache-dir /path/to/store/cached/reader /path/to/input output.ome.tiff
Added in version 6.2.0.
- -no-sas
Do not preserve the OME-XML StructuredAnnotation elements:
bfconvert -no-sas /path/to/input output.ome.tiff
Added in version 6.2.0.
- -no-sequential
Do not assume that planes are written in sequential order:
bfconvert -no-sequential /path/to/input output.ome.tiff
Added in version 6.8.0.
- -swap DIMENSIONORDER
Overrides the default input dimension order:
bfconvert -swap XYZTC /path/to/input output.ome.tiff
Added in version 6.9.0.
- -fill UNSIGNED_BYTE
Sets the fill value to use for undefined pixels. Valid values are 0-255, with 0 representing a black pixel and 255 representing a white pixel. The value set here will be applied to all bytes in an undefined pixel, e.g. setting to 128 (0x80) on a uint16 image will result in a pixel value of 32896 (0x8080). The default fill value is typically 0, but some readers may have different defaults.
Added in version 6.13.0.
- -precompressed
Enables transfer of compressed bytes from input dataset directly to output without decompression. Most input and output formats do not support this option, currently this is implemented in the Aperio SVS input and DICOM output. Do not use -crop, -fill, or -autoscale, or pyramid generation options:
bfconvert -precompressed /path/to/input /path/to/output
For an example of this option being used see below using the CMU-1.svs file from OpenSlide:
bfconvert -noflat -precompressed -compression JPEG CMU-1.svs CMU-1.dcm
Added in version 7.1.0.
- -extra-metadata METADATA FILE
Enables the writing of additional supplemental metadata from an external file during the conversion process . Most output formats do not support this option, currently this is implemented for outputting the DICOM format. For DICOM the additional metadata file can be in the format of a .json file
bfconvert -extra-metadata /path/to/extra-metadata /path/to/input /path/to/output
For an example of this option being used see below:
$ cat hierarchy-test.json { "BodyPartExamined": { "Value": "BRAIN", "VR": "CS", "Tag": "(0018,0015)" "ResolutionStrategy": "IGNORE" }, "ContributingEquipmentSequence": { "VR": "SQ", "Tag": "(0018,a001)", "Sequence": { "Manufacturer": { "Value": "PixelMed", "VR": "LO", "Tag": "(0008,0070)" }, "ContributionDateTime": { "Value": "20210710234601.105+0000", "VR": "DT", "Tag": "(0018,a002)" } } "ResolutionStrategy": "REPLACE" } } $ bfconvert -extra-metadata hierarchy-test.json test.fake hierarchy-test-json.dcmAdded in version 7.1.0.
Validating XML in an OME-TIFF
The XML stored in an OME-TIFF file can be validated using the command line tools.
Both the tiffcomment and xmlvalid commands are used; tiffcomment extracts the XML from the file and xmlvalid validates the XML and prints any errors to the console.
For example:
xmlvalid /path/to/file.ome.tiff
and
xmlvalid /path/to/file.xml
will perform validatation for an ome.xml file and xml file, respectively.
Also:
tiffcomment "/path/to/file.ome.tiff" | xmlvalid
will perform the extraction and validation all at once.
Typical successful output of xmlvalid is:
[~/Work/bftools]$ ./xmlvalid sample.ome
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd
Validating sample.ome
No validation errors found.
[~/Work/bftools]$
If any errors are found they are reported. When correcting errors it is usually best to work from the top of the file as errors higher up can cause extra errors further down. In this example the output shows 3 errors but there are only 2 mistakes in the file:
[~/Work/bftools]$ ./xmlvalid broken.ome
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2010-06/ome.xsd
Validating broken.ome
cvc-complex-type.4: Attribute 'SizeY' must appear on element 'Pixels'.
cvc-enumeration-valid: Value 'Non Zero' is not facet-valid with respect
to enumeration '[EvenOdd, NonZero]'. It must be a value from the enumeration.
cvc-attribute.3: The value 'Non Zero' of attribute 'FillRule' on element
'ROI:Shape' is not valid with respect to its type, 'null'.
Error validating document: 3 errors found
[~/Work/bftools]$
If the XML is found to have validation errors, the tiffcomment command can be used to overwrite the XML in the OME-TIFF file with corrected XML. The XML can be displayed in an editor window:
tiffcomment -edit /path/to/file.ome.tiff
or the new XML can be read from a file:
tiffcomment -set new-comment.xml /path/to/file.ome.tiff
Editing XML in an OME-TIFF
To edit the XML in an OME-TIFF file you can use tiffcomment, one of the Bio-Formats tools.
Note
The tiffcomment tool requires that the ImageDescription tag is present in the TIFF file and will error otherwise.
To use the built in editor run:
tiffcomment -edit sample.ome.tif
To extract or view the XML run:
tiffcomment sample.ome.tif
To inject replacement XML into a file run:
tiffcomment -set 'newmetadata.xml' sample.ome.tif
List formats by domain
Each supported file format has one or more imaging domains associated with it. To print the list of formats associated with each imaging domain:
domainlist
The command does not accept any arguments. The known image domains are defined by:
List supported file formats
A detailed list of supported formats can be displayed using the formatlist command.
The default behavior is to print a plain-text list of formats:
formatlist
- -txt
Prints the list of formats as plain-text:
formatlist -txt
- -html
Prints the list of formats as HTML:
formatlist -html
- -xml
Prints the list of formats as XML:
formatlist -xml
- -help
Displays the usage information:
formatlist -help
Display file in ImageJ
Files can be displayed from the command line in ImageJ. The Bio-Formats importer plugin for ImageJ is used to open the file.
The command takes a single argument:
ijview /file/to/open
If the input file is not specified, ImageJ will show a file chooser window.
The Bio-Formats import options window will then appear, after which the image(s) will be displayed.
If the BF_DEVEL environment variable is set, the ImageJ jar
<jars/ij.jar> must be included in the classpath.
Format XML data
The xmlindent command formats and adds indenting to XML so that it is easier to read. Indenting is currently set to 3 spaces.
If an XML file name is not specified, the XML to indent will be read from standard output. Otherwise, one or more file names can be specified:
xmlindent /path/to/xml
xmlindent /path/to/first-xml /path/to/second-xml
The formatted XML from each file will be printed in the order in which the files were specified.
By default, extra whitespace may be added to CDATA elements. To preserve the contents of CDATA elements:
xmlindent -valid /path/to/xml
Create a high-content screen for testing
The mkfake command creates a high-content screen for testing. The image data will be meaningless, but it allows testing of screen, plate, and well metadata without having to find appropriately-sized screens from real acquisitions.
If no arguments are specified, mkfake prints usage information.
To create a single screen with default plate dimensions:
mkfake default-screen.fake
This will create a directory that represents one screen with a single plate containing one well, one field, and one acquisition of the plate (see PlateAcquisition).
- -plates PLATES
To change the number of plates in the screen:
mkfake -plates 3 three-plates.fake
- -runs RUNS
To change the number of acquisitions for each plate:
mkfake -runs 4 four-plate-acquisitions.fake
- -rows ROWS
To change the number of rows of wells in each plate:
mkfake -rows 8 eight-row-plate.fake
- -columns COLUMNS
To change the number of columns of wells in each plate:
mkfake -columns 12 twelve-column-plate.fake
- -fields FIELDS
To change the number of fields per well:
mkfake -fields 2 two-field-plate.fake
It is often most useful to use the arguments together to create a realistic screen, for example:
mkfake -rows 16 -columns 24 -plates 2 -fields 3 two-384-well-plates.fake
- -debug DEBUG
As with other command line tools, debugging output can be enabled if necessary:
mkfake -debug debug-screen.fake
Installation
Download bftools.zip, unzip it into a new folder.
Note
As of Bio-Formats 5.0.0, this zip now contains the bundled jar
and you no longer need to download bioformats_package.jar
separately.
The zip file contains both Unix scripts and Windows batch files.
Tools available
Currently available tools include:
- showinf
Prints information about a given image file to the console, and displays the image itself in the Bio-Formats image viewer (see Displaying images and metadata for more information).
- ijview
Displays the given image file in ImageJ using the Bio-Formats Importer plugin. See Display file in ImageJ for details.
- bfconvert
Converts an image file from one format to another. Bio-Formats must support writing to the output file (see Converting a file to different format for more information).
- formatlist
Displays a list of supported file formats in HTML, plaintext or XML. See List supported file formats for details.
- xmlindent
A simple XML prettifier similar to xmllint --format but more robust in that it attempts to produce output regardless of syntax errors in the XML. See Format XML data for details.
- xmlvalid
A command-line XML validation tool, useful for checking an OME-XML document for compliance with the OME-XML schema. See Validating XML in an OME-TIFF for details.
- tiffcomment
Dumps the comment from the given TIFF file’s first IFD entry; useful for examining the OME-XML block in an OME-TIFF file (also see Editing XML in an OME-TIFF).
- domainlist
Displays a list of imaging domains and the supported formats associated with each domain. See List formats by domain for more information.
- mkfake
Creates a “fake” high-content screen with configurable dimensions. This is useful for testing how HCS metadata is handled, without requiring real image data from an acquired screen. See Create a high-content screen for testing for more information.
Some of these tools also work in combination, for example Validating XML in an OME-TIFF uses both tiffcomment and xmlvalid.
Running any of these commands without any arguments will print usage
information to help you. When run with the -version argument, showinf
and bfconvert will display the version of Bio-Formats that is being used
(version number, build date, and Git commit reference).
Command-line environment
A set of environment variables can be passed to all command-line utilities:
BF_CPExtra directories to be added to the autodetected command-line classpath e.g. for external reader JARs. Default: empty.
BF_FLAGSAdditional flags to be sent to the JVM. Default: empty.
BF_MAX_MEMMaximum heap size to be allocated to the JVM. Default: 512m.
BF_PROFILEEnable profiling - see Profiling for more information. Default: off.
BF_PROFILE_DEPTHMaximum profiling depth if profiling is activated. Default: 30.
Using the tools directly from source
Firstly, obtain a copy of the sources and build them (see Obtaining and building Bio-Formats). You can configure the scripts to use your source tree instead of bioformats_package.jar in the same directory by following these steps:
Point your CLASSPATH to the checked-out directory and the JAR files in the jar folder.
E.g. on Windows with Java 1.8 or later, if you have checked out the source at
C:\code\bio-formats, set your CLASSPATH environment variable to the valueC:\code\bio-formats\jar\*;C:\code\bio-formats. You can access the environment variable configuration area by right-clicking on My Computer, choosing Properties, Advanced tab, Environment Variables button.
Compile the source with
ant compile.Set the
BF_DEVELenvironment variable to any value (the variable just needs to be defined).
Version checker
If you run bftools outside of the OMERO environment, you may encounter an
issue with the automatic version checker causing a tool to crash when trying
to connect to upgrade.openmicroscopy.org.uk. The error message will look
something like this:
Failed to compare version numbers
java.io.IOException: Server returned HTTP response code: 400 for URL:
http://upgrade.openmicroscopy.org.uk?version=4.4.8;os.name=Linux;os.
version=2.6.32-358.6.2.el6.x86_64;os.arch=amd64;java.runtime.version=
1.6.0_24-b24;java.vm.vendor=Sun+Microsystems+Inc.;bioformats.caller=
Bio-Formats+utilities
To avoid this issue, call the tool with the -no-upgrade parameter.
Profiling
For debugging errors or investigating performance issues, it can be useful to
use profiling tools while running Bio-Formats. The command-line tools can
invoke the HPROF agent library to profile Heap and CPU usage. Setting the
BF_PROFILE environment variable allows to turn profiling on, e.g.:
BF_PROFILE=true showinf -nopix -no-upgrade myfile
See also
OMERO
OMERO 5 uses Bio-Formats to read original files from over 140 file formats. Please refer to the OMERO documentation for further information.
Many other software packages can use Bio-Formats to read and write microscopy formats (click on the package for further details):
Image server applications
BISQUE
The BISQUE (Bio-Image Semantic Query User Environment) Database, developed at the Center for Bio-Image Informatics at UCSB, was developed for the exchange and exploration of biological images. The Bisque system supports several areas useful for imaging researchers from image capture to image analysis and querying. The bisque system is centered around a database of images and metadata. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content.
Bisque integrates with Bio-Formats by calling the showinf command line tool.
OME Server
The OME server is a set of software that interacts with a database to manage images, image metadata, image analysis and analysis results. The OME system is capable of leveraging Bio-Formats to import files.
Please note - the OME server is no longer maintained and has now been superseded by the OMERO server. Support for the OME server has been entirely removed in the 5.0.0 version of Bio-Formats; the following instructions can still be used with the 4.4.x versions.
Installation
For OME Perl v2.6.1 and later, the command line installer automatically downloads the latest loci_tools.jar and places it in the proper location. This location is configurable, but is /OME/java/loci_tools.jar by default.
For a list of what was recognized for a particular import into the OME server, go to the Image details page in the web interface, and click the “Image import” link in the upper right hand box.
Bio-Formats is capable of parsing original metadata for supported formats, and standardizes what it can into the OME data model. For the rest, it expresses the metadata in OME terms as key/value pairs using an OriginalMetadata custom semantic type. However, this latter method of metadata representation is of limited utility, as it is not a full conversion into the OME data model.
Bio-Formats is enabled in OME v2.6.1 for all formats except:
OME-TIFF
Metamorph HTD
Deltavision DV
Metamorph STK
Bio-Rad PIC
Zeiss LSM
TIFF
BMP
DICOM
OME-XML
The above formats have their own Perl importers that override Bio-Formats, meaning that Bio-Formats is not used to process them by default. However, you can override this behavior (except for Metamorph HTD, which Bio-Formats does not support) by editing an OME database configuration value:
% psql ome
To see the current file format reader list:
ome=# select value from configuration where name='import_formats';
value
------------------------------------------------------------------------------
['OME::ImportEngine::OMETIFFreader','OME::ImportEngine::MetamorphHTDFormat',
'OME::ImportEngine::DVreader','OME::ImportEngine::STKreader',
'OME::ImportEngine::BioradReader','OME::ImportEngine::LSMreader',
'OME::ImportEngine::TIFFreader','OME::ImportEngine::BMPreader',
'OME::ImportEngine::DICOMreader','OME::ImportEngine::XMLreader',
'OME::ImportEngine::BioFormats']
(1 row)
To remove extraneous readers from the list:
ome=# update configuration set value='[\'OME::ImportEngine::MetamorphHTDFormat\',
\'OME::ImportEngine::XMLreader\',\'OME::ImportEngine::BioFormats\']' where
name='import_formats';
UPDATE 1
ome=# select value from configuration where name='import_formats';
value
------------------------------------------------------------------------------
['OME::ImportEngine::MetamorphHTDFormat','OME::ImportEngine::XMLreader',
'OME::ImportEngine::BioFormats']
(1 row)
To reset things back to how they were:
ome=# update configuration set value='[\'OME::ImportEngine::OMETIFFreader\',
\'OME::ImportEngine::MetamorphHTDFormat\',\'OME::ImportEngine::DVreader\',
\'OME::ImportEngine::STKreader\',\'OME::ImportEngine::BioradReader\',
\'OME::ImportEngine::LSMreader\',\'OME::ImportEngine::TIFFreader\',
\'OME::ImportEngine::BMPreader\',\'OME::ImportEngine::DICOMreader\',
\'OME::ImportEngine::XMLreader\',\'OME::ImportEngine::BioFormats\']' where
name='import_formats';
Lastly, please note that Li-Cor L2D files cannot be imported into an OME server. Since the OME perl server has been discontinued, we have no plans to fix this limitation.
Upgrading
OME server is not supported by Bio-Formats versions 5.0.0 and above. To take advantage of more recent improvements to Bio-Formats, you must switch to OMERO server.
Source Code
The source code for the Bio-Formats integration with OME server spans three languages, using piped system calls in both directions to communicate, with imported pixels written to OMEIS pixels files. The relevant source files are:
OmeisImporter.java – omebf Java command line tool
BioFormats.pm – Perl module for OME Bio-Formats importer
omeis.c – OMEIS C functions for Bio-Formats (search for “bioformats” case insensitively to find relevant sections)
Libraries and scripting applications
FARSIGHT
FARSIGHT is a collection of modules for image analysis created by LOCI’s collaborators at the University of Houston. These open source modules are built on the ITK library and thus can take advantage of ITK’s support for Bio-Formats to process otherwise unsupported image formats.
The principal FARSIGHT module that benefits from Bio-Formats is the Nucleus Editor, though in principle any FARSIGHT-based code that reads image formats via the standard ITK mechanism will be able to leverage Bio-Formats.
i3dcore
i3dcore, also known as the CBIA 3D image representation library, is a 3D image processing library developed at the Centre for Biomedical Image Analysis. Together with i3dalgo and i4dcore, i3dcore forms a continuously developed templated cross-platform C++ suite of libraries for multidimensional image processing and analysis.
i3dcore is capable of reading images with Bio-Formats using Java for C++ (java4cpp).
ImgLib
ImgLib2 is a multidimensional image processing library. It provides a general mechanism for writing image analysis algorithms, without writing case logic for bit depth, or worrying about the source of the pixel data (arrays in memory, files on disk, etc.).
The SCIFIO project provides an ImgOpener utility class for reading data into ImgLib2 data structures using Bio-Formats.
ITK
The Insight Toolkit (ITK) is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data.
ITK provides an ImageIO plug-in structure that works via discovery through a dependency injection scheme. This allows a program built on ITK to load plug-ins for reading and writing different image types without actually linking to the ImageIO libraries required for those types. Such encapsulation automatically grants two major boons: firstly, programs can be easily extended just by virtue of using ITK (developers do not have to specifically accommodate or anticipate what plug-ins may be used). Secondly, the architecture provides a distribution method for open source software, like Bio-Formats, which have licenses that might otherwise exclude them from being used with other software suites.
The SCIFIO ImageIO plugin provides an ITK imageIO base that uses Bio-Formats to read and write supported life sciences file formats. This plugin allows any program built on ITK to read any of the image types supported by Bio-Formats.
Qu for MATLAB
Qu for MATLAB is a MATLAB toolbox for the visualization and analysis of multi-channel 4-dimensional datasets targeted to the field of biomedical imaging, developed by Aaron Ponti.
Uses Bio-Formats to read files
Open source software available under the Mozilla Public License
See also
Numerical data processing applications
GNU Octave
GNU Octave is a high-level interpreted language, primarily intended for numerical computations. Being an array programming language, it is naturally suited for image processing and handling of N dimensional datasets. Octave is distributed under the terms of the GNU General Public License.
The Octave language is MATLAB compatible so that programs are easily portable. Indeed, the Octave bioformats package is exactly the same as MATLAB’s, the only difference being the installation steps.
Requirements
The bioformats package requires Octave version 4.0.0 or later with support for java:
$ octave
>> OCTAVE_VERSION
ans = 4.0.0
>> usejava ("jvm")
ans = 1
Installation
Download bioformats_package.jar and place it somewhere sensible for your system (in Linux, this will probably be /usr/local/share/java or ~/.local/share/java for a system-wide or user installation respectively).
Add bioformats_package.jar to Octave’s static javaclasspath (see Octave’s documentation).
Download the Octave package.
Start octave and install the package with:
>> pkg install path-to-bioformats-octave-version.tar.gz
Usage
Usage instructions are the same as MATLAB. The only difference is that you need to explicitly load the package. This is done by running at the Octave prompt:
>> pkg load bioformats
Upgrading
To use a newer version of Bio-Formats, repeat the install instructions. Do not follow the MATLAB instructions.
IDL
IDL (Interactive Data Language) is a popular data visualization and analysis platform used for interactive processing of large amounts of data including images.
IDL possesses the ability to interact with Java applications via its IDL-Java bridge. Karsten Rodenacker has written a script that uses Bio-Formats to read in image files to IDL.
Installation
Download the ij_read_bio_formats.pro script from Karsten Rodenacker’s IDL goodies (?) web site. See the comments at the top of the script for installation instructions and caveats.
Upgrading
To use a newer version of Bio-Formats, overwrite the requisite JAR files with the newer version and restart IDL.
KNIME
KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform. KNIME supports image import using Bio-Formats using the KNIME Image Processing (a.k.a. KNIP) plugin.
MATLAB
MATLAB is a high-level language and interactive environment that facilitates rapid development of algorithms for performing computationally intensive tasks.
Calling Bio-Formats from MATLAB is fairly straightforward, since MATLAB has built-in interoperability with Java. We have created a toolbox for reading and writing image files. Note the minimum recommended MATLAB version is R2017b.
Note
It is possible to run Bio-Formats 6 on earlier MATLAB versions using a JVM version 8 or greater although using a different JVM than the one shipped with MATLAB can affect other functionalities. Please refer to the MATLAB Answers for more information.
Installation
Download the MATLAB toolbox from the Bio-Formats
downloads page.
Unzip bfmatlab.zip and add the unzipped bfmatlab folder to
your MATLAB path.
Usage
Please see Using Bio-Formats in MATLAB for usage instructions. If you intend to extend the existing .m files, please also see the developer page for more information on how to use Bio-Formats in general.
Performance
In our tests (MATLAB R14 vs. java 1.6.0_20), the script executes at approximately half the speed of our showinf command line tool, due to overhead from copying arrays.
Troubleshooting
If you encounter an error trying to open JPEG-2000 data in MATLAB but the file will open e.g. in Fiji using Bio-Formats, it may be due to conflicting versions of JAI ImageIO in different JARs. As discussed on the component page, JAI ImageIO is no longer maintained and you will likely need to remove the conflicting JAR(s) as a workaround.
Upgrading
To use a newer version of Bio-Formats, overwrite the content of the
bfmatlab folder with the newer version of the
toolbox and restart MATLAB.
Alternative scripts
Several other groups have developed their own MATLAB scripts that use Bio-Formats, including the following:
VisAD
The VisAD visualization toolkit is a Java component library for interactive and collaborative visualization and analysis of numerical data. VisAD uses Bio-Formats to read many image formats, notably TIFF.
Installation
The visad.jar file has Bio-Formats bundled inside, so no further installation is necessary.
Upgrading
It should be possible to use a newer version of Bio-Formats by
putting the latest
bioformats_package.jar or
formats-gpl.jar before visad.jar
in the class path. Alternately, you can create a “VisAD Lite” using the
make lite command from VisAD source, and use the resultant
visad-lite.jar, which is a stripped down version of VisAD without sample
applications or Bio-Formats bundled in.
R
OME does not currently provide an R implementation for Bio-Formats. However, there are options provided by the community:
Bioconductor RBioFormats
Bioconductor is a project to develop, support, and disseminate free open source software that facilitates rigorous and reproducible analysis of data from current and emerging biological assays. Most Bioconductor components are distributed as R packages, this includes RBioFormats. RBioFormats is an R package which interfaces the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.
Installation
To install this package, start R (version “4.3”) and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("RBioFormats")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RBioFormats")
See also
- RBioFormats
Website for the RBioFormats package
- Using Bio-Formats in R
Section of the developer documentation describing the R wrapper for Bio-Formats used by RBioFormats
Visualization and analysis applications
Bitplane Imaris
Imaris is Bitplane’s core scientific software module that delivers all the necessary functionality for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets. Combining speed, precision and ease-of-use, Imaris provides a complete set of features for working with three- and four-dimensional multi-channel images of any size, from a few megabytes to multiple gigabytes in size.
As of version 7.2, Imaris integrates with Fiji overview, which includes Bio-Formats. See this page for a detailed list of Imaris’ features.
CellProfiler
CellProfiler—developed by the Broad Institute Imaging Platform—is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. CellProfiler uses Bio-Formats to read images from disk, as well as write movies.
Installation
The CellProfiler distribution comes with Bio-Formats included, so no further installation is necessary.
Upgrading
It should be possible to use a newer version of Bio-Formats by replacing the bundled bioformats_package.jar with a newer version.
For example, on Mac OS X, Ctrl+click the CellProfiler icon, choose Show Package Contents, and replace the following file:
Contents/Resources/bioformats/jars/bioformats_package.jar
See also
- CellProfiler
Website of the CellProfiler software
- Using Bio-Formats in Python
Section of the developer documentation describing the Python wrapper for Bio-Formats used by CellProfiler
Comstat2
Comstat2 is a Java-based computer program for the analysis and treatment of biofilm images in 3D. It is the Master’s project of Martin Vorregaard.
Comstat2 uses the Bio-Formats Importer plugin for ImageJ to read files in TIFF and Leica LIF formats.
Endrov
Endrov (EV) is a multi-purpose image analysis program developed by the Thomas Burglin group at Karolinska Institute, Department of Biosciences and Nutrition.
Installation
The EV distribution comes bundled with the core Bio-Formats library (bio-formats.jar), so no further installation is necessary.
Upgrading
It should be possible to use a newer version of Bio-Formats by
downloading the latest
formats-gpl.jar
and putting it into the libs folder of the EV distribution,
overwriting the old file.
You could also include some optional libraries, to add support for additional formats, if desired.
FocalPoint
FocalPoint is an image browser, similar to Windows Explorer or other file manager application, specifically designed to work with more complex image types. FocalPoint uses Bio-Formats to generate thumbnails for some formats.
Installation
FocalPoint is bundled with Bio-Formats, so no further installation is necessary.
Upgrading
It should be possible to use a newer version of Bio-Formats by overwriting the old loci_tools.jar within the FocalPoint distribution. For Mac OS X, you will have to control click the FocalPoint program icon, choose “Show Package Contents” and navigate into Contents/Resources/Java to find the loci_tools.jar file.
Graphic Converter
Graphic Converter is a Mac OS application for opening, editing, and organizing photos. Versions 6.4.1 and later use Bio-Formats to open all file formats supported by Bio-Formats.
Icy
Icy is an open-source image analysis and visualization software package that combines a user-friendly graphical interface with the ability to write scripts and plugins that can be uploaded to a centralized website. It uses Bio-Formats internally to read images and acquisition metadata, so no further installation is necessary.
Iqm
Iqm is an image processing application written in Java. It is mainly constructed around the Java JAI library and furthermore it incorporates the functionality of the popular ImageJ image processing software.
Because iqm integrates with ImageJ, it can take advantage of the Bio-Formats ImageJ plugin to read image data.
Micro-Manager
Micro-Manager is a software framework for implementing advanced and novel imaging procedures, extending functionality, customization and rapid development of specialized imaging applications.
Micro-Manager offers the functionality for saving the acquired images in
TIFF/OME-TIFF format. Based on the mode of saving and the configuration
settings, the acquired image can be saved with or without a companion file
(*metadata.txt):
Micro-Manager saving option |
Micro-Manager saving format |
Companion file |
Bio-Formats reading |
Reader users |
|---|---|---|---|---|
Save as separate image files |
TIFF |
Yes |
Full support |
|
Save as image stack file |
OME-TIFF |
No |
Pixel data plus minimal metadata* |
|
Save as image stack file |
OME-TIFF |
Yes** |
Full Support |
* Not all acquisition metadata is converted to OME-XML.
** A small change in the acquisition side facilitates better handling of
the metadata from the Bio-Formats side:
and then select “Create metadata.txt
file with Image Stack Files” in the text box.
MIPAV
The MIPAV (Medical Image Processing, Analysis, and Visualization) application—developed at the Center for Information Technology at the National Institutes of Health—enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. You can use Bio-Formats as a plugin for MIPAV to read images in the formats it supports.
Installation
Follow these steps to install the Bio-Formats plugin for MIPAV:
Download bioformats_package.jar and drop it into your MIPAV folder.
Download the plugin source code into your user
mipav/pluginsfolder.From the command line, compile the plugin with:
cd mipav/plugins javac -cp $MIPAV:$MIPAV/bioformats\_package.jar \\ PlugInBioFormatsImporter.java
where $MIPAV is the location of your MIPAV installation.
Add bioformats_package.jar to MIPAV’s class path:
How to do so depends on your platform.
E.g., in Mac OS X, edit the
mipav.app/Contents/Info.plistfile.
Run MIPAV and a new “BioFormatsImporter - read image” menu item will appear in the Plugins > File submenu.
See the readme file for more information.
To upgrade, just overwrite the old bioformats_package.jar with the latest one. You may want to download the latest version of MIPAV first, to take advantage of new features and bug-fixes.
QuPath
QuPath is an open-source application for whole slide image analysis and visualization. QuPath can be configured to use Bio-Formats by installing the QuPath Bio-Formats extension
Vaa3D
Vaa3D, developed by the Peng Lab at the HHMI Janelia Farm Research Campus, is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects.
Vaa3D can use Bio-Formats via the Bio-Formats C++ bindings to read images.
VisBio
VisBio is a biological visualization tool designed for easy visualization and analysis of multidimensional image data. VisBio uses Bio-Formats to import files as the Bio-Formats library originally grew out of our efforts to continually expand the file format support within VisBio.
Installation
VisBio is bundled with Bio-Formats, so no further installation is necessary.
Upgrading
It should be possible to use a newer version of Bio-Formats by overwriting the old bio-formats.jar and optional libraries within the VisBio distribution. For Mac OS X, you will have to control click the VisBio program icon, choose “Show Package Contents” and navigate into Contents/Resources/Java to find the JAR files.
XuvTools
XuvTools is automated 3D stitching software for biomedical image data. As of release 1.8.0, XuvTools uses Bio-Formats to read image data.
Developer Documentation
The following sections describe various things that are useful to know when working with Bio-Formats. It is recommended that you obtain the Bio-Formats source by following the directions in the Source code section. Referring to the Javadocs as you read over these pages should help, as the notes will make more sense when you see the API.
For a complete list of supported formats, see the Bio-Formats supported formats table.
For a few working examples of how to use Bio-Formats, see these Github pages and the bio-formats-examples repository.
Introduction to Bio-Formats
Overview for developers
From the rest of the Bio-Formats developer documentation one may piece together a correct and useful understanding of what Bio-Formats does and how it does it. This section gives a high-level tour of these technical details, for those new to working on Bio-Formats itself, making it easier to understand how the information from the other sections fits into the big picture.
Terms and concepts
Bio-Formats can read image data from files for many formats, and can write image data to files for some formats. An image may have many two-dimensional “planes” of pixel intensity values. Each pixel on a plane is identified by its x, y values. Planes within an image may be identified by various dimensions including z (third spatial dimension), c (channel, e.g. wavelength) or t (time). Planes may be divided into tiles, which are rectangular subsections of a plane; this is helpful in handling very large planes. A file (or set of related files) on disk may contain multiple images: each image is identified by a unique series number.
An image is more than a set of planes: it also has metadata. Bio-Formats distinguishes core metadata, such as the x, y, z, c, t dimensions of the image, from format-specific original metadata, e.g. information about the microscope and its settings, which is represented as a dictionary of values indexed by unique keys. Metadata apply to the image data as a whole, or separately to specific series within it.
Bio-Formats is able to translate the above metadata into a further form, OME metadata. The translation may be partial or incomplete, but remains very useful for allowing the metadata of images from different file formats to be used and compared in a common format defined by the OME data model.
Implementation
Bio-Formats is primarily a Java project. It can be used from MATLAB and there is also a separate C++ implementation (OME Files C++). The source code is available for download and sometimes the user community contributes code back into Bio-Formats by opening a pull request on GitHub. Bio-Formats is built from source with Ant or Maven and some of the Bio-Formats source code is generated from other files during the build process. The resulting JARs corresponding to official Bio-Formats releases are available for download.
Readers and writers for different image file formats are implemented in separate Java classes. Readers for related formats may reflect that relationship in the Java class hierarchy. Simple standalone command-line tools are provided with Bio-Formats, but it is more commonly used as a third-party library by other applications. Various examples show how one may use Bio-Formats in different ways in writing a new application that reads or writes image data. A common pattern is to initialize a reader based on the image data’s primary file, then query that reader for the metadata and planes of interest.
The set of readers is easily modified. The readers.txt file lists the readers to try in determining an image file’s format, and there are many useful classes and methods among the Bio-Formats Java code to assist in writing new readers and writers.
Obtaining and building Bio-Formats
Note
Bio-Formats requires Java 8 or above
Source code
The source code for this Bio-Formats release is available from the downloads site. This release and the latest Bio-Formats source code are also available from the Git repository. This may be accessed using the repository path:
git@github.com:openmicroscopy/bioformats.git
More information about Git and client downloads are available from the Git project website. You can also browse the Bio-Formats source on GitHub
Note
Windows users must set git to use core.autocrlf=input to
ensure that Bio-Formats uses LF rather than CRLF line endings,
otherwise the build will fail (Genshi can’t process code templates
with CRLF line endings, leading to broken sources being
generated). This can be set globally in the registry when
installing msysgit or by editing etc/gitconfig
in the git installation directory. Annoyingly, these settings
appear to override per-user and per-repository configuration
values, requiring these to be set globally.
Lastly, you can browse the Bio-Formats Javadocs online, or generate them yourself using the “docs” Ant target.
Source code structure
The Bio-Formats code is divided into several projects. Core components are located in subfolders of the components folder, with some components further classified into components/forks, depending on the nature of the project. See the Component overview for more information, including associated build targets for each component.
Each project has a corresponding Maven POM file, which can be used to work with the project in your favorite IDE, or from the command line, once you have cloned the source.
Building from source
Instructions for several popular options follow. In all cases, make sure that the prerequisites are installed before you begin.
If you are interested in working on the Bio-Formats source code itself, you can load it into your favorite IDE, or develop with your favorite text editor.
NetBeans
NetBeans comes with Maven support built in. To import the Bio-Formats source, perform the following steps:
Select from the menu - choose the top-level path to bioformats.git and click
In the ‘Projects’ tab on the left-hand side, expand the ‘Bio-Formats projects’ entry - you should now have a series of folders including ‘Other Sources’, ‘Modules’ and ‘Dependencies.
Expand the ‘Modules’ folder to give a list of components and then double-click the desired project(s) to work with them.
Alternately, you can clone the source directly from NetBeans into a project by selecting from the menu.
Eclipse
Eclipse uses the “Maven Integration for Eclipse” (m2e) plugin to work with
Maven projects. It is more flexible than Eclipse’s built-in project
management because m2e transparently converts between project dependencies
and JAR dependencies (stored in the Maven repository in
~/.m2/repository) on the build path, depending on which projects are
currently open.
We recommend using Eclipse 4.3 (Kepler) or later, specifically - “Eclipse IDE for Java developers”. It comes with m2e installed (http://eclipse.org/downloads/compare.php?release=kepler).
You can import the Bio-Formats source by choosing from the menu and browsing to the top-level folder of your Bio-Formats working copy. Alternatively, run the Eclipse Maven target with mvn eclipse:eclipse to create the Eclipse project files, then use .
IntelliJ IDEA
IntelliJ IDEA can build Bio-Formats using either Maven or Ant. Go to and browse to the top-level folder of your Bio-Formats working copy. Select or select the Maven tab on the right of the screen.
Command line
If you prefer developing code with a text editor such as vim or emacs, you can use the Ant or Maven command line tools to compile Bio-Formats. The Bio-Formats source tree provides parallel build systems for both Ant and Maven, so you can use either one to build the code.
For a list of Ant targets, run:
ant -p
In general, ant jars or ant tools is the correct command.
When using Maven, Bio-Formats is configured to run the “install” target
by default, so all JARs will be copied into your local Maven repository
in ~/.m2/repository. Simply run:
mvn
With either Ant or Maven, you can use similar commands in any subproject folder to build just that component.
Component overview
The Bio-Formats code repository is divided up into separate components.
The Ant targets to build each component from the repository root are noted in the component descriptions below. Unless otherwise noted, each component can also be built with Maven by running mvn in the component’s subdirectory. The Maven module name for each component (as it is shown in most IDEs) is also noted in parenthesis.
Core components
The most commonly used and actively modified components.
Internal testing components
These components are used heavily during continuous integration testing, but are less relevant for active development work.
Forks of existing projects
All components
bio-formats-plugins (Bio-Formats Plugins for ImageJ):
Ant: jar-bio-formats-plugins
Everything pertaining to the Bio-Formats plugins for ImageJ lives in this
component. Note that when built, this component produces
bio-formats_plugins.jar (instead of bio-formats-plugins.jar) to
be in keeping with ImageJ plugin naming conventions.
bio-formats-tools (Bio-Formats command line tools):
Ant: jar-bio-formats-tools
The classes that implement the showinf, bfconvert, and mkfake command line tools are contained in this component. Note that this is built with the jar-bio-formats-tools Ant target, and not the tools target (which is the Ant equivalent of bundles).
bundles (bioformats_package bundle, LOCI Tools bundle):
Ant: tools
This is only needed by the Maven build system, and is used to aggregate all of
the individual .jar files into bioformats_package.jar. There should
not be any code here, just build system files.
This is a fork of JAI ImageIO. JAI ImageIO is no longer maintained; the most active fork is jai-imageio-core on GitHub. JAI provides support for decoding YCbCr JPEG-2000 data. This is primarily needed for reading images from histology/pathology formats in formats-gpl. There are no dependencies on other components.
The status of this component means that you may encounter errors due to conflicting JARs e.g. between Bio-Formats and other toolboxes within Fiji or MATLAB, especially when trying to open JPEG-2000 data. In this case, you will need to remove the conflicting JAR(s) as a workaround.
forks/turbojpeg (libjpeg-turbo Java bindings):
Ant: jar-turbojpeg
This is a fork of libjpeg-turbo. There are not any real code changes, but having this as a separate component allows us to package the libjpeg-turbo Java API together with all of the required binaries into a single .jar file using native-lib-loader. There are no dependencies on other components.
formats-api (Bio-Formats API):
Ant: jar-formats-api
This defines all of the high level interfaces and abstract classes for reading and writing files. There are no file format readers or writers actually implemented in this component, but it does contain the majority of the API that defines Bio-Formats. formats-bsd and formats-gpl implement this API to provide file format readers and writers. ome-common and ome-xml are both required as part of the interface definitions.
formats-bsd (BSD Bio-Formats readers and writers):
Ant: jar-formats-bsd
This contains readers and writers for formats which have a publicly available specification, e.g. TIFF. Everything in the component is BSD-licensed.
formats-gpl (Bio-Formats library):
Ant: jar-formats-gpl
The majority of the file format readers and some file format writers are contained in this component. Everything in the component is GPL-licensed (in contrast with formats-bsd). Most file formats represented in this component do not have a publicly available specification.
test-suite (Bio-Formats testing framework):
Ant: jar-tests
All tests that operate on files from our data repository (i.e. integration tests) are included in this component. These tests are primarily run by the continuous integration jobs, and verify that there are no regressions in reading images or metadata.
External components
The following have been decoupled from the Bio-Formats code repository and are now available as separate build dependencies:
Decoupled OME data model components:
Usage examples for Bio-Formats with Maven and Gradle.
The Sphinx source repository for this manual.
Provides I/O classes that unify reading from files on disk, streams or files in memory, compressed streams, and non-file URLs. The primary entry points are Location, RandomAccessInputStream (for reading), and RandomAccessOutputStream (for writing).
In addition to I/O, there are several classes to assist in working with XML (XMLTools), date/timestamps (DateTools), logging configuration (DebugTools), and byte arithmetic (DataTools).
Provides classes for encoding and decoding compressed data for a variety of compression formats. ome-common is a required dependency for I/O and service loading.
This is a fork of the mdbtools-java project. There are numerous bug fixes, as well as changes to reduce the memory required for large files. There are no dependencies on other components.
This is a fork of Apache POI, which allows reading of Microsoft OLE document files. We have made substantial changes to support files larger than 2GB and reduce the amount of memory required to open a file. I/O is also handled by classes from ome-common, which allows OLE files to be read from memory.
Java implementation of the Metakit database specification. This uses classes from ome-common and is used by formats-gpl, but is otherwise independent of the main Bio-Formats API.
This component contains classes that represent the OME-XML schema. Some classes are committed to the Git repository, but the majority are generated at build time by using XSD-FU to parse the OME-XML schema files. Classes from this component are used by Bio-Formats to read and write OME-XML, but they can also be used independently.
All released and in-progress OME-XML schema files are contained in this component. The specification component is also the location of all XSLT stylesheets for converting between OME-XML schema versions, as well as example OME-XML files in each of the released schema versions.
MIPAV stubs.
This component provides empty classes that mirror third-party dependencies which are required at compile time but cannot be included in the build system (usually due to licensing issues). The build succeeds since required class names are present with the correct method signatures; the end user is then expected to replace the stub .jar files at runtime.
This component contains the Java bindings for jxrlib, an open source implementation of the JPEG-XR image format standard.
Reading files
Basic file reading
Bio-Formats provides several methods for retrieving data from files in an arbitrary (supported) format. These methods fall into three categories: raw pixels, core metadata, and format-specific metadata. All methods described here are present and documented in loci.formats.IFormatReader. In general, it is recommended that you read files using an instance of loci.formats.ImageReader. While it is possible to work with readers for a specific format, ImageReader contains additional logic to automatically detect the format of a file and delegate subsequent calls to the appropriate reader.
Prior to retrieving pixels or metadata, it is necessary to call setId(java.lang.String) on the reader instance, passing in the name of the file to read. Some formats allow multiple series (5D image stacks) per file; in this case you may wish to call setSeries(int) to change which series is being read.
Raw pixels are always retrieved one plane at a time. Planes are returned as raw byte arrays, using one of the openBytes methods.
Core metadata is the general term for anything that might be needed to work with the planes in a file. A list of core metadata fields is given in the table below together with the appropriate accessor method:
Core metadata field |
API method |
|---|---|
image width |
|
image height |
|
number of series per file |
|
total number of images per series |
|
number of slices in the current series |
|
number of timepoints in the current series |
|
number of actual channels in the current series |
|
number of channels per image |
|
the ordering of the images within the current series |
|
whether each image is RGB |
|
whether the pixel bytes are in little-endian order |
|
whether the channels in an image are interleaved |
|
the type of pixel data in this file |
All file formats are guaranteed to accurately report core metadata.
Bio-Formats also converts and stores additional information which can be stored and retrieved
from the OME-XML Metadata. These fields can be accessed in a similar way to the core metadata above.
An example of such values would be the physical size of dimensions X, Y and Z. The accessor methods
for these properties return a Length object which
contains both the value and unit of the dimension. These lengths can also be converted to other units using
value(ome.units.unit.Unit)
An example of reading and converting these physical sizes values can be found in
ReadPhysicalSize.java.
Format-specific metadata refers to any other data specified in the file - this includes acquisition and hardware parameters, among other things. This data is stored internally in a java.util.Hashtable, and can be accessed in one of two ways: individual values can be retrieved by calling getMetadataValue(java.lang.String), which gets the value of the specified key. Note that the keys in this Hashtable are different for each format, hence the name “format-specific metadata”.
See Bio-Formats metadata processing for more information on the metadata capabilities that Bio-Formats provides.
See also
- IFormatReader
Source code of the
loci.formats.IFormatReaderinterfaceOrthogonalReader.javaExample of reading XZ and YZ image planes from a file
File reading extras
The previous section described how to read pixels as they are stored in the file. However, the native format is not necessarily convenient, so Bio-Formats provides a few extras to make file reading more flexible.
The loci.formats.ReaderWrapper API that implements
loci.formats.IFormatReaderallows to define “wrapper” readers that take a reader in the constructor, and manipulate the results somehow, for convenience. Using them is similar to the java.io InputStream/OutputStream model: just layer whichever functionality you need by nesting the wrappers.The table below summarizes a few wrapper readers of interest:
Wrapper reader
Functionality
Allows pixel data to be returned as BufferedImages instead of raw byte arrays
Uses advanced pattern matching heuristics to group files that belong to the same dataset
Makes sure that all planes are grayscale - RGB images are split into 3 separate grayscale images
Merges grayscale images to RGB if the number of channels is greater than 1
Converts indexed color images to RGB images
Provides an API for retrieving the minimum and maximum pixel values for each channel
Provides an API for changing the dimension order of a file
Caches the state of the reader into a memoization file
loci.formats.ImageTools and loci.formats.gui.AWTImageTools provide a number of methods for manipulating BufferedImages and primitive type arrays. In particular, there are methods to split and merge channels in a BufferedImage/array, as well as converting to a specific data type (e.g. convert short data to byte data).
Troubleshooting
Importing multi-file formats (Leica LEI, PerkinElmer, FV1000 OIF, ICS, and Prairie TIFF, to name a few) can fail if any of the files are renamed. There are “best guess” heuristics in these readers, but they are not guaranteed to work in general. So please do not rename files in these formats.
If you are working on a Macintosh, make sure that the data and resource forks of your image files are stored together. Bio-Formats does not handle separated forks (the native QuickTime reader tries, but usually fails).
Bio-Formats file readers are not thread-safe. If files are read within a parallelized environment, a new reader must be fully initialized in each parallel session. See Improving reading performance about ways to improve file reading performance in multi-threaded mode.
Writing files
The loci.formats.IFormatWriter API is very similar to the reader API, in that files are written one plane at time (rather than all at once).
The file formats which can be written using Bio-Formats are marked in the supported formats table with a green tick in the ‘export’ column. These include, but are not limited to:
TIFF (uncompressed, LZW, JPEG, or JPEG-2000)
OME-TIFF (uncompressed, LZW, JPEG, or JPEG-2000)
JPEG
PNG
AVI (uncompressed)
QuickTime (uncompressed)
Encapsulated PostScript (EPS)
OME-XML (not recommended)
All writers allow the output file to be changed before the last plane has been written. This allows you to write to any number of output files using the same writer and output settings (compression, frames per second, etc.), and is especially useful for formats that do not support multiple images per file.
See also
- IFormatWriter
Source code of the
loci.formats.IFormatWriterinterface- loci.formats.tools.ImageConverter
Source code of the
loci.formats.tools.ImageConverterclass- Further details on exporting raw pixel data to OME-TIFF files
Examples of OME-TIFF writing
Using Bio-Formats as a Java library
Using Bio-Formats as a Java library
Bio-Formats as a Maven, Gradle or Ivy dependency
All released .jar artifacts are published to and can be obtained from
the OME Artifactory. The
“Client Settings” section of the Artifactory main page provides example code
snippets for inclusion into your Gradle, Maven or Ivy project, which will
enable the use of this repository.
Changed in version 6.12.0.
As of Bio-Formats 6.12.0 consumers will have to directly declare a dependency for their chosen SLF4J logging framework. See Logging for further details.
Examples of getting started with Bio-Formats using Maven or Gradle are given in the https://github.com/ome/bio-formats-examples repository. OMERO uses Ivy to manage its Java dependencies including Bio-Formats.
Note
In order to retrieve the NetCDF dependency of Bio-Formats, it is necessary
to configure the Unidata releases repository in addition to Maven Central and
the OME artifactory in your https://github.com/ome/bio-formats-examples/blob/master/pom.xml, https://github.com/ome/bio-formats-examples/blob/master/build.gradle or
ivy.xml file.
Bio-Formats as a Java library
Alternatively Bio-Formats can be used by including its component jar files.
You can download formats-gpl.jar to
use it as a library. Just add formats-gpl.jar to your CLASSPATH or
build path. You will also need ome-common.jar for common I/O functions,
ome-xml.jar for metadata standardization, and a
SLF4J binding for Logging.
Dependencies
The complete list of third-party dependencies for formats-gpl.jar is as follows:
Package |
Maven name |
License |
|---|---|---|
cisd:jhdf5:19.04.0 |
||
cisd:base:18.09.0 |
||
commons-io:commons-io:2.7 |
||
org.apache.commons:commons-lang3:3.10 |
||
com.adobe.xmp:xmpcore:6.1.11 |
||
com.beust:jcommander:1.27 |
||
com.drewnoakes:metadata-extractor:2.18.0 |
||
io.airlift:aircompressor:0.21 |
||
com.esotericsoftware.kryo:kryo:4.0.2 |
||
com.esotericsoftware:reflectasm:1.11.3 |
||
org.ow2.asm:asm:5.0.4 |
||
com.esotericsoftware.minlog:minlog:1.3 |
||
com.google.guava:guava:32.0.0-jre |
||
com.jgoodies:jgoodies-common:1.7.0 |
||
com.jgoodies:jgoodies-forms:1.7.2 |
||
commons-lang:commons-lang:2.6 |
||
commons-logging:commons-logging:1.2 |
||
edu.ucar:cdm:5.3.3 |
||
joda-time:joda-time:2.2 |
||
junit:junit:4.10 |
||
org.beanshell:bsh:2.0b4 |
||
org.hamcrest:hamcrest-core:1.2.1 |
||
org.objenesis:objenesis:2.5.1 |
||
org.perf4j:perf4j:0.9.16 |
||
org.scijava:native-lib-loader:2.1.4 |
||
org.slf4j:slf4j-api:2.0.9 |
||
org.testng:testng:6.8 |
||
org.yaml:snakeyaml:1.32 |
||
xalan:serializer:2.7.3 |
||
xalan:xalan:2.7.3 |
||
xerces:xercesImpl:2.12.2 |
||
xml-apis:xml-apis:1.4.01 |
||
io.minio:minio:5.0.2 |
||
com.google.http-client:google-http-client-xml:1.20.0 |
||
com.google.http-client:google-http-client:1.20.0 |
||
xpp3:xpp3:1.1.4c |
||
com.squareup.okhttp3:okhttp:3.7.0 |
||
com.squareup.okio:okio:1.12.0 |
||
javax.xml.bind:jaxb-api:2.3.0 |
||
org.json:json:20230227 |
||
org.xerial:sqlite-jdbc:3.28.0 |
||
com.google.guava:failureaccess:1.0.1 |
||
com.google.guava:listenablefuture:9999.0-empty-to-avoid-conflict-with-guava |
||
com.google.code.findbugs:jsr305:3.0.2 |
||
org.checkerframework:checker-qual:2.11.1 |
||
com.google.errorprone:error_prone_annotations:2.3.4 |
||
com.google.j2objc:j2objc-annotations:1.3 |
||
edu.ucar:httpservices:5.3.3 |
||
org.apache.httpcomponents:httpclient:4.5.9 |
||
commons-codec:commons-codec:1.11 |
||
org.apache.httpcomponents:httpmime:4.5.9 |
||
com.mchange:c3p0:0.9.5.3 |
||
com.mchange:mchange-commons-java:0.2.15 |
||
com.fasterxml.jackson.core:jackson-core:2.14.1 |
||
com.fasterxml.jackson.core:jackson-annotations:2.14.1 |
||
com.fasterxml.jackson.core:jackson-databind:2.14.1 |
The below are optional dependencies :
Package |
Maven name |
License |
|---|---|---|
ch.qos.logback:logback-classic:1.3.14 |
||
ch.qos.logback:logback-core:1.3.14 |
As described in Versioning policy, the minor version number of a Bio-Formats release will always be increased if the version of a non-OME/external dependency is bumped.
Dependency lists for any component can be generated by checking out the code as described in Source code and then running:
cd components/$COMPONENT_NAME
mvn dependency:tree
Examples of usage
File reading and performance:
MultiFileExample - Simple example of how to open multiple files simultaneously.
ParallelRead - Reads all files in given directory in parallel, using a separate thread for each.
ReadWriteInMemory - Tests the Bio-Formats I/O logic to and from byte arrays in memory.
OrthogonalReader - Reads image data in XZ and YZ order.
File writing:
MinimumWriter - A command line utility demonstrating the minimum amount of metadata needed to write a file.
FileExport - Write a file in any supported output format.
TiledExport - Shows how to convert a file one tile at a time, instead of one plane at a time (needed for very large images).
FileExportSPW - Write a file with plate (OME SPW) metadata.
File compression:
makeLZW - Converts the given image file to an LZW-compressed TIFF.
Metadata extract/print:
GetPhysicalMetadata - Uses Bio-Formats to extract some basic standardized (format-independent) metadata.
ReadPhysicalSize - Reads physical size information uses the units API to display in micrometers.
ImageInfo - A more involved command line utility for thoroughly reading an input file, printing some information about it, and displaying the pixels onscreen using the Bio-Formats viewer.
PrintTimestamps - A command line example demonstrating how to extract timestamps from a file.
PrintLensNA - Uses Bio-Formats to extract lens numerical aperture in a format-independent manner from a dataset.
PrintROIs - A simple example of how to retrieve ROI data parsed from a file.
SubResolutionExample - Demonstration of the sub-resolution API.
Metadata add/edit:
EditImageName - Edits the given file’s image name (but does not save back to disk).
EditTiffComment - Allows raw user TIFF comment editing for the given TIFF files.
writeMapAnnotations - Example method to write MapAnnotations to the ome-xml.
CommentSurgery - Edits a TIFF ImageDescription comment, particularly the OME-XML comment found in OME-TIFF files.
Image converters:
ImageConverter - A simple command line tool for converting between formats.
FileConvert - Converts a file in any supported format to any supported output format.
ConvertToOmeTiff - Converts the given files to OME-TIFF format.
WritePreCompressedPlanes - Writes the pixels from a set of JPEG files to a single TIFF. The pixel data is used as-is, so no decompression or re-compression is performed.
GeneratePyramidResolutions - Convert a file containing a single large image to a pyramid OME-TIFF.
TiledReaderWriter - Convert a file to OME-TIFF one tile at a time.
OverlappedTiledWriter - Convert a file to OME-TIFF one tile at a time, when the image size is not a multiple of the tile size.
SimpleTiledWriter - Convert a file to OME-TIFF using automatic tiling.
ImageJ plugins:
Simple_Read - A simple ImageJ plugin demonstrating how to use Bio-Formats to read files into ImageJ (see ImageJ overview).
Read_Image - An ImageJ plugin that uses Bio-Formats to build up an image stack, reading image planes one by one (see ImageJ overview).
Mass_Importer - A simple plugin for ImageJ that demonstrates how to open all image files in a directory using Bio-Formats, grouping files with similar names to avoiding opening the same dataset more than once (see ImageJ overview).
Image processing utilities:
SewTiffs - Stitches the first plane from a collection of TIFFs into a single file.
SumPlanes - Sums together the image planes from the given file,and saves the result to a 16-bit TIFF.
A Note on Java Web Start (bioformats_package.jar vs. formats-gpl.jar)
To use Bio-Formats with your Java Web Start application, we recommend using formats-gpl.jar rather than bioformats_package.jar—the latter is merely a bundle of formats-gpl.jar plus all its optional dependencies.
The bioformats_package.jar bundle is intended as a convenience (e.g. to simplify installation as an ImageJ plugin), but is by no means the only solution for developers. We recommend using formats-gpl.jar as a separate entity depending on your needs as a developer.
The bundle is quite large because we have added support for several formats that need large helper libraries (e.g. Imaris’ HDF-based format). However, these additional libraries are optional; Bio-Formats has been coded using reflection so that it can both compile and run without them.
When deploying a JNLP-based application, using bioformats_package.jar directly is not the best approach, since every time Bio-Formats is updated, the server would need to feed another 15+ MB JAR file to the client. Rather, Web Start is a case where you should keep the JARs separate, since JNLP was designed to make management of JAR dependencies trivial for the end user. By keeping formats-gpl.jar and the optional dependencies separate, only a <1 MB JAR needs to be updated when formats-gpl.jar changes.
As a developer, you have the option of packaging formats-gpl.jar with as many or as few optional libraries as you wish, to cut down on file size as needed. You are free to make whatever kind of “stripped down” version you require. You could even build a custom formats-gpl.jar that excludes certain classes, if you like.
Units of measurement
Since Bio-Formats 5.1 and the adoption of the 2015-01 OME Data Model, the data model and the corresponding Bio-Formats model and metadata APIs have added support for units of measurement. Previously, the units for various properties such as the physical size of an image, stage position, confocal pinhole size, light wavelengths etc. were fixed in the model. This was however somewhat inflexible, and not appropriate for imaging modalities at widely different scales. The solution to this was to add a unit of measurement to each of these properties. The image size, for example, was previously specified to be stored in micrometers but may now be specified in any SI length unit of choice, or one of the supported non-SI length units. This permits the preservation of the unit used by a proprietary file format or used at acquisition time, for example nanometers, millimeters, meters, or inches or thousandths of an inch could be used instead.
At the OME-XML level, the properties continue to use the old attribute
names. They are supplemented by an additional attribute with a
Unit suffix, for example the PhysicalSizeX attribute and its
companion PhysicalSizeXUnit attribute.
At the API level, two classes are used:
Unit<T>represents a unit system for a given dimension such as length, pressure or time.
Quantityrepresents a value and unit in a given unit system; this is subclassed for each of the supported dimensions such as
Length,Pressureetc. For example theLengthclass could represent the value and unit of 5.3 µm and thePressureclass 956 mbar.
All of the model and metadata APIs pass Quantity objects in place
of raw numerical values. Updating your code will require replacing
the use of raw values with quantities. Where your code needs to deal
with the quantity in a specific unit, for example µm, you will need to
perform an explicit unit conversion to transform the value to the
required unit.
The three situations you will need to deal with are:
getting a quantity from a
getmethod in the APIconverting a quantity to a desired unit
setting a quantity with a
setmethod in the API (possibly also requiring the creation of a quantity)
Examples of how to use units and quantities for these purposes are
shown in the sections Reading files (ReadPhysicalSize
example which uses getPixelsPhysicalSize and also demonstrates
unit conversion) and Further details on exporting raw pixel data to OME-TIFF files
(setPixelsPhysicalSize).
Exporting files using Bio-Formats
This guide pertains to version 4.2 and later.
Basic conversion
The first thing we need to do is set up a reader:
// create a reader that will automatically handle any supported format
IFormatReader reader = new ImageReader();
// tell the reader where to store the metadata from the dataset
MetadataStore metadata;
try {
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
metadata = service.createOMEXMLMetadata();
}
catch (DependencyException exc) {
throw new FormatException("Could not create OME-XML store.", exc);
}
catch (ServiceException exc) {
throw new FormatException("Could not create OME-XML store.", exc);
}
reader.setMetadataStore(metadata);
// initialize the dataset
reader.setId("/path/to/file");
Now, we set up our writer:
// create a writer that will automatically handle any supported output format
IFormatWriter writer = new ImageWriter();
// give the writer a MetadataRetrieve object, which encapsulates all of the
// dimension information for the dataset (among many other things)
OMEXMLService service = factory.getInstance(OMEXMLService.class);
writer.setMetadataRetrieve(service.asRetrieve(reader.getMetadataStore()));
// initialize the writer
writer.setId("/path/to/output/file");
Note that the extension of the file name passed to ‘writer.setId(…)’ determines the file format of the exported file.
Now that everything is set up, we can start writing planes:
for (int series=0; series<reader.getSeriesCount(); series++) {
reader.setSeries(series);
writer.setSeries(series);
for (int image=0; image<reader.getImageCount(); image++) {
writer.saveBytes(image, reader.openBytes(image));
}
}
Finally, make sure to close both the reader and the writer. Failure to do so can cause:
file handle leaks
memory leaks
truncated output files
Fortunately, closing the files is very easy:
reader.close();
writer.close();
Converting to multiple files
The recommended method of converting to multiple files is to use a single IFormatWriter, like so:
// you should have set up a reader as in the first example
ImageWriter writer = new ImageWriter();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
writer.setMetadataRetrieve(service.asRetrieve(reader.getMetadataStore()));
// replace this with your own filename definitions
// in this example, we're going to write half of the planes to one file
// and half of the planes to another file
String[] outputFiles =
new String[] {"/path/to/file/1.tiff", "/path/to/file/2.tiff"};
writer.setId(outputFiles[0]);
int planesPerFile = reader.getImageCount() / outputFiles.length;
for (int file=0; file<outputFiles.length; file++) {
writer.changeOutputFile(outputFiles[file]);
for (int image=0; image<planesPerFile; image++) {
int index = file * planesPerFile + image;
writer.saveBytes(image, reader.openBytes(index));
}
}
reader.close();
writer.close();
The advantage here is that the relationship between the files is preserved when converting to formats that support multi-file datasets internally (namely OME-TIFF). If you are only converting to graphics formats (e.g. JPEG, AVI, MOV), then you could also use a separate IFormatWriter for each file, like this:
OMEXMLService service = factory.getInstance(OMEXMLService.class);
// again, you should have set up a reader already
String[] outputFiles = new String[] {"/path/to/file/1.avi", "/path/to/file/2.avi"};
int planesPerFile = reader.getImageCount() / outputFiles.length;
for (int file=0; file<outputFiles.length; file++) {
ImageWriter writer = new ImageWriter();
writer.setMetadataRetrieve(service.asRetrieve(reader.getMetadataStore()));
writer.setId(outputFiles[file]);
for (int image=0; image<planesPerFile; image++) {
int index = file * planesPerFile + image;
writer.saveBytes(image, reader.openBytes(index));
}
writer.close();
}
Known issues
Further details on exporting raw pixel data to OME-TIFF files
This document explains how to export pixel data to OME-TIFF using Bio-Formats version 4.2 and later.
Working example code is provided in
FileExport.java - code from that class
is referenced here in part. You will need to have bioformats_package.jar in
your Java CLASSPATH in order to compile FileExport.java.
The first thing that must happen is we must create the object that stores OME-XML metadata. This is done as follows:
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata omexml = service.createOMEXMLMetadata();
The ‘omexml’ object can now be used in our code to store OME-XML metadata, and by the file format writer to retrieve OME-XML metadata.
Now that we have somewhere to put metadata, we need to populate as much metadata as we can. The minimum amount of metadata required is:
endianness of the pixel data
the order in which dimensions are stored
the bit depth of the pixel data
the number of channels
the number of timepoints
the number of Z sections
the width (in pixels) of an image
the height (in pixels) of an image
the number of samples per channel (3 for RGB images, 1 otherwise)
We populate that metadata as follows:
omexml.setImageID("Image:0", 0);
omexml.setPixelsID("Pixels:0", 0);
// specify that the pixel data is stored in big-endian order
// replace 'TRUE' with 'FALSE' to specify little-endian order
omexml.setPixelsBinDataBigEndian(Boolean.TRUE, 0, 0);
omexml.setPixelsDimensionOrder(DimensionOrder.XYCZT, 0);
omexml.setPixelsType(PixelType.UINT16, 0);
omexml.setPixelsSizeX(new PositiveInteger(width), 0);
omexml.setPixelsSizeY(new PositiveInteger(height), 0);
omexml.setPixelsSizeZ(new PositiveInteger(zSectionCount), 0);
omexml.setPixelsSizeC(new PositiveInteger(channelCount *
samplesPerChannel), 0);
omexml.setPixelsSizeT(new PositiveInteger(timepointCount), 0);
for (int channel=0; channel<channelCount; channel++) {
omexml.setChannelID("Channel:0:" + channel, 0, channel);
omexml.setChannelSamplesPerPixel(new PositiveInteger(samplesPerChannel),
0, channel);
}
Unit<Length> unit = UNITS.MICROMETER;
Length physicalSizeX = new Length(1.0, unit);
Length physicalSizeY = new Length(1.5, unit);
Length physicalSizeZ = new Length(2, unit);
omexml.setPixelsPhysicalSizeX(physicalSizeX, 0);
omexml.setPixelsPhysicalSizeY(physicalSizeY, 0);
omexml.setPixelsPhysicalSizeZ(physicalSizeZ, 0);
There is much more metadata that can be stored; please see the Javadoc for loci.formats.meta.MetadataStore for a complete list.
Now that we have defined all of the metadata, we need to create a file writer:
ImageWriter writer = new ImageWriter();
Now we must associate the ‘omexml’ object with the file writer:
writer.setMetadataRetrieve(omexml);
The writer now knows to retrieve any metadata that it needs from ‘omexml’.
We now tell the writer which file it should write to:
writer.setId("output-file.ome.tiff");
It is critical that the file name given to the writer ends with “.ome.tiff” or “.ome.tif”, as it is the file name extension that determines which format will be written.
Now that everything is set up, we can save the image data. This is done plane by plane, and we assume that the pixel data is stored in a 2D byte array ‘pixelData’:
int sizeC = omexml.getPixelsSizeC(0).getValue();
int sizeZ = omexml.getPixelsSizeZ(0).getValue();
int sizeT = omexml.getPixelsSizeT(0).getValue();
int samplesPerChannel = omexml.getChannelSamplesPerPixel(0).getValue();
sizeC /= samplesPerChannel;
int imageCount = sizeC * sizeZ * sizeT;
for (int image=0; image<imageCount; image++) {
writer.saveBytes(image, pixelData[image]);
}
}
Finally, we must tell the writer that we are finished, so that the output file can be properly closed:
writer.close();
There should now be a complete OME-TIFF file at whichever path was specified above.
Tiled reading and writing in Bio-Formats
Reading tiled images
The reading of tiled images is straightforward and can be done in much the same way as reading a full image. In this case, to read an individual tile, we pass to the reader parameters for the x and y coordinates of the tile to read and the height and width of tile desired.
byte[] tile = reader.openBytes(image, tileX, tileY, tileSizeX, tileSizeY);
For TIFF-based readers, if the image has been written using tiles, then the tile width and height used can be found as below. These values can then be used with the above command to read the correct tiles individually.
IFD tileIFd = reader.getIFDs().get(0);
int tileHeight = tileIFd.getIFDIntValue(IFD.TILE_LENGTH);
int tileWidth = tileIFd.getIFDIntValue(IFD.TILE_WIDTH);
Introduction to tiled writing
Tiled writing is currently supported for TIFF-based formats. To set up an image writer to use tiling the following 2 API functions are provided:
public int setTileSizeX(int tileSize) throws FormatException
public int setTileSizeY(int tileSize) throws FormatException
Each function takes in an integer parameter for the desired tile size. As not all tile sizes are supported, the image writer will round the requested value to the nearest supported tile size. The return value will contain the actual tiling size which will be used by the writer.
To find out the tiling size currently being used at any point there are 2 further API functions to get the current tile size for a writer. If tiling is not being used or is not supported then the full image height and width will be returned.
public int getTileSizeX() throws FormatException
public int getTileSizeY() throws FormatException
The tiling parameters for writers must be set after the image metadata is set. An example of initializing a writer for tiling is shown below.
// set up the writer and associate it with the output file
writer = new OMETiffWriter();
writer.setMetadataRetrieve(omexml);
writer.setInterleaved(reader.isInterleaved());
// set the tile size height and width for writing
this.tileSizeX = writer.setTileSizeX(tileSizeX);
this.tileSizeY = writer.setTileSizeY(tileSizeY);
writer.setId(outputFile);
Simple tiled writing
The simplest way to write a tiled image is to set the tiling parameters on your image writer as above and have the writer automatically handle the tiling. Once the tile sizes have been set you may simply read and write your image files as normal.
// set up the writer and associate it with the output file
writer = new OMETiffWriter();
writer.setMetadataRetrieve(omexml);
writer.setInterleaved(reader.isInterleaved());
// set the tile size height and width for writing
this.tileSizeX = writer.setTileSizeX(tileSizeX);
this.tileSizeY = writer.setTileSizeY(tileSizeY);
writer.setId(outputFile);
- Full working example code is provided in
SimpleTiledWriter.java- code from that class is referenced here in part. You will need to havebioformats_package.jarin your JavaCLASSPATHin order to compileSimpleTiledWriter.java.
Reading and writing using tiling
For the most efficient reading and writing of tiles you may instead wish to read in and write out the individual image tiles one at a time.
To do this you can set up the reader and writer as in the previous example above. In this case, when setting the tile height and width used it is important to store the return values which will be the valid tile size used by the writer.
// set the tile height and width and store the actual values used by the writer
int tileSizeX = writer.setTileSizeX(tileSizeX);
int tileSizeY = writer.setTileSizeY(tileSizeY);
This time for each image you must determined the number of tiles using the actual tile height and width being used.
int width = reader.getSizeX();
int height = reader.getSizeY();
// Determined the number of tiles to read and write
int nXTiles = width / tileSizeX;
int nYTiles = height / tileSizeY;
if (nXTiles * tileSizeX != width) nXTiles++;
if (nYTiles * tileSizeY != height) nYTiles++;
Now each tile can be read and written individually.
for (int y=0; y<nYTiles; y++) {
for (int x=0; x<nXTiles; x++) {
// The x and y coordinates for the current tile
int tileX = x * tileSizeX;
int tileY = y * tileSizeY;
// Read tiles from the input file and write them to the output OME-Tiff
buf = reader.openBytes(image, tileX, tileY, tileSizeX, tileSizeY);
writer.saveBytes(image, buf, tileX, tileY, tileSizeX, tileSizeY);
}
}
- Full working example code is provided in
TiledReaderWriter.java- code from that class is referenced here in part. You will need to havebioformats_package.jarin your JavaCLASSPATHin order to compileTiledReaderWriter.java.
Tiles which overlap image size
It may not always be the case that the tile size divides evenly into the image height and width.
In these scenarios in which the last column or row of tiles overlaps with the image boundary, a smaller tile
is instead read or written for the final row or column. If a full sized tile with padding is written then a
loci.formats.FormatException will be thrown for Invalid tile size.
To deal with this we can modify the previous tiled writing example to check if the tile size will overlap the image boundaries. If it will not overlap then the full tile size is used, if it does then the tile size for that tile is modified to reflect the partial tile.
// If the last tile row or column overlaps the image size then only a partial tile
// is read or written. The tile size used is adjusted to account for any overlap.
int effTileSizeX = (tileX + tileSizeX) < width ? tileSizeX : width - tileX;
int effTileSizeY = (tileY + tileSizeY) < height ? tileSizeY : height - tileY;
// Read tiles from the input file and write them to the output OME-Tiff
buf = reader.openBytes(image, tileX, tileY, effTileSizeX, effTileSizeY);
writer.saveBytes(image, buf, tileX, tileY, effTileSizeX, effTileSizeY);
- Full working example code is provided in
OverlappedTiledWriter.java- code from that class is referenced here in part. You will need to havebioformats_package.jarin your JavaCLASSPATHin order to compileOverlappedTiledWriter.java.
Working with whole slide images
Bio-Formats supports many whole slide image formats, but effectively working with this type of data requires some extra considerations. Each file contains images representing one or more physical slides, with each slide typically stored at multiple resolutions. The width and height of a full resolution whole slide image often exceed 100,000 pixels, so the uncompressed image size may be several gigabytes. This means that only part of the full resolution image can be accessed at any given time.
JPEG or JPEG-2000 compression is typically used such that the size on disk is often less than 100MB. Most whole slide formats split each image into many small tiles of 1024×1024 pixels or smaller and compress each tile independently, though some (e.g. Hamamatsu ndpi) compress the whole image at once. Many supported whole slide formats are based upon TIFF, with vendor-specific extensions for metadata or tile storage. Notable exceptions include Zeiss CZI and cellSens VSI.
The original full resolution image and its resolutions are collectively referred to as an image pyramid. File formats which support image pyramids are noted by the Pyramid column in the supported formats table.
By default, openBytes will load from the full resolution image in the first pyramid stored in the file. Each resolution of each pyramid is stored as a separate series, and can be accessed by calling setSeries prior to retrieving pixel data.
There are additional API methods that can be used to make pyramids easier to work with. These can be enabled by calling setFlattenedResolutions(false) prior to setId.
After setFlattenedResolutions(false), each series represents an entire image pyramid and not
just a single resolution. Calling setSeries(...) then skips over
all other resolutions in the same pyramid, to either the next pyramid (if
multiple pyramids are stored), or the thumbnail or barcode image (if present).
To access the smaller resolutions in the pyramid, use the getResolutionCount()
and setResolution(int) methods.
Most formats only store one pyramid per fileset, but some (e.g. cellSens VSI) allow multiple pyramids. Almost all formats allow a thumbnail, slide overview, and/or slide barcode image. Bio-Formats always stores these images as separate series, after all of the pyramids. Be careful to check the pixel type for the extra images, as the type and channel count will often differ from that of the pyramid(s).
For an example of how to use the pyramid resolution API, see https://github.com/ome/bio-formats-examples/blob/master/src/main/java/SubResolutionExample.java.
Bio-Formats also provides some visibility into how the tiles are stored via the getOptimalTileWidth() and getOptimalTileHeight() methods. This is a suggestion of the size of tiles to be passed to openBytes(int, byte[], int, int, int, int), in order to minimize the number of tile decompressions. In most cases, and especially for the largest resolution, the whole image can’t be loaded at once. The amount of memory allocated is not a factor in being able to load the whole image, as no more than 2GB of pixel data can be stored in a single byte array and most full resolution images will exceed this limit.
Pyramids in OME-TIFF
Bio-Formats 6.0.0 and later can read and write image pyramids in the OME-TIFF format.
Reading OME-TIFF pyramids uses the same API as described above. Writing OME-TIFF pyramids requires the resolution dimensions
to be specified in an IPyramidStore object. GeneratePyramidResolutions
shows a simple example of how to do this.
The bfconvert command line tool will also
automatically write pyramids if the input file has at least one pyramid, the output format is OME-TIFF,
and the bfconvert -noflat option is specified.
Internal OMERO pyramid format
For files that contain very large images and are not in a format that supports pyramids, OMERO will generate its own image pyramid to improve visualization performance. Bio-Formats can read these generated pyramids, but cannot currently write them outside of OMERO. For details of how to read image pyramids with Bio-Formats, see Working with whole slide images
OMERO handles pyramid generation automatically for files that do not already have a stored pyramid, use a supported pixel type, and have images that exceed a specific XY size. The default XY size threshold is 3192×3192, but this can be configured in OMERO if necessary. Common formats for which a pyramid will be generated include Gatan DM3, MRC, and TIFF. Dedicated whole slide imaging formats such as SVS typically contain their own image pyramid, in which case an OMERO pyramid will not be generated.
For further information, see the OMERO pyramid specification.
In-memory reading and writing in Bio-Formats
Bio-Formats readers and writers are traditionally used to handle image files from disk. However it is also possible to achieve reading and writing of files from in-memory sources. This is handled by mapping the in-memory data to a file location using Location.mapFile().
Location.mapFile(fileName, byteArrayHandle);
This file location is not created on disk but rather maps internally to the in-memory data provided.
Reading file from memory
In order for Bio-Formats to read a file from memory it must be available in a byte array. For this example an input file is read from disk into a byte array.
// read in entire file
System.out.println("Reading file into memory from disk...");
File inputFile = new File(path);
int fileSize = (int) inputFile.length();
DataInputStream in = new DataInputStream(new FileInputStream(inputFile));
byte[] inBytes = new byte[fileSize];
in.readFully(inBytes);
System.out.println(fileSize + " bytes read.");
This data can now be handled by a Bio-Formats reader. This is achieved by providing a mapping from the in-memory data to a suitable filename which will be used by the reader. The filename used must have the same suffix as the original data type.
// determine input file suffix
String fileName = inputFile.getName();
int dot = fileName.lastIndexOf(".");
String suffix = dot < 0 ? "" : fileName.substring(dot);
// map input id string to input byte array
String inId = "inBytes" + suffix;
Location.mapFile(inId, new ByteArrayHandle(inBytes));
Once the in-memory data has been mapped to a suitable filename the data can be handled by the reader as normal.
// read in entire file
System.out.println("Reading file into memory from disk...");
File inputFile = new File(path);
int fileSize = (int) inputFile.length();
DataInputStream in = new DataInputStream(new FileInputStream(inputFile));
byte[] inBytes = new byte[fileSize];
in.readFully(inBytes);
System.out.println(fileSize + " bytes read.");
Writing to memory
To use a writer to output to memory rather than an output file a similar process is required. First a mapping is created between a suitable output filename and the in-memory data.
// map output id string to output byte array
String outId = fileName + ".ome.tif";
ByteArrayHandle outputFile = new ByteArrayHandle();
Location.mapFile(outId, outputFile);
The mapped filename can now be passed to initialize the writer as standard.
// write data to byte array using ImageWriter
System.out.println();
System.out.print("Writing planes to destination in memory: ");
ImageWriter writer = new ImageWriter();
writer.setMetadataRetrieve(omeMeta);
writer.setId(outId);
The data can then be written to memory using the same read and write loop which would normally be used to write a file to disk.
byte[] plane = null;
for (int i=0; i<imageCount; i++) {
if (plane == null) {
// allow reader to allocate a new byte array
plane = reader.openBytes(i);
}
else {
// reuse previously allocated byte array
reader.openBytes(i, plane);
}
writer.saveBytes(i, plane);
System.out.print(".");
}
reader.close();
writer.close();
System.out.println();
byte[] outBytes = outputFile.getBytes();
outputFile.close();
If desired the data written to memory can then be flushed to disk and written to an output file location.
// flush output byte array to disk
System.out.println();
System.out.println("Flushing image data to disk...");
File outFile = new File(fileName + ".ome.tif");
DataOutputStream out = new DataOutputStream(new FileOutputStream(outFile));
out.write(outBytes);
out.close();
See also
ReadWriteInMemory.java - Full source code which is
referenced here in part. You will need to have bioformats_package.jar in your
Java CLASSPATH in order to compile ReadWriteInMemory.java.
Logging
Logging frameworks
Bio-Formats uses SLF4J as a logging API. SLF4J is a facade and needs to be bound to a logging framework at deployment time. Two underlying logging frameworks are currently supported by Bio-Formats. Bio-Formats does not impose any specific SLF4J binding on downstream consumers as per the recommended SLF4J best practices. Some recommended bindings are as follows:
logback is the recommended framework and natively implements the SLF4J API. A logback version of 1.2.x is recommended as Bio-Formats has a hard dependency for slf4j-api 1.7.30. This means that logback versions 1.3.x and higher are not yet supported in Bio-Formats as they rely on slf4j-api 2.x.
log4j is the other logging framework supported by Bio-Formats and is primarily used in the MATLAB environment.
Examples of declaring these dependencies using Maven or Gradle are given in the Bio-Formats examples repository.
Initialization
The DebugTools class contains a series of framework-agnostic methods for the initialization and control of the logging system. This class uses reflection to detect the underlying logging framework and delegate the method calls to either Log4jTools or LogbackTools.
The main methods are described below:
DebugTools.enableLogging()will initialize the underlying logging framework. This call will result in a no-op if logging has been initialized either via a binding-specific configuration file (see logback configuration) or via a prior call toDebugTools.enableLogging().DebugTools.enableLogging(level)will initialize the logging framework under the same conditions as described above and set the root logger level if the initialization was succesful.DebugTools.setRootLevel(level)will override the level of the root logger independently of how the logging system was initialized.DebugTools.enableIJLogging()(logback-only) will add an ImageJ-specific appender to the root logger.
Changed in version 5.2.0: Prior to Bio-Formats 5.2.0, DebugTools.enableLogging(level)
unconditionally set the logging and root logger level. Use
DebugTools.setRootLevel(level) to restore this behavior.
Converting files from FV1000 OIB/OIF to OME-TIFF
This document explains how to convert a file from FV1000 OIB/OIF to OME-TIFF using Bio-Formats version 4.2 and later.
Working example code is provided in
FileConvert.java - code from that
class is referenced here in part. You will need to have
bioformats_package.jar in your Java CLASSPATH in order to compile
FileConvert.java.
The first thing that must happen is we must create the object that stores OME-XML metadata. This is done as follows:
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata omexml = service.createOMEXMLMetadata();
The ‘omexml’ object can now be used by both a file format reader and a file format writer for storing and retrieving OME-XML metadata.
Now that have somewhere to put metadata, we need to create a file reader and writer:
ImageReader reader = new ImageReader();
ImageWriter writer = new ImageWriter();
Now we must associate the ‘omexml’ object with the file reader and writer:
reader.setMetadataStore(omexml);
writer.setMetadataRetrieve(omexml);
The reader now knows to store all of the metadata that it parses into ‘omexml’, and the writer knows to retrieve any metadata that it needs from ‘omexml’.
We now tell the reader and writer which files will be read from and written to, respectively:
reader.setId("input-file.oib");
writer.setId("output-file.ome.tiff");
It is critical that the file name given to the writer ends with “.ome.tiff” or “.ome.tif”, as it is the file name extension that determines which format will be written.
Now that everything is set up, we can convert the image data. This is done plane by plane:
for (int series=0; series<reader.getSeriesCount(); series++) {
reader.setSeries(series);
writer.setSeries(series);
byte[] plane = new byte[FormatTools.getPlaneSize(reader)];
for (int image=0; image<reader.getImageCount(); image++) {
reader.openBytes(image, plane);
writer.saveBytes(image, plane);
}
}
The body of the outer ‘for’ loop may also be replaced with the following:
reader.setSeries(series);
writer.setSeries(series);
for (int image=0; image<reader.getImageCount(); image++) {
byte[] plane = reader.openBytes(image);
writer.saveBytes(image, plane);
}
But note that this will be a little slower.
Finally, we must tell the reader and writer that we are finished, so that the input and output files can be properly closed:
reader.close();
writer.close();
There should now be a complete OME-TIFF file at whichever path was specified above.
Using Bio-Formats in MATLAB
This section assumes that you have installed the MATLAB toolbox as instructed in the MATLAB user information page. Note the minimum recommended MATLAB version is R2017b.
As described in Using Java Libraries, every installation of MATLAB includes a JVM allowing use of the Java API and third-party Java libraries. All the helper functions included in the MATLAB toolbox make use of the Bio-Formats Java API. Please refer to the Javadocs for more information.
Increasing JVM memory settings
The default JVM settings in MATLAB can result in
java.lang.OutOfMemoryError: Java heap space exceptions when opening large
image files using Bio-Formats. Information about the Java heap space usage in
MATLAB can be retrieved using:
java.lang.Runtime.getRuntime.maxMemory
MATLAB Preferences (R2010a+)
Default JVM settings can be increased by Java Heap Memory Preferences of MATLAB (R2010a onwards) using . We recommend to use 512 MB in general, but you don’t need to decrease the value if the default value is bigger than 512 MB.
However, the maximum value allowed in the Preferences GUI (typically set to 25% of Physical Memory, whihc you can ask by the memory MATLAB command) can still be too small
for your purpose. In that case, you can directly edit matlab.prf file in the
folder specified by the prefdir MATLAB function
(eg. 'C:\Users\xxxxxxx\AppData\Roaming\MathWorks\MATLAB\R2018b'). Find the
parameter JavaMemHeapMax in the file and increase the number that follows
the capital I (in MB) to increase the maximum Java heap memory size. The
change will be reflected by the Preferences as above.
JavaMemHeapMax=I25000
You will see a warning message as above.
java.opts
Alternatively, this can also be done by creating a java.opts file in
the startup directory
and overriding the default memory settings (see this page
for more information). We recommend using -Xmx512m (meaning 512 MB) in your java.opts
file.
Calling:
bfCheckJavaMemory()
will also throw a warning if the runtime memory is lower than the recommended value.
If errors of type java.lang.OutOfMemoryError: PermGen space are thrown
while using Bio-Formats with the Java bundled with MATLAB, you
may try to increase the default values of -XX:MaxPermSize and
-XX:PermSize via the java.opts file.
Opening an image file
The first thing to do is initialize a file with the bfopen function:
data = bfopen('/path/to/data/file');
This function returns an n-by-4 cell array, where n is the number of
series in the dataset. If s is the series index between 1 and n:
The
data{s, 1}element is anm-by-2 cell array, wheremis the number of planes in thes-th series. Iftis the plane index between 1 andm:The
data{s, 1}{t, 1}element contains the pixel data for thet-th plane in thes-th series.The
data{s, 1}{t, 2}element contains the label for thet-th plane in thes-th series.
The
data{s, 2}element contains original metadata key/value pairs that apply to thes-th series.The
data{s, 3}element contains color lookup tables for each plane in thes-th series.The
data{s, 4}element contains a standardized OME metadata structure, which is the same regardless of the input file format, and contains common metadata values such as physical pixel sizes - see OME metadata below for examples.
Accessing planes
Here is an example of how to unwrap specific image planes for easy access:
seriesCount = size(data, 1);
series1 = data{1, 1};
series2 = data{2, 1};
series3 = data{3, 1};
metadataList = data{1, 2};
% etc
series1_planeCount = size(series1, 1);
series1_plane1 = series1{1, 1};
series1_label1 = series1{1, 2};
series1_plane2 = series1{2, 1};
series1_label2 = series1{2, 2};
series1_plane3 = series1{3, 1};
series1_label3 = series1{3, 2};
Displaying images
If you want to display one of the images, you can do so as follows:
series1_colorMap1 = data{1, 3}{1, 1};
figure('Name', series1_label1);
if isempty(series1_colorMap1)
colormap(gray);
else
colormap(series1_colorMap1);
end
imagesc(series1_plane1);
This will display the first image of the first series with its associated
color map (if present). If you would prefer not to apply the color maps
associated with each image, simply comment out the calls to colormap.
If you have the image processing toolbox, you could instead use:
imshow(series1_plane1, []);
You can also create an animated movie (assumes 8-bit unsigned data):
cmap = gray(256);
for p = 1 : size(series1, 1)
M(p) = im2frame(uint8(series1{p, 1}), cmap);
end
if feature('ShowFigureWindows')
movie(M);
end
Retrieving metadata
There are two kinds of metadata:
Original metadata is a set of key/value pairs specific to the input format of the data. It is stored in the
data{s, 2}element of the data structure returned bybfopen.OME metadata is a standardized metadata structure, which is the same regardless of input file format. It is stored in the
data{s, 4}element of the data structure returned bybfopen, and contains common metadata values such as physical pixel sizes, instrument settings, and much more. See the OME Model and Formats documentation for full details.
Original metadata
To retrieve the metadata value for specific keys:
% Query some metadata fields (keys are format-dependent)
metadata = data{1, 2};
subject = metadata.get('Subject');
title = metadata.get('Title');
To print out all of the metadata key/value pairs for the first series:
metadataKeys = metadata.keySet().iterator();
for i=1:metadata.size()
key = metadataKeys.nextElement();
value = metadata.get(key);
fprintf('%s = %s\n', key, value)
end
OME metadata
Conversion of metadata to the OME standard is one of Bio-Formats’ primary features. The OME metadata is always stored the same way, regardless of input file format.
To access physical voxel and stack sizes of the data:
omeMeta = data{1, 4};
stackSizeX = omeMeta.getPixelsSizeX(0).getValue(); % image width, pixels
stackSizeY = omeMeta.getPixelsSizeY(0).getValue(); % image height, pixels
stackSizeZ = omeMeta.getPixelsSizeZ(0).getValue(); % number of Z slices
voxelSizeXdefaultValue = omeMeta.getPixelsPhysicalSizeX(0).value(); % returns value in default unit
voxelSizeXdefaultUnit = omeMeta.getPixelsPhysicalSizeX(0).unit().getSymbol(); % returns the default unit type
voxelSizeX = omeMeta.getPixelsPhysicalSizeX(0).value(ome.units.UNITS.MICROMETER); % in µm
voxelSizeXdouble = voxelSizeX.doubleValue(); % The numeric value represented by this object after conversion to type double
voxelSizeY = omeMeta.getPixelsPhysicalSizeY(0).value(ome.units.UNITS.MICROMETER); % in µm
voxelSizeYdouble = voxelSizeY.doubleValue(); % The numeric value represented by this object after conversion to type double
voxelSizeZ = omeMeta.getPixelsPhysicalSizeZ(0).value(ome.units.UNITS.MICROMETER); % in µm
voxelSizeZdouble = voxelSizeZ.doubleValue(); % The numeric value represented by this object after conversion to type double
For more information about the methods to retrieve the metadata, see the MetadataRetrieve Javadoc page.
To convert the OME metadata into a string, use the dumpXML() method:
omeXML = char(omeMeta.dumpXML());
Changing the logging level
By default, bfopen uses bfInitLogging to initialize the logging system
at the WARN level. To change the root logging level, use the
DebugTools methods as
described in the Logging section.
% Set the logging level to DEBUG
loci.common.DebugTools.setRootLevel('DEBUG');
Reading from an image file
The main inconvenience of the bfopen.m function is that it loads all the content of an image regardless of its size.
To access the file reader without loading all the data, use the low-level bfGetReader.m function:
reader = bfGetReader('path/to/data/file');
You can then access the OME metadata using the getMetadataStore()
method:
omeMeta = reader.getMetadataStore();
Individual planes can be queried using the bfGetPlane.m function:
series1_plane1 = bfGetPlane(reader, 1);
To switch between series in a multi-image file, use the setSeries(int) method. To retrieve a plane given a set of (z, c, t) coordinates, these coordinates must be linearized first using getIndex(int, int, int)
% Read plane from series iSeries at Z, C, T coordinates (iZ, iC, iT)
% All indices are expected to be 1-based
reader.setSeries(iSeries - 1);
iPlane = reader.getIndex(iZ - 1, iC -1, iT - 1) + 1;
I = bfGetPlane(reader, iPlane);
Saving files
The basic code for saving a 5D array into an OME-TIFF file is located in the bfsave.m function.
For instance, the following code will save a single image of 64 pixels by 64 pixels with 8 unsigned bits per pixels:
plane = zeros(64, 64, 'uint8');
bfsave(plane, 'single-plane.ome.tiff');
And the following code snippet will produce an image of 64 pixels by 64 pixels with 2 channels and 2 timepoints:
plane = zeros(64, 64, 1, 2, 2, 'uint8');
bfsave(plane, 'multiple-planes.ome.tiff');
By default, bfsave will create a minimal OME-XML metadata object
containing basic information such as the pixel dimensions, the dimension order
and the pixel type.
To customize the OME metadata, it is possible to create a metadata object
from the input array using createMinimalOMEXMLMetadata.m, add custom
metadata and pass this object directly to bfsave:
plane = zeros(64, 64, 1, 2, 2, 'uint8');
metadata = createMinimalOMEXMLMetadata(plane);
pixelSize = ome.units.quantity.Length(java.lang.Double(.05), ome.units.UNITS.MICROMETER);
metadata.setPixelsPhysicalSizeX(pixelSize, 0);
metadata.setPixelsPhysicalSizeY(pixelSize, 0);
pixelSizeZ = ome.units.quantity.Length(java.lang.Double(.2), ome.units.UNITS.MICROMETER);
metadata.setPixelsPhysicalSizeZ(pixelSizeZ, 0);
bfsave(plane, 'metadata.ome.tiff', 'metadata', metadata);
The dimension order of the file on disk can be specified in two ways:
either by passing an OME-XML metadata option as a key/value pair as shown above
or as an optional positional argument of
bfsave
If a metadata object is passed to bfsave, its dimension order stored
internally will take precedence.
For more information about the methods to store the metadata, see the MetadataStore Javadoc page.
Improving reading performance
Initializing a Bio-Formats reader can consume substantial time and memory. Most of the initialization time is spend in the setId(java.lang.String) call. Various factors can impact the performance of this step including the file size, the amount of metadata in the image and also the file format itself.
One solution to improve reading performance is to use Bio-Formats memoization functionalities with the loci.formats.Memoizer reader wrapper. By essence, the speedup gained from memoization will only happen after the first initialization of the reader for a particular file.
The simplest way to make use the Memoizer functionalities in MATLAB is
illustrated by the following example:
% Construct an empty Bio-Formats reader
r = bfGetReader();
% Decorate the reader with the Memoizer wrapper
r = loci.formats.Memoizer(r);
% Initialize the reader with an input file
% If the call is longer than a minimal time, the initialized reader will
% be cached in a file under the same directory as the initial file
% name .large_file.bfmemo
r.setId(pathToFile);
% Perform work using the reader
% Close the reader
r.close()
% If the reader has been cached in the call above, re-initializing the
% reader will use the memo file and complete much faster especially for
% large data
r.setId(pathToFile);
% Perform additional work
% Close the reader
r.close()
If the time required to call setId(java.lang.String) method is larger
than DEFAULT_MINIMUM_ELAPSED or the minimum value
passed in the constructor, the initialized reader will be cached in a memo
file under the same folder as the input file. Any subsequent call to
setId() with a reader decorated by the Memoizer on the same input file
will load the reader from the memo file instead of performing a full reader
initialization.
More constructors are described in the Memoizer javadocs allowing to control the minimal initialization time required before caching the reader and/or to define a root directory under which the reader should be cached.
As Bio-Formats is not thread-safe, reader memoization offers a new solution to increase reading performance when doing parallel work. For instance, the following example shows how to combine memoization and MATLAB parfor to do work on a single file in a parallel loop:
% Construct a Bio-Formats reader decorated with the Memoizer wrapper
r = loci.formats.Memoizer(bfGetReader(), 0);
% Initialize the reader with an input file to cache the reader
r.setId(pathToFile);
% Close reader
r.close()
nWorkers = 4;
% Enter parallel loop
parfor i = 1 : nWorkers
% Initialize logging at INFO level
bfInitLogging('INFO');
% Initialize a new reader per worker as Bio-Formats is not thread safe
r2 = javaObject('loci.formats.Memoizer', bfGetReader(), 0);
% Initialization should use the memo file cached before entering the
% parallel loop
r2.setId(pathToFile);
% Perform work
% Close the reader
r2.close()
end
Using Bio-Formats in Python
OME does not currently provide a Python implementation for Bio-Formats. However, there are several options you can use to read images from Python via Bio-Formats:
AICSImageIO
The AICSImageIO project includes support for Bio-Formats:
from aicsimageio import AICSImage
cells = AICSImage('/path/to/my/cells.ome.tif')
import napari
napari.view_image(cells.xarray_data)
napari.run()
PyImageJ
The PyImageJ project enables use of ImageJ2, which includes the SCIFIO library, which wraps Bio-Formats. In this way, you can open Bio-Formats-supported formats as NumPy arrays:
import imagej
ij = imagej.init('sc.fiji:fiji')
jcells = ij.io().open('/path/to/my/cells.ome.tif')
cells = ij.py.from_java(jcells)
import napari
napari.view_image(cells)
napari.run()
python-bioformats
The CellProfiler project has implemented a Python wrapper around Bio-Formats used by the CellProfiler software which can be installed using pip:
pip install python-bioformats
See also
- https://pypi.org/project/python-bioformats
Source code of the CellProfiler Python wrapper for Bio-Formats
Using Bio-Formats in R
OME does not currently provide an R implementation for Bio-Formats. However, there are options provided by the community:
Bioconductor RBioFormats
The RBioFormats project from Bioconductor provides an R package which interfaces the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("RBioFormats")
# To view documentation for the version of this package installed in your system
browseVignettes("RBioFormats")
For further details and examples of how to use the package, please see the API documentation
Using Bio-Formats in .NET
OME does not currently provide a .NET implementation for Bio-Formats. However, there are options you can use to read images from .NET via Bio-Formats:
Bioformats.NET6
The Bioformats.NET6 project provides Bio-Formats libraries converted to DLL, built with IKVM 8.7.1 Maven SDK for .NET6. To install add the below to your project file. Note that due to formatting the release version has extra whitespace surrounding it that can be removed :
<PropertyGroup>
<MavenAdditionalRepositories>ome=https://artifacts.openmicroscopy.org/artifactory/maven/;edu.ucar=https://maven.scijava.org/content/repositories/public/;</MavenAdditionalRepositories>
</PropertyGroup>
<ItemGroup>
<MavenReference Include="bioformats_package">
<GroupId>ome</GroupId>
<ArtifactId>bioformats_package</ArtifactId>
<Version> 7.3.0 </Version>
</MavenReference>
<MavenReference Include="cdm-core">
<GroupId>edu.ucar</GroupId>
<ArtifactId>cdm-core</ArtifactId>
<Version>5.3.3</Version>
</MavenReference>
</ItemGroup>
Interfacing with Bio-Formats from non-Java code
Bio-Formats is written in Java, and is easiest to use with other Java code. However, it is possible to call Bio-Formats from a program written in another language. But how to do so depends on your program’s needs.
Technologically, there are two broad categories of solutions: in-process approaches, and inter-process communication.
For details, see LOCI’s article, Interfacing from non-Java code.
Example in-process solution: Bio-Formats JACE C++ bindings (note that this is a legacy project and no longer actively maintained).
See also
Using Bio-Formats as a native C++ library
Note
See the OME-Files C++ downloads page for more information.
Contributing to Bio-Formats
Code formatting
Note, these guidelines do not cover:
third-party code imported into the source tree, which is covered by the guidelines for the upstream projects
released schema files which would require re-releasing if changed by reindenting
All languages
Use spaces to indent; do not ever use tabs
Java
All Java code is formatted with:
an indentation size of two spaces
braces use the Java variant of K&R style
XML
All XML code is formatted with:
an indentation size of two spaces
attributes on multiple lines aligned vertically after the element name.
Testing code changes
Automated tests
The Bio-Formats testing framework component contains most of the infrastructure to run automated tests against the data repository.
After checking out source code and building all the JAR files (see
Obtaining and building Bio-Formats), switch to the test-suite component and run the tests using the ant test-automated target:
$ cd components/test-suite
$ ant -Dtestng.directory=$DATA/metamorph -Dtestng.configDirectory=$CONFIG/metamorph test-automated
where $DATA is the path to the full data repository and $CONFIG is the path to the configuration repository.
Multiple options can be passed to the ant test-automated target
by setting the testng.${option} option via the command line. Useful options
are described below.
- testng.directory
Mandatory option. Specifies the root of the data directory to be tested:
$ ant -Dtestng.directory=$DATA/metamorph -Dtestng.configDirectory=$CONFIG/metamorph test-automated
On Windows, the arguments to the test command must be quoted:
> ant "-Dtestng.directory=$DATA\metamorph" "-Dtestng.configDirectory=$CONFIG\metamorph" test-automated
- testng.configDirectory
Mandatory option. Specifies the root of the directory containing the configuration files. This directory must have the same hierarchy as the one specified by
testng.directoryand contain.bioformatsconfiguration files:$ ant -Dtestng.directory=/path/to/data -Dtestng.configDirectory=/path/to/config test-automated
- testng.configSuffix
Specifies an optional suffix for the configuration files:
$ ant -Dtestng.directory=/path/to/data -Dtestng.configSuffix=win test-automated
- testng.memory
Specifies the amount of memory to be allocated to the JVM:
$ ant -Dtestng.directory=$DATA -Dtestng.memory=4g test-automated
Default: 512m.
- testng.threadCount
Specifies the number of threads to use for testing:
$ ant -Dtestng.directory=$DATA -Dtestng.threadCount=4 test-automated
Default: 1.
You should now see output similar to this:
Buildfile: build.xml
init-title:
[echo] ----------=========== bio-formats-testing-framework ===========----------
...
test-automated:
[testng] 17:05:28,713 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 17:05:28,713 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
[testng] 17:05:28,713 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 17:05:28,713 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/opt/ome/bioformats/components/test-suite/logback.xml]
[testng] 17:05:28,835 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 17:05:28,837 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [stdout]
[testng] 17:05:28,876 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 17:05:28,878 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [SIFT]
[testng] 17:05:28,891 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 17:05:28,891 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to INFO
[testng] 17:05:28,891 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 17:05:28,892 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 17:05:28,892 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
[testng] 17:05:28,894 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@706a04ae - Registering current configuration as safe fallback point
[testng] [2015-08-18 17:05:28,904] [main] testng.directory = /ome/data_repo/test_per_commit/
[testng] 17:05:28,908 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 17:05:28,909 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [logfile-main]
[testng] 17:05:28,955 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2015-08-18_17-05-28.log]
[testng] [2015-08-18 17:05:28,963] [main] testng.multiplier = 1.0
[testng] [2015-08-18 17:05:28,964] [main] testng.in-memory = false
[testng] [2015-08-18 17:05:28,964] [main] user.language = en
[testng] [2015-08-18 17:05:28,964] [main] user.country = US
[testng] [2015-08-18 17:05:28,964] [main] Maximum heap size = 455 MB
[testng] Scanning for files...
[testng] [2015-08-18 17:05:32,258] [main] ----------------------------------------
[testng] [2015-08-18 17:05:32,258] [main] Total files: 480
[testng] [2015-08-18 17:05:32,258] [main] Scan time: 3.293 s (6 ms/file)
[testng] [2015-08-18 17:05:32,258] [main] ----------------------------------------
[testng] Building list of tests...
and then eventually:
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 19110, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 16 minutes 42 seconds
In most cases, test failures should be logged in the main console output as:
[testng] [2015-08-18 17:13:13,625] [pool-1-thread-1] SizeZ: FAILED (Series 0 (expected 2, actual 1))
To identify the file, look for the initialization line preceding the test failures under the same thread:
[testng] [2015-08-18 17:13:12,376] [pool-1-thread-1] Initializing /ome/data_repo/test_per_commit/ome-tiff/img_bk_20110701.ome.tif:
The console output is also recorded under components/test-suite/target
as bio-formats-software-test-main-$DATE.log where “$DATE” is the date
on which the tests started in “yyyy-MM-dd_hh-mm-ss” format. The detailed report
of each thread is recorded under
bio-formats-software-pool-$POOL-thread-$THREAD-main-$DATE.log
Configuration files can be generated for files or directories using the
ant gen-config target. This generation target supports the same options as ant test-automated:
$ ant -Dtestng.directory=/path/to/data -Dtestng.configDirectory=/path/to/config -Dtestng.memory=4g -Dtestng.threadCount=6 gen-config
MATLAB tests
Tests for the Bio-Formats MATLAB toolbox are written using the xunit framework and are located under https://github.com/ome/bioformats/tree/develop/components/formats-gpl/test/matlab.
To run these tests, you will need to download or clone matlab-xunit, a xUnit framework with JUnit-compatible XML output. Then add this package together with the Bio-Formats MATLAB to your MATLAB path:
% Add the matlab-xunit toolbox to the MATLAB path
addpath('/path/to/matlab-xunit');
% Add the Bio-Formats MATLAB source to the MATLAB path
% For developers working against the source code
addpath('/path/to/bioformats/components/formats-gpl/matlab');
addpath('/path/to/bioformats/artifacts');
% For developers working against a built artifact, e.g. a release
% addpath('/path/to/bfmatlab');
You can run all the MATLAB tests using runxunit:
cd /path/to/bioformats/components/formats-gpl/test/matlab
runxunit
Individual test classes can be run by passing the name of the class:
cd /path/to/bioformats/components/formats-gpl/test/matlab
runxunit TestBfsave
Individual test methods can be run by passing the name of the class and the name of the method:
cd /path/to/bioformats/components/formats-gpl/test/matlab
runxunit TestBfsave:testLZW
Finally, to output the test results under XML format, you can use the -xmlfile option:
cd /path/to/bioformats/components/formats-gpl/test/matlab
runxunit -xmlfile test-output.xml
Generating test images
Sometimes it is nice to have a file of a specific size or pixel type for testing. Bio-Formats defines an internal format used for generating test images. Test images recognized by Bio-Formats:
must have an extension of type .fake
must encode the image metadata using key-value pairs separated by = either in the filename or in a companion file
may be accompanied by an INI-style companion file. A companion file must use the same basename as the fake file and be suffixed with .ini
Filename format
To generate an image file (that contains a gradient image):
touch "my-special-test-file&pixelType=uint8&sizeX=8192&sizeY=8192.fake"
Whatever is before the first & is the image name; the remaining key-value
pairs, each preceded with &, set the pixel type and image dimensions. Just
replace the values with whatever you need for testing. See
Key-value pairs for the full description of available key/value
pairs.
Companion file
You can put metadata values in a separate UTF-8 encoded .fake.ini file
with the same basename as the fake file:
touch my-special-test-file.fake
echo "pixelType=uint8" >> my-special-test-file.fake.ini
echo "sizeX=8192" >> my-special-test-file.fake.ini
echo "sizeY=8192" >> my-special-test-file.fake.ini
In fact, just the .fake.ini file alone suffices:
echo "pixelType=uint8" >> my-special-test-file.fake.ini
echo "sizeX=8192" >> my-special-test-file.fake.ini
echo "sizeY=8192" >> my-special-test-file.fake.ini
If you include a “[GlobalMetadata]” section to the ini file, then all the included values will be accessible from the global metadata map:
echo "[GlobalMetadata]" >> my-special-test-file.fake.ini
echo "my.key=some.value" >> my-special-test-file.fake.ini
The .ini file can also contain one section for each series, which allows metadata such as
exposure times and positions to be set for each plane:
echo "[series_0]" >> my-special-test-file.fake.ini
echo "ExposureTime_0=10" >> my-special-test-file.fake.ini
echo "ExposureTimeUnit_0=ms" >> my-special-test-file.fake.ini
echo "PositionX_0=5" >> my-special-test-file.fake.ini
echo "PositionY_0=-5" >> my-special-test-file.fake.ini
echo "PositionZ_0=1" >> my-special-test-file.fake.ini
echo "PositionXUnit_0=mm" >> my-special-test-file.fake.ini
echo "PositionYUnit_0=mm" >> my-special-test-file.fake.ini
echo "PositionZUnit_0=mm" >> my-special-test-file.fake.ini
Several keys have support for units and can be expressed as KEY=VALUE UNIT where UNIT is the symbol of the desired unit:
touch "physicalSizesUnits&physicalSizeX=1nm&physicalSizeY=1nm&physicalSizeZ=1.5km.fake"
echo "physicalSizeX=1 nm" >> physicalSizes.fake.ini
echo "physicalSizeY=10 pm" >> physicalSizes.fake.ini
echo "physicalSizeZ=.002 mm" >> physicalSizes.fake.ini
High-content screening
To generate a simple plate file:
touch "simple-plate&plates=1&plateAcqs=1&plateRows=1&plateCols=1&fields=1.fake"
touch "default-plate&plates=1.fake"
touch "default-plate&screens=0&plates=1.fake"
These will each create a single plate without a containing screen, by default
in the first two cases. In the third case setting screens to zero is used
to document the lack of a screen. As above a .fake.ini file can be
used.
To generate a simple screen file:
touch "default-screen&screens=1.fake"
This will create a screen containing a single simple plate.
To generate a valid plate at least one of screens, plates,
plateAcqs, plateRows, plateCols and fields must be greater
than zero. If this condition is met then any other plate-specific values set
to zero will be ignored and the defaults used. So, for example, the file:
one-key-set&screens=0&plates=0&plateRows=0&plateCols=0&plateAcqs=0&fields=1.fake
will create a simple plate with no screen.
Regions
To generate a fake file containing regions of interest:
touch "regions&points=10.fake"
touch "regions&ellipses=20.fake"
touch "regions&rectangles=5&lines=25.fake"
Replace regions in the above examples with the desired image or plate which will contain the regions, e.g.
touch "HCSanalysis&plates=1&plateRows=16&plateCols=24&rectangles=100.fake"
For each shape type, the value will specify the number of regions of interest to create where each region of interest contains a single shape of the input type. By convention, all generated regions of interests are not associated to any given Z, C or T plane.
Sub-resolutions
Added in version 6.0.0.
To generate a fake file containing sub-resolutions:
touch "pyramid1&sizeX=20000&sizeY=10000&resolutions=8.fake"
touch "pyramid2&sizeX=20000&sizeY=10000&resolutions=4&resolutionScale=4.fake"
The resolutions and resolutionScale specify the number of
sub-resolutions for each plane and the downsampling factor between
consecutive sub-resolutions.
Key-value pairs
There are several other keys that can be added, a complete list of these, with their default values, is shown below.
Key |
Value |
Default |
|---|---|---|
sizeX |
number of pixels wide |
512 |
sizeY |
number of pixels tall |
512 |
sizeZ |
number of Z sections |
1 |
sizeC |
number of channels |
1 |
sizeT |
number of timepoints |
1 |
thumbSizeX |
number of pixels wide, for the thumbnail |
0 |
thumbSizeY |
number of pixels tall, for the thumbnail |
0 |
pixelType |
pixel type |
uint8 |
bitsPerPixel |
number of valid bits (<= number of bits implied by pixel type) |
0 |
rgb |
number of channels that are merged together |
1 |
dimOrder |
dimension order (e.g. XYZCT) |
XYZCT |
orderCertain |
whether or not the dimension order is certain |
true |
little |
whether or not the pixel data should be little-endian |
true |
interleaved |
whether or not merged channels are interleaved |
false |
indexed |
whether or not a color lookup table is present |
false |
falseColor |
whether or not the color lookup table is just for making the image look pretty |
false |
metadataComplete |
whether or not the metadata is complete |
true |
thumbnail |
whether or not |
false |
series |
number of series (Images) |
1 |
lutLength |
number of entries in the color lookup table |
3 |
scaleFactor |
the scaling factor for the pixel values on each plane |
1 |
exposureTime |
time of exposure |
null |
acquisitionDate |
timestamp formatted as “yyyy-MM-dd_HH-mm-ss” |
null |
screens |
number of screens |
0 |
plates |
number of plates to generate |
0 [1] |
plateAcqs |
number of plate runs |
0 [1] |
plateRows |
number of rows per plate |
0 [1] |
plateCols |
number of columns per plate |
0 [1] |
fields |
number of fields per well |
0 [1] |
withMicrobeam |
whether or not a microbeam should be added to the experiment (HCS only) |
false |
annLong, annDouble, annMap, annComment, annBool, annTime, annTag, annTerm, annXml |
number of annotations of the given type to generate |
0 |
physicalSizeX |
real width of the pixels, supports units defaulting to microns |
|
physicalSizeY |
real height of the pixels, supports units defaulting to microns |
|
physicalSizeZ |
real depth of the pixels, supports units defaulting to microns |
|
ChannelName_x |
the channel name for channel x |
|
color |
the default color for all channels [3] |
null |
color_x |
the color for channel x, overrides the default color for that channel [3] |
|
ellipses, labels, lines, points, polygons, polylines, rectangles |
the number of ROIs containing one shape of the given type to generate |
|
ExposureTime_x |
floating point exposure time for plane |
|
ExposureTimeUnit_x |
string defining the units for the corresponding |
seconds |
PositionX_x |
floating point X position for plane |
|
PositionXUnit_x |
string defining the units for the corresponding |
microns |
PositionY_x |
floating point Y position for plane |
|
PositionYUnit_x |
string defining the units for the corresponding |
microns |
PositionZ_x |
floating point Z position for plane |
|
PositionZUnit_x |
string defining the units for the corresponding |
microns |
resolutions |
number of pyramid levels or sub-resolutions for each series |
1 |
resolutionScale |
for images with sub-resolutions, scaling factor between consecutive pyramid levels |
2 |
sleepOpenBytes |
number of milliseconds to sleep for when openBytes is called |
0 |
sleepInitFile |
number of milliseconds to sleep for when initFile is called |
0 |
For full details of these keys, how unset and default values are handled and further examples see loci.formats.in.FakeReader.
You can often work with the .fake file directly, but in some cases
support for those files is disabled and so you will need to convert the
file to something else. Make sure that you have Bio-Formats built and
the JARs in your CLASSPATH (individual JARs or just
bioformats_package.jar):
bfconvert test&pixelType=uint8&sizeX=8192&sizeY=8192.fake test.tiff
If you do not have the command line tools installed, substitute loci.formats.tools.ImageConverter for bfconvert.
Writing a new file format reader
This document is a brief guide to writing new Bio-Formats file format readers.
All format readers should extend either loci.formats.FormatReader or an existing reader.
Methods to override
isSingleFile(java.lang.String) Whether or not the named file is expected to be the only file in the dataset. This only needs to be overridden for formats whose datasets can contain more than one file.
isThisType(loci.common.RandomAccessInputStream) Check the first few bytes of a file to determine if the file can be read by this reader. You can assume that index 0 in the stream corresponds to the index 0 in the file. Return true if the file can be read; false if not (or if there is no way of checking).
fileGroupOption(java.lang.String) Returns an indication of whether or not the files in a multi-file dataset can be handled individually. The return value should be one of the following:
FormatTools.MUST_GROUP: the files cannot be handled separately
FormatTools.CAN_GROUP: the files may be handled separately or as a single unit
FormatTools.CANNOT_GROUP: the files must be handled separately
This method only needs to be overridden for formats whose datasets can contain more than one file.
getSeriesUsedFiles(boolean) You only need to override this if your format uses multiple files in a single dataset. This method should return a list of all files associated with the given file name and the current series (i.e. every file needed to display the current series). If the
noPixelsflag is set, then none of the files returned should contain pixel data. For an example of how this works, see loci.formats.in.PerkinElmerReader. It is recommended that the first line of this method beFormatTools.assertId(currentId, true, 1)- this ensures that the file name is non-null.openBytes(int, byte[], int, int, int, int) Returns a byte array containing the pixel data for a specified subimage from the given file. The dimensions of the subimage (upper left X coordinate, upper left Y coordinate, width, and height) are specified in the final four int parameters. This should throw a FormatException if the image number is invalid (less than 0 or >= the number of images). The ordering of the array returned by openBytes should correspond to the values returned by isLittleEndian and isInterleaved. Also, the length of the byte array should be [image width * image height * bytes per pixel]. Extra bytes will generally be truncated. It is recommended that the first line of this method be
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h)- this ensures that all of the parameters are valid.initFile(java.lang.String) The majority of the file parsing logic should be placed in this method. The idea is to call this method once (and only once!) when the file is first opened. Generally, you will want to start by calling
super.initFile(String). You will also need to set up the stream for reading the file, as well as initializing any dimension information and metadata. Most of this logic is up to you; however, you should populate the core variable (see loci.formats.CoreMetadata).Note that each variable is initialized to 0 or null when
super.initFile(String)is called. Also,super.initFile(String)constructs a Hashtable called metadata where you should store any relevant metadata.The most common way to set up the OME-XML metadata for the reader is to initialize the MetadataStore using the makeFilterMetadata() method and populate the Pixels elements of the metadata store from the
corevariable using the MetadataTools.populatePixels(MetadataStore, FormatReader) method:# Initialize the OME-XML metadata from the core variable MetadataStore store = makeFilterMetadata(); MetadataTools.populatePixels(store, this);
If the reader includes metadata at the plane level, you can initialize the Plane elements under the Pixels using MetadataTools.populatePixels(MetadataStore, FormatReader, doPlane):
MetadataTools.populatePixels(store, this, true);
Once the metadatastore has been initialized with the core properties, additional metadata can be added to it using the setter methods. Note that for each of the model components, the
setObjectID()method should be called before any of thesetObjectProperty()methods, e.g.:# Add an oil immersion objective with achromat String objectiveID = MetadataTools.createLSID("Objective", 0, 0); store.setObjectiveID(objectiveID, 0, 0); store.setObjectiveImmersion(getImmersion("Oil"), 0, 0);
close(boolean) Cleans up any resources used by the reader. Global variables should be reset to their initial state, and any open files or delegate readers should be closed.
Note that if the new format is a variant of a format currently supported by Bio-Formats, it is more efficient to make the new reader a subclass of the existing reader (rather than subclassing loci.formats.FormatReader). In this case, it is usually sufficient to override initFile(java.lang.String) and isThisType(byte[]).
Every reader also has an instance of loci.formats.CoreMetadata. All readers should populate the fields in CoreMetadata, which are essential to reading image planes.
If you read from a file using something other than
loci.common.RandomAccessInputStream or
loci.common.Location,
you must use the file name returned by Location.getMappedId(String), not
the file name passed to the reader.
Thus, a stub for initFile(String) might look like this:
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
RandomAccessInputStream in = new RandomAccessInputStream(id);
// alternatively,
//FileInputStream in = new FileInputStream(Location.getMappedId(id));
// read basic file structure and metadata from stream
}
For more details, see loci.common.Location.mapId(java.lang.String, java.lang.String) and loci.common.Location.getMappedId(java.lang.String).
Variables to populate
There are a number of global variables defined in loci.formats.FormatReader that should be populated in the constructor of any implemented reader.
These variables are:
suffixNecessary Indicates whether or not a file name suffix is required; true by default
suffixSufficient Indicates whether or not a specific file name suffix guarantees that this reader can open a particular file; true by default
hasCompanionFiles Indicates whether or not there is at least one file in a dataset of this format that contains only metadata (no images); false by default
datasetDescription A brief description of the layout of files in datasets of this format; only necessary for multi-file datasets
domains An array of imaging domains for which this format is used. Domains are defined in loci.formats.FormatTools.
Other useful things
loci.common.RandomAccessInputStream is a hybrid RandomAccessFile/InputStream class that is generally more efficient than either RandomAccessFile or InputStream, and implements the DataInput interface. It is recommended that you use this for reading files.
loci.common.Location provides an API similar to java.io.File, and supports File-like operations on URLs. It is highly recommended that you use this instead of File. See the Javadocs for additional information.
loci.common.DataTools provides a number of methods for converting bytes to shorts, ints, longs, etc. It also supports reading most primitive types directly from a RandomAccessInputStream (or other DataInput implementation).
loci.formats.ImageTools provides several methods for manipulating primitive type arrays that represent images. Consult the source or Javadocs for more information.
If your reader relies on third-party code which may not be available to all users, it is strongly suggested that you make a corresponding service class that interfaces with the third-party code. Please see Bio-Formats service and dependency infrastructure for a description of the service infrastructure, as well as the loci.formats.services package.
Several common image compression types are supported through subclasses of loci.formats.codec.BaseCodec. These include JPEG, LZW, LZO, Base64, ZIP and RLE (PackBits).
If you wish to convert a file’s metadata to OME-XML (strongly encouraged), please see Bio-Formats metadata processing for further information.
Once you have written your file format reader, add a line to the readers.txt file with the fully qualified name of the reader, followed by a ‘#’ and the file extensions associated with the file format. Note that loci.formats.ImageReader, the master file format reader, tries to identify which format reader to use according to the order given in readers.txt, so be sure to place your reader in an appropriate position within the list.
The easiest way to test your new reader is by calling “java loci.formats.tools.ImageInfo <file name>”. If all goes well, you should see all of the metadata and dimension information, along with a window showing the images in the file. loci.formats.ImageReader can take additional parameters; a brief listing is provided below for reference, but it is recommended that you take a look at the contents of loci.formats.tools.ImageInfo to see exactly what each one does.
Argument |
Action |
|---|---|
-version |
print the library version and exit |
file |
the image file to read |
-nopix |
read metadata only, not pixels |
-nocore |
do not output core metadata |
-nometa |
do not parse format-specific metadata table |
-nofilter |
do not filter metadata fields |
-thumbs |
read thumbnails instead of normal pixels |
-minmax |
compute min/max statistics |
-merge |
combine separate channels into RGB image |
-nogroup |
force multi-file datasets to be read as individual files |
-stitch |
stitch files with similar names |
-separate |
split RGB image into separate channels |
-expand |
expand indexed color to RGB |
-omexml |
populate OME-XML metadata |
-normalize |
normalize floating point images* |
-fast |
paint RGB images as quickly as possible* |
-debug |
turn on debugging output |
-range |
specify range of planes to read (inclusive) |
-series |
specify which image series to read |
-swap |
override the default input dimension order |
-shuffle |
override the default output dimension order |
-map |
specify file on disk to which name should be mapped |
-preload |
pre-read entire file into a buffer; significantly reduces the time required to read the images, but requires more memory |
-crop |
crop images before displaying; argument is ‘x,y,w,h’ |
-autoscale |
used in combination with ‘-fast’ to automatically adjust brightness and contrast |
-novalid |
do not perform validation of OME-XML |
-omexml-only |
only output the generated OME-XML |
-format |
read file with a particular reader (e.g., ZeissZVI) |
* = may result in loss of precision
If you wish to test using TestNG,
loci.tests.testng.FormatReaderTestprovides several basic tests that work with all Bio-Formats readers. See the FormatReaderTest source code for additional information.For more details, please look at the source code and Javadocs. Studying existing readers is probably the best way to get a feel for the API; we would recommend first looking at loci.formats.in.ImarisReader (this is the most straightforward one). loci.formats.in.LIFReader and InCellReader are also good references that show off some of the nicer features of Bio-Formats.
If you have questions about Bio-Formats, please contact the forums.
Adding format/reader documentation pages
Documentation pages for the supported formats and readers are auto-generated during the build. This page explains how to amend/extend this part of the Bio-Formats documentation.
Formats
The supported formats pages are generated as part of the documentation build using maven. The metadata for each format is contained in format-pages.txt and the build generates a reStructuredText file for each format as well as an index page for all supported formats using Velocity.
The format-pages.txt is an INI file where each section corresponds to
a particular format given by the section header. Multiple key/values should be
defined for each section:
pagename
The name of the output reStructuredText file. If unspecified, the section
header will be used to generate the filename.
extensions
The list of extensions supported for the format
owner
The owner of the file format
developer
The developer of the file format
bsd
A `yes/no` flag specifying whether the format readers/writers are under
the BSD license
versions
A comma-separated list of all versions supported for this format
weHave
A bullet-point list describing the supporting material we have for this
format including specification and sample datasets
weWant
A bullet-point list describing the supporting material we would like to
have for this format
pixelRating
metadataRating
opennessRating
presenceRating
utilityRating
See :term:`Ratings legend and definitions`. Available choices are:
`Poor`, `Fair`, `Good`, `Very Good`, `Outstanding`.
The `metadataRating` should be set as follows:
* base `metadataRating` is the smaller of `opennessRating` and `pixelsRating`
* increment `metadataRating` by 1 if any combination of `Instrument.ID` plus `Image.InstrumentRef`,
or `Channel.EmissionWavelength`, or `Channel.ExcitationWavelength` are supported
* increment `metadataRating` by 1 if any SPW metadata is supported or :term:`pyramid` is ``yes``
reader
A string or a comma-separated list of all readers for this format
mif
set to ``true`` if the format can store multiple Images (in OME-XML
terminology) or series (in Bio-Formats API terminology)
pyramid
set to ``yes`` if the format can store a single image at multiple
resolutions
notes
Additional relevant information e.g. that we cannot distribute
specification documents to third parties
options
A link to additional reader and writer options documentation where they
are available for the format
Dataset structure table
The summary table listing the extensions for each reader is generated by the build process reading their extensions and descriptions from all Bio-Formats readers (BSD and GPL). A reStructuredText file with a table summary of all file extensions is created.
Readers
The metadata pages for each reader are generated by the build process parsing
their metadata support from all Bio-Formats readers (BSD and GPL). An
intermediate meta-support.txt file is created which is then converted
into one reStructuredText page for each reader as well as a metadata summary
reStructuredText file using Velocity.
Bio-Formats service and dependency infrastructure
Description
The Bio-Formats service infrastructure is an interface driven pattern
for dealing with external and internal dependencies. The design goal was
mainly to avoid the cumbersome usage of ReflectedUniverse where
possible and to clearly define both service dependency and interface
between components. This is generally referred to as dependency
injection,
dependency
inversion
or component based
design.
It was decided, at this point, to forgo the usage of potentially more powerful but also more complicated solutions such as:
The Wikipedia page for dependency injection contains many other implementations in many languages.
An added benefit is the potential code reuse possibilities as a result of decoupling of dependency and usage in Bio-Formats readers. Implementations of the initial Bio-Formats services were completed as part of BioFormatsCleanup and tickets #463 and #464.
Writing a service
Interface – The basic form of a service is an interface which inherits from loci.common.services.Service. Here is a very basic example using the (now removed)
OMENotesServicepublic interface OMENotesService extends Service { /** * Creates a new OME Notes instance. * @param filename Path to the file to create a Notes instance for. */ public void newNotes(String filename); }
Implementation – This service then has an implementation, which is usually located in the Bio-Formats component or package which imports classes from an external, dynamic or other dependency. Again looking at the
OMENotesService:public class OMENotesServiceImpl extends AbstractService implements OMENotesService { /** * Default constructor. */ public OMENotesServiceImpl() { checkClassDependency(Notes.class); } /* (non-Javadoc) * @see loci.formats.dependency.OMENotesService#newNotes() */ public void newNotes(String filename) { new Notes(null, filename); } }
Style
Extension of
AbstractServiceto enable uniform runtime dependency checking is recommended. Java does not check class dependencies until classes are first instantiated so if you do not do this, you may end up withClassNotFoundor the like exceptions being emitted from your service methods. This is to be strongly discouraged. If a service has unresolvable classes on its CLASSPATH instantiation should fail, not service method invocation.Service methods should not burden the implementer with numerous checked exceptions. Also external dependency exception instances should not be allowed to directly leak from a service interface. Please wrap these using a
ServiceException.By convention both the interface and implementation are expected to be in a package named
loci.*.services. This is not a hard requirement but should be followed where possible.
Registration – A service’s interface and implementation must finally be registered with the loci.common.services.ServiceFactory via the
services.propertiesfile. Following theOMENotesServiceagain, here is an example registration:... # OME notes service (implementation in legacy ome-notes component) loci.common.services.OMENotesService=loci.ome.notes.services.OMENotesServiceImpl ...
Using a service
OMENotesService service = null;
try {
ServiceFactory factory = new ServiceFactory();
service = factory.getInstance(OMENotesService.class);
}
catch (DependencyException de) {
LOGGER.info("", de);
}
...
Scripts for performing development tasks
The tools directory contains several scripts which are useful
for building and performing routine updates to the code base.
bump_maven_version.py
This updates the Maven POM version numbers for all pom.xml files that set groupId to ome. The script takes a single argument, which is the new version. For example, to update the POM versions prior to release:
./tools/bump_maven_version.py 5.1.0
and to switch back to snapshot versions immediately after release:
./tools/bump_maven_version.py 5.1.1-SNAPSHOT
test-build
This is the script used by Travis to test each commit. It compiles and runs tests on each of the components in the Bio-Formats repository according to the arguments specified. Valid arguments are:
clean: cleans the Maven build directories
maven: builds all Java components using Maven and runs unit tests
ant: builds all Java components using Ant and runs unit tests
all: equivalent of clean maven ant
update_copyright
This updates the end year in the copyright blocks of all source code files. The command takes no arguments, and sets the end year to be the current year. As update_copyright is a Bash script, it is not intended to be run on Windows.
See open Trac tickets for Bio-Formats and the various Trello boards for information on work currently planned or in progress.
For more general guidance about how to contribute to OME projects, see the Contributing developers documentation.
Formats
Bio-Formats supports over 140 different file formats. The Dataset Structure Table explains the file extension you should choose to open/import a dataset in any of these formats, while the Supported Formats table lists all of the formats and gives an indication of how well they are supported and whether Bio-Formats can write, as well as read, each format. The Summary of supported metadata fields table shows an overview of the OME data model fields populated for each format.
Further information on each individual format is also provided (click on the entries in the supported formats table).
We are always looking for examples of files to help us provide better support for different formats. If you would like to help, you can upload files to Zenodo and let us know. If you have any questions, or would prefer not to use Zenodo, please contact us via the Image.sc forum. If your format is already supported, please refer to the ‘we would like to have’ section on the individual page for that format, to see if your dataset would be useful to us.
All the example files we have permission to share publicly are freely available from our sample image downloads site.
Dataset Structure Table
This table shows the extension of the file that you should choose if you want to open/import a dataset in a particular format.
Format name |
File to choose |
Structure of files |
|---|---|---|
AIM |
.aim |
Single file |
ARF |
.arf |
Single file |
Adobe Photoshop |
.psd |
Single file |
Adobe Photoshop TIFF |
.tif, .tiff |
Single file |
Alicona AL3D |
.al3d |
Single file |
Amersham Biosciences GEL |
.gel |
Single file |
Amira |
.am, .amiramesh, .grey, .hx, .labels |
Single file |
Analyze 7.5 |
.img, .hdr |
One .img file and one similarly-named .hdr file |
Andor SIF |
.sif |
Single file |
Animated PNG |
.png |
Single file |
Aperio AFI |
.afi |
One .afi file and several similarly-named .svs files |
Aperio SVS |
.svs |
Single file |
Audio Video Interleave |
.avi |
Single file |
BD Pathway |
.exp, .tif |
Multiple files (.exp, .dye, .ltp, …) plus one or more directories containing .tif and .bmp files |
BDV |
.xml, .h5 |
Single file |
Bio-Rad GEL |
.1sc |
Single file |
Bio-Rad PIC |
.pic, .xml, .raw |
One or more .pic files and an optional lse.xml file |
Bio-Rad SCN |
.scn |
Single file |
Bitplane Imaris |
.ims |
Single file |
Bitplane Imaris 3 (TIFF) |
.ims |
Single file |
Bitplane Imaris 5.5 (HDF) |
.ims |
Single file |
Bruker |
(no extension) |
One ‘fid’ and one ‘acqp’ plus several other metadata files and a ‘pdata’ directory |
Burleigh |
.img |
Single file |
Canon RAW |
.cr2, .crw, .jpg, .thm, .wav |
Single file |
CellH5 (HDF) |
.ch5 |
Single file |
CellSens VSI |
.vsi, .ets |
One .vsi file and an optional directory with a similar name that contains at least one subdirectory with .ets files |
CellVoyager |
.tif, .xml |
Directory with 2 master files ‘MeasurementResult.xml’ and ‘MeasurementResult.ome.xml’, used to stitch together several TIF files. |
CellWorx |
.pnl, .htd, .log |
One .htd file plus one or more .pnl files and optionally one or more .log files |
Cellomics C01 |
.c01, .dib |
One or more .c01 files |
Compix Simple-PCI |
.cxd |
Single file |
DICOM |
.dic, .dcm, .dicom, .jp2, .j2ki, .j2kr, .raw, .ima |
One or more .dcm or .dicom files |
DNG |
.cr2, .crw, .jpg, .thm, .wav, .tif, .tiff |
Single file |
Deltavision |
.dv, .r3d, .r3d_d3d, .dv.log, .r3d.log |
One .dv, .r3d, or .d3d file and up to two optional .log files |
ECAT7 |
.v |
Single file |
Encapsulated PostScript |
.eps, .epsi, .ps |
Single file |
Evotec Flex |
.flex, .mea, .res |
One directory containing one or more .flex files, and an optional directory containing an .mea and .res file. The .mea and .res files may also be in the same directory as the .flex file(s). |
Extended leica file |
.xlef |
Single file |
FEI TIFF |
.tif, .tiff |
Single file |
FEI/Philips |
.img |
Single file |
Flexible Image Transport System |
.fits, .fts |
Single file |
FlowSight |
.cif |
Single file |
Fuji LAS 3000 |
.img, .inf |
Single file |
Gatan DM2 |
.dm2 |
Single file |
Gatan Digital Micrograph |
.dm3, .dm4 |
Single file |
Graphics Interchange Format |
.gif |
Single file |
Hamamatsu Aquacosmos |
.naf |
Single file |
Hamamatsu HIS |
.his |
Single file |
Hamamatsu NDPI |
.ndpi |
Single file |
Hamamatsu NDPIS |
.ndpis |
One .ndpis file and at least one .ndpi file |
Hamamatsu VMS |
.vms |
One .vms file plus several .jpg files |
Hitachi |
.txt |
One .txt file plus one similarly-named .tif, .bmp, or .jpg file |
I2I |
.i2i |
Single file |
IMAGIC |
.hed, .img |
One .hed file plus one similarly-named .img file |
IMOD |
.mod |
Single file |
INR |
.inr |
Single file |
IPLab |
.ipl |
Single file |
IVision |
.ipm |
Single file |
Imacon |
.fff |
Single file |
Image Cytometry Standard |
.ics, .ids |
One .ics and possibly one .ids with a similar name |
Image-Pro Sequence |
.seq, .ips |
Single file |
Image-Pro Workspace |
.ipw |
Single file |
Improvision TIFF |
.tif, .tiff |
Single file |
InCell 1000/2000 |
.xdce, .xml, .tiff, .tif, .xlog |
One .xdce file with at least one .tif/.tiff or .im file |
InCell 3000 |
.frm |
Single file |
Inveon |
.hdr |
One .hdr file plus one similarly-named file |
Ionpath MIBI |
.tif, tiff |
Single file |
JEOL |
.dat, .img, .par |
A single .dat file or an .img file with a similarly-named .par file |
JPEG |
.jpg, .jpeg, .jpe |
Single file |
JPEG-2000 |
.jp2, .j2k, .jpf |
Single file |
JPK Instruments |
.jpk |
Single file |
JPX |
.jpx |
Single file |
KLB |
.klb |
Single file |
Khoros XV |
.xv |
Single file |
Kodak Molecular Imaging |
.bip |
Single file |
LEO |
.sxm, .tif, .tiff |
Single file |
LI-FLIM |
.fli |
Single file |
Laboratory Imaging |
.lim |
Single file |
Lavision Imspector |
.msr |
Single file |
Leica |
.lei, .tif, .tiff, .raw |
One .lei file with at least one .tif/.tiff file and an optional .txt file |
Leica Image File Format |
.lif |
Single file |
Leica Object Format |
.lof |
Single file |
Leica SCN |
.scn |
Single file |
Leica TCS TIFF |
.tif, .tiff, .xml |
Single file |
Li-Cor L2D |
.l2d, .scn, .tif |
One .l2d file with one or more directories containing .tif/.tiff files |
MIAS |
.tif, .tiff, .txt |
One directory per plate containing one directory per well, each with one or more .tif/.tiff files |
MINC MRI |
.mnc |
Single file |
Medical Research Council |
.mrc, .st, .ali, .map, .rec, .mrcs |
Single file |
MetaXpress TIFF |
.htd, .tif |
One .htd file plus one or more .tif files |
Metamorph STK |
.stk, .nd, .scan, .tif, .tiff |
One or more .stk or .tif/.tiff files plus an optional .nd or .scan file |
Metamorph TIFF |
.tif, .tiff |
One or more .tif/.tiff files |
Micro-Manager |
.tif, .tiff, .txt, .xml |
A file ending in ‘metadata.txt’ plus one or more .tif files |
MicroCT |
.vff |
Directory with XML file and one .tif/.tiff file per plane |
Mikroscan TIFF |
.tif, .tiff |
Single file |
Minolta MRW |
.mrw |
Single file |
Molecular Imaging |
.stp |
Single file |
Multiple-image Network Graphics |
.mng |
Single file |
NIfTI |
.nii, .img, .hdr, .nii.gz |
A single .nii file or a single .nii.gz file or one .img file and a similarly-named .hdr file |
NOAA-HRD Gridded Data Format |
(no extension) |
Single file |
NRRD |
.nrrd, .nhdr |
A single .nrrd file or one .nhdr file and one other file containing the pixels |
Nikon Elements TIFF |
.tif, .tiff |
Single file |
Nikon ND2 |
.nd2, .jp2 |
Single file |
Nikon NEF |
.nef, .tif, .tiff |
Single file |
Nikon TIFF |
.tif, .tiff |
Single file |
OBF |
.obf, .msr |
OBF file |
OME-TIFF |
.ome.tiff, .ome.tif, .ome.tf2, .ome.tf8, .ome.btf, .companion.ome |
One or more .ome.tiff files |
OME-XML |
.ome, .ome.xml |
Single file |
Olympus .omp2info |
.omp2info |
One .omp2info file and at least one .oir or .vsi file |
Olympus APL |
.apl, .tnb, .mtb, .tif |
One .apl file, one .mtb file, one .tnb file, and a directory containing one or more .tif files |
Olympus FV1000 |
.oib, .oif, .pty, .lut |
Single .oib file or one .oif file and a similarly-named directory containing .tif/.tiff files |
Olympus Fluoview/ABD TIFF |
.tif, .tiff |
One or more .tif/.tiff files, and an optional .txt file |
Olympus OIR |
.oir |
Single file |
Olympus SIS TIFF |
.tif, .tiff |
Single file |
Olympus ScanR |
.dat, .xml, .tif |
One .xml file, one ‘data’ directory containing .tif/.tiff files, and optionally two .dat files |
Olympus Slidebook |
.sld, .spl |
Single file |
Openlab LIFF |
.liff |
Single file |
Openlab RAW |
.raw |
Single file |
Oxford Instruments |
.top |
Single file |
PCO-RAW |
.pcoraw, .rec |
A single .pcoraw file with a similarly-named .rec file |
PCX |
.pcx |
Single file |
PICT |
.pict, .pct |
Single file |
POV-Ray |
.df3 |
Single file |
Perkin Elmer Densitometer |
.hdr, .img |
One .hdr file and a similarly-named .img file |
Perkin-Elmer Nuance IM3 |
.im3 |
Single file |
PerkinElmer |
.ano, .cfg, .csv, .htm, .rec, .tim, .zpo, .tif |
One .htm file, several other metadata files (.tim, .ano, .csv, …) and either .tif files or .2, .3, .4, etc. files |
PerkinElmer Columbus |
.xml |
Directory with XML file and one .tif/.tiff file per plane |
PerkinElmer Operetta |
.tif, .tiff, .xml |
Directory with XML file and one .tif/.tiff file per plane |
PerkinElmer Vectra/QPTIFF |
.tiff, .tif, .qptiff |
Single file |
PicoQuant Bin |
.bin |
Single file |
Portable Any Map |
.pbm, .pgm, .ppm |
Single file |
Prairie TIFF |
.tif, .tiff, .cfg, .env, .xml |
One .xml file, one .cfg file, and one or more .tif/.tiff files |
Princeton Instruments SPE |
.spe |
Single file |
Pyramid TIFF |
.tif, .tiff |
Single file |
Quesant AFM |
.afm |
Single file |
QuickTime |
.mov |
Single file |
RCPNL |
.rcpnl |
One .dv, .r3d, or .d3d file and up to two optional .log files |
RHK Technologies |
.sm2, .sm3 |
Single file |
SBIG |
(no extension) |
Single file |
SM Camera |
(no extension) |
Single file |
SPC FIFO Data |
.spc, .set |
One .spc file and similarly named .set file |
SPCImage Data |
.sdt |
Single file |
SPIDER |
.spi |
Single file |
Seiko |
.xqd, .xqf |
Single file |
SimplePCI TIFF |
.tif, .tiff |
Single file |
Simulated data |
.fake |
Single file |
SlideBook 7 SLD (native) |
.sldy |
Single file |
Slidebook TIFF |
.tif, .tiff |
Single file |
Tagged Image File Format |
.tif, .tiff, .tf2, .tf8, .btf |
Single file |
Tecan Spark Cyto |
.db |
SQLite database, TIFF files, optional analysis output |
Text |
.txt, .csv |
Single file |
TillVision |
.vws, .pst, .inf |
One .vws file and possibly one similarly-named directory |
TopoMetrix |
.tfr, .ffr, .zfr, .zfp, .2fl |
Single file |
Trestle |
.tif |
One .tif file plus several other similarly-named files (e.g. .FocalPlane-, .sld, .slx, .ROI) |
Truevision Targa |
.tga |
Single file |
UBM |
.pr3 |
Single file |
Unisoku STM |
.hdr, .dat |
One .HDR file plus one similarly-named .DAT file |
VG SAM |
.dti |
Single file |
Varian FDF |
.fdf |
Single file |
Veeco |
.hdf |
Single file |
Ventana .bif |
.bif |
Single file |
Visitech XYS |
.xys, .html |
One .html file plus one or more .xys files |
Volocity Library |
.mvd2, .aisf, .aiix, .dat, .atsf |
One .mvd2 file plus a ‘Data’ directory |
Volocity Library Clipping |
.acff |
Single file |
WA Technology TOP |
.wat |
Single file |
Windows Bitmap |
.bmp |
Single file |
Yokogawa CV7000 |
.wpi |
Directory with XML files and one .tif/.tiff file per plane |
Zeiss AxioVision TIFF |
.tif, .xml |
Single file |
Zeiss CZI |
.czi |
Single file |
Zeiss LMS |
.lms |
Single file |
Zeiss Laser-Scanning Microscopy |
.lsm, .mdb |
One or more .lsm files; if multiple .lsm files are present, an .mdb file should also be present |
Zeiss Vision Image (ZVI) |
.zvi |
Single file |
Zip |
.zip |
Single file |
Flex Support
OMERO.importer supports importing analyzed Flex files from an Opera system.
Basic configuration is done via the importer.ini. Once the user has
run the Importer once, this file will be in the following location:
C:\Documents and Settings\<username>\omero\importer.ini
The user will need to modify or add the [FlexReaderServerMaps]
section of the INI file as follows:
…
[FlexReaderServerMaps]
CIA-1 = \\\\hostname1\\mount;\\\\archivehost1\\mount
CIA-2 = \\\\hostname2\\mount;\\\\archivehost2\\mount
where the key of the INI file line is the value of the “Host” tag in
the .mea measurement XML file (here: <Host name="CIA-1">) and
the value is a semicolon-separated list of escaped UNC path names to
the Opera workstations where the Flex files reside.
Once this resolution has been encoded in the configuration file and
you have restarted the importer, you will be able to select the .mea
measurement XML file from the Importer user interface as the import
target.
Supported Formats
Ratings legend and definitions
Format |
Extensions |
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.sld |
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.sldy |
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.tif |
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.aim |
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.al3d |
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.gel |
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.am, .amiramesh, .grey, .hx, .labels |
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.cif |
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.img, .hdr |
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.sif |
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.png |
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.afi, .svs |
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.svs |
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.htd, .pnl |
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.avi |
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.tiff, .tif, .tf2, .tf8, .btf |
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.tfr, .ffr, .zfr, .zfp, .2fl |
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Bio-Formats currently supports 161 formats
- Ratings legend and definitions
Outstanding
Very good
Good
Fair
Poor
- Pixels
Our estimation of Bio-Formats’ ability to reliably extract complete and accurate pixel values from files in that format. The better this score, the more confident we are that Bio-Formats will successfully read your file without displaying an error message or displaying an erroneous image.
- Metadata
Our certainty in the thoroughness and correctness of Bio-Formats’ metadata extraction and conversion from files of that format into standard OME-XML. The better this score, the more confident we are that all meaningful metadata will be parsed and populated as OME-XML.
- Openness
This is not a direct expression of Bio-Formats’ performance, but rather indicates the level of cooperation the format’s controlling interest has demonstrated toward the scientific community with respect to the format. The better this score, the more tools (specification documents, source code, sample files, etc.) have been made available.
- Presence
This is also not directly related to Bio-Formats, but instead represents our understanding of the format’s popularity, and is also as a measure of compatibility between applications. The better this score, the more common the format and the more software packages include support for it.
- Utility
Our opinion of the format’s suitability for storing metadata-rich microscopy image data. The better this score, the wider the variety of information that can be effectively stored in the format.
- Export
This indicates whether Bio-Formats is capable of writing the format (Bio-Formats can read every format on this list).
- BSD
This indicates whether format is BSD-licensed. By default, format readers and writers are GPL-licensed.
- Multiple Images
This indicates whether the format can store multiple Images (in OME-XML terminology) or series (in Bio-Formats API terminology).
- Pyramid
This indicates whether the format can store a single image at multiple resolutions, typically referred to as an image pyramid.
3i SlideBook
Extensions: .sld
Developer: Intelligent Imaging Innovations
Owner: Intelligent Imaging Innovations
Support
BSD-licensed: 
Export:
Officially Supported Versions: 4.1, 4.2, 5.0, 5.5, 6.0
Reader: SlidebookReader (Source Code, Supported Metadata Fields)
We currently have:
Numerous SlideBook datasets
We would like to have:
A SlideBook specification document
More SlideBook datasets (preferably acquired with the most recent SlideBook software)
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
We strongly encourage users to export their .sld files to OME-TIFF using the SlideBook software. Bio-Formats is not likely to support the full range of metadata that is included in .sld files, and so exporting to OME-TIFF from SlideBook is the best way to ensure that all metadata is preserved. Free software from 3i can export the files to OME-TIFF post-acquisition, see https://www.intelligent-imaging.com/slidebook.
3i also develops a native SlideBook reader which works with Bio-Formats. See http://www.openmicroscopy.org/info/slidebook for details.
See also
3i SlideBook 7
Extensions: .sldy
Developer: Intelligent Imaging Innovations
Owner: Intelligent Imaging Innovations
Support
BSD-licensed: 
Export:
Officially Supported Versions:
Reader: SlideBook7Reader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a small number of datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Andor Bio-Imaging Division (ABD) TIFF
Extensions: .tif
Developer: Andor Bioimaging Department
Owner: Andor Technology
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: FluoviewReader (Source Code, Supported Metadata Fields)
We currently have:
an ABD-TIFF specification document (from 2005 November, in PDF)
a few ABD-TIFF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
With a few minor exceptions, the ABD-TIFF format is identical to the Fluoview TIFF format.
AIM
Extensions: .aim
Developer: SCANCO Medical AG
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: AIMReader (Source Code, Supported Metadata Fields)
We currently have:
one .aim file
We would like to have:
an .aim specification document
more .aim files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Alicona 3D
Extensions: .al3d
Owner: Alicona Imaging
Support
BSD-licensed:
Export:
Officially Supported Versions: 1.0
Reader: AliconaReader (Source Code, Supported Metadata Fields)
We currently have:
an AL3D specification document (v1.0, from 2003, in PDF)
a few AL3D datasets
We would like to have:
more AL3D datasets (Z series, T series, 16-bit)
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Known deficiencies:
Support for 16-bit AL3D images is present, but has never been tested.
Texture data is currently ignored.
Amersham Biosciences Gel
Extensions: .gel
Developer: Molecular Dynamics
Owner: Cytiva
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: GelReader (Source Code, Supported Metadata Fields)
We currently have:
a GEL specification document (Revision 2, from 2001 Mar 15, in PDF)
a few GEL datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
See also
Amira Mesh
Extensions: .am, .amiramesh, .grey, .hx, .labels
Developer: Visage Imaging
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: AmiraReader (Source Code, Supported Metadata Fields)
We currently have:
a few Amira Mesh datasets
We would like to have:
more Amira Mesh datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Amnis FlowSight
Extensions: .cif
Owner: Amnis (now owned by Merck)
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: FlowSightReader (Source Code, Supported Metadata Fields)
We currently have:
a few sample datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Analyze 7.5
Extensions: .img, .hdr
Developer: Mayo Foundation Biomedical Imaging Resource
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: AnalyzeReader (Source Code, Supported Metadata Fields)
We currently have:
several Analyze 7.5 datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Andor SIF
Extensions: .sif
Developer: Andor Bioimaging Department
Owner: Andor Technology
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: SIFReader (Source Code, Supported Metadata Fields)
We currently have:
a small number of Andor SIF datasets
We would like to have:
an Andor SIF specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Animated PNG
Extensions: .png
Developer: The Animated PNG Project
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: APNGReader (Source Code, Supported Metadata Fields)
Writer: APNGWriter (Source Code)
Freely Available Software:
We currently have:
several APNG files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Aperio AFI
Extensions: .afi, .svs
Owner: Leica Biosystems
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: AFIReader (Source Code, Supported Metadata Fields)
We currently have:
several AFI datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
See also
Aperio SVS TIFF
Extensions: .svs
Owner: Leica Biosystems
Support
BSD-licensed:
Export:
Officially Supported Versions: 8.0, 8.2, 9.0
Reader: SVSReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
many SVS datasets
an SVS specification document
the ability to generate additional SVS datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
See also
Applied Precision CellWorX
Extensions: .htd, .pnl
Developer: Applied Precision, Inc.
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: CellWorxReader (Source Code, Supported Metadata Fields)
We currently have:
a few CellWorX datasets
We would like to have:
a CellWorX specification document
more CellWorX datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
AVI (Audio Video Interleave)
Extensions: .avi
Developer: Microsoft
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: AVIReader (Source Code, Supported Metadata Fields)
Writer: AVIWriter (Source Code)
Freely Available Software:
We currently have:
several AVI datasets
We would like to have:
more AVI datasets, including:
files with audio tracks and/or multiple video tracks
files compressed with a common unsupported codec
2+ GB files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats can save image stacks as AVI (uncompressed).
The following codecs are supported for reading:
Microsoft Run-Length Encoding (MSRLE)
Microsoft Video (MSV1)
Raw (uncompressed)
JPEG
See also
Axon Raw Format
Extensions: .arf
Owner: INDEC BioSystems
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: ARFReader (Source Code, Supported Metadata Fields)
We currently have:
one ARF dataset
We would like to have:
more ARF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
BD Pathway
Extensions: .exp, .tif
Owner: BD Biosciences
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: BDReader (Source Code, Supported Metadata Fields)
We currently have:
a few BD Pathway datasets
We would like to have:
more BD Pathway datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Becker & Hickl SPC FIFO
Extensions: .spc
Owner: Becker-Hickl
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: SPCReader (Source Code, Supported Metadata Fields)
We currently have:
We would like to have:
more SPC sample files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Only files containing frame, line and pixel clock information are currently supported
Becker & Hickl SPCImage
Extensions: .sdt
Owner: Becker-Hickl
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: SDTReader (Source Code, Supported Metadata Fields)
We currently have:
an SDT specification document (from 2008 April, in PDF)
an SDT specification document (from 2006 June, in PDF)
Becker & Hickl’s SPCImage software
a large number of SDT datasets
the ability to produce new datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Big Data Viewer
Extensions: .xml, .h5
Owner: Tobias Pietzsch
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: BDVReader (Source Code, Supported Metadata Fields)
We currently have:
a BDV specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Bio-Rad Gel
Extensions: .1sc
Owner: Bio-Rad
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: BioRadGelReader (Source Code, Supported Metadata Fields)
We currently have:
software that can read Bio-Rad Gel files
several Bio-Rad Gel files
reverse-engineered Bio-Rad Gel (1sc) file format specification
Bio-Rad’s Image Lab 5.2.1 software
We would like to have:
more Bio-Rad Gel files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Python3 package of a Bio-Rad Gel Format (1sc) reader
pip3 install biorad1sc_readerIncludes command-line utilities
bio1sc2tiff - convert 1sc file image to tiff
bio1scmeta - report all metadata in a 1sc file
bio1scread - report details on internal 1sc file structure
Bio-Rad PIC
Extensions: .pic, .raw, .xml
Developer: Bio-Rad
Owner: ZEISS International
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: BioRadReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a PIC specification document (v4.5, in PDF)
an older PIC specification document (v4.2, from 1996 December 16, in DOC)
a large number of PIC datasets
the ability to produce new datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Commercial applications that support this format include:
Bio-Rad SCN
Extensions: .scn
Developer: Bio-Rad
Owner: Bio-Rad
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: BioRadSCNReader (Source Code, Supported Metadata Fields)
We currently have:
a few Bio-Rad .scn files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Bitplane Imaris
Extensions: .ims
Owner: Oxford Instruments (formerly Bitplane)
Support
BSD-licensed:
Export:
Officially Supported Versions: 2.7, 3.0, 5.5
Readers:
ImarisHDFReader (Source Code, Supported Metadata Fields)
ImarisTiffReader (Source Code, Supported Metadata Fields)
ImarisReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
an Imaris (RAW) specification document (from no later than 1997 November 11, in HTML)
Bitplane’s bfFileReaderImaris3N code (from no later than 2005, in C++)
several older Imaris (RAW) datasets
one Imaris 3 (TIFF) dataset
several Imaris 5.5 (HDF) datasets
We would like to have:
an Imaris 3 (TIFF) specification document
more Imaris 3 (TIFF) datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
- There are three distinct Imaris formats:
the old binary format (introduced in Imaris version 2.7)
Imaris 3, a TIFF variant (introduced in Imaris version 3.0)
Imaris 5.5, an HDF variant (introduced in Imaris version 5.5)
Bruker MRI
Developer: Bruker
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: BrukerReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a few Bruker MRI datasets
We would like to have:
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Burleigh
Extensions: .img
Owner: Burleigh Instruments
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: BurleighReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read Burleigh files (from ImageSXM)
a few Burleigh files
We would like to have:
a Burleigh file format specification
more Burleigh files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Canon DNG
Extensions: .cr2, .crw
Developer: Canon
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: DNGReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a few example datasets
We would like to have:
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
CellH5
Extensions: .ch5
Developer: CellH5
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: CellH5Reader (Source Code, Supported Metadata Fields)
Writer: CellH5Writer (Source Code)
Freely Available Software:
We currently have:
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Cellomics
Extensions: .c01, .dib
Developer: Thermo Fisher Scientific
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: CellomicsReader (Source Code, Supported Metadata Fields)
We currently have:
a few Cellomics .c01 datasets
We would like to have:
a Cellomics .c01 specification document
more Cellomics .c01 datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
cellSens VSI
Extensions: .vsi
Developer: Olympus
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: CellSensReader (Source Code, Supported Metadata Fields)
We currently have:
a few example datasets
a VSI specification document (v1.6, 2012 November 27, in PDF)
a VSI specification document (v1.3, 2010 February 5, in PDF)
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
CellVoyager
Extensions: .xml, .tif
Owner: Yokogawa
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: CellVoyagerReader (Source Code, Supported Metadata Fields)
We currently have:
a few example datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
CV7000
Extensions: .wpi, .tif
Owner: Yokogawa
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: CV7000Reader (Source Code, Supported Metadata Fields)
We currently have:
many example datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Additional options are available for reading or writing this format type, see Additional reader and writer options for information.
DeltaVision
Extensions: .dv, .r3d, .rcpnl
Owner: Cytiva (formerly GE Healthcare, Applied Precision)
Support
BSD-licensed:
Export:
Officially Supported Versions:
Readers:
DeltavisionReader (Source Code, Supported Metadata Fields)
RCPNLReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a DV specification document (v2.10 or newer, in HTML)
numerous DV datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
The Deltavision format is based on the Medical Research Council (MRC) file format.
Commercial applications that support DeltaVision include:
RCPNL is a variant of the DeltaVision format and requires a separate reader.
DICOM
Extensions: .dcm, .dicom
Developer: DICOM Standards Committee
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: DicomReader (Source Code, Supported Metadata Fields)
Writer: DicomWriter (Source Code)
Freely Available Software:
Sample Datasets:
We currently have:
numerous DICOM datasets (see above)
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
DICOM stands for “Digital Imaging and Communication in Medicine”.
Bio-Formats supports uncompressed, baseline JPEG, JPEG-2000 (lossy and lossless), and RLE lossless transfer syntaxes.
Support for reading and writing DICOM whole slide images (DICOM WSI format) was implemented through collaboration with NCI Imaging Data Commons and has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN2612015000031.
If you have a problematic DICOM file which you cannot send us for privacy reasons, please send us the exact error message and be aware that it may take several attempts to fix the problem blind.
See also
ECAT7
Extensions: .v
Developer: Siemens
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: Ecat7Reader (Source Code, Supported Metadata Fields)
We currently have:
a few ECAT7 files
We would like to have:
an ECAT7 specification document
more ECAT7 files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
EPS (Encapsulated PostScript)
Extensions: .eps, .epsi, .ps
Developer: Adobe
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: EPSReader (Source Code, Supported Metadata Fields)
Writer: EPSWriter (Source Code)
Freely Available Software:
We currently have:
a few EPS datasets
the ability to produce new datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats can save individual planes as EPS.
Certain types of compressed EPS files are not supported.
Evotec/PerkinElmer Opera Flex
Extensions: .flex, .mea, .res
Developer: Evotec Technologies, now PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: FlexReader (Source Code, Supported Metadata Fields)
We currently have:
many Flex datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
FEI
Extensions: .img
Developer: FEI
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: FEIReader (Source Code, Supported Metadata Fields)
We currently have:
a few FEI files
We would like to have:
a specification document
more FEI files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
FEI TIFF
Extensions: .tiff
Developer: FEI
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: FEITiffReader (Source Code, Supported Metadata Fields)
We currently have:
a few FEI TIFF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
FITS (Flexible Image Transport System)
Extensions: .fits
Developer: National Radio Astronomy Observatory
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: FitsReader (Source Code, Supported Metadata Fields)
We currently have:
a FITS specification document (NOST 100-2.0, from 1999 March 29, in HTML)
several FITS datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
See also
Gatan Digital Micrograph
Extensions: .dm3, .dm4
Owner: Gatan
Support
BSD-licensed:
Export:
Officially Supported Versions: 3, 4
Reader: GatanReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
Gatan’s ImageReader2003 code (from 2003, in C++)
numerous DM3 datasets
We would like to have:
a DM3 specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Applications that support .dm3 files include Datasqueeze.
Note that the Gatan Reader does not currently support stacks.
Gatan Digital Micrograph 2
Extensions: .dm2
Developer: Gatan
Support
BSD-licensed:
Export:
Officially Supported Versions: 2
Reader: GatanDM2Reader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read DM2 files (from ImageSXM)
a few DM2 files
We would like to have:
an official DM2 specification document
more DM2 files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
GE MicroCT
Extensions: .vff
Developer: GE Healthcare
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: MicroCTReader (Source Code, Supported Metadata Fields)
We currently have:
several public MicroCT datasets from the CIBC Dataset Archive
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
GIF (Graphics Interchange Format)
Extensions: .gif
Developer: CompuServe
Owner: Unisys
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: GIFReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a GIF specification document (Version 89a, from 1990, in HTML)
numerous GIF datasets
the ability to produce new datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Hamamatsu Aquacosmos NAF
Extensions: .naf
Developer: Hamamatsu
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: NAFReader (Source Code, Supported Metadata Fields)
We currently have:
a few NAF files
We would like to have:
a specification document
more NAF files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Hamamatsu HIS
Extensions: .his
Owner: Hamamatsu
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: HISReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read HIS files (from ImageSXM)
several HIS files
We would like to have:
an HIS specification
more HIS files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Hamamatsu ndpi
Extensions: .ndpi, .ndpis
Developer: Hamamatsu
Support
BSD-licensed:
Export:
Officially Supported Versions:
Readers:
NDPIReader (Source Code, Supported Metadata Fields)
NDPISReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
many example datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Hamamatsu VMS
Extensions: .vms
Developer: Hamamatsu
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: HamamatsuVMSReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a few example datasets
We would like to have:
an official specification document
more example datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Hitachi S-4800
Extensions: .txt, .tif, .bmp, .jpg
Developer: Hitachi
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: HitachiReader (Source Code, Supported Metadata Fields)
We currently have:
several Hitachi S-4800 datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
I2I
Extensions: .i2i
Developer: Biomedical Imaging Group, UMass Medical School
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: I2IReader (Source Code, Supported Metadata Fields)
We currently have:
several example datasets
a specification document
an ImageJ plugin that can read I2I data
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
ICS (Image Cytometry Standard)
Extensions: .ics, .ids
Developer: P. Dean et al.
Support
BSD-licensed:
Export:
Officially Supported Versions: 1.0, 2.0
Reader: ICSReader (Source Code, Supported Metadata Fields)
Writer: ICSWriter (Source Code)
Freely Available Software:
We currently have:
numerous ICS datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
ICS version 1.0 datasets have two files - an .ics file that contains all of the metadata in plain-text format, and an .ids file that contains all of the pixel data.
ICS version 2.0 datasets are a single .ics file that contains both pixels and metadata.
Commercial applications that can support ICS include:
Imacon
Extensions: .fff
Owner: Hasselblad
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: ImaconReader (Source Code, Supported Metadata Fields)
We currently have:
one Imacon file
We would like to have:
more Imacon files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
ImagePro Sequence
Extensions: .seq
Owner: Media Cybernetics
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: SEQReader (Source Code, Supported Metadata Fields)
We currently have:
the Image-Pro Plus software
a few SEQ datasets
the ability to produce more datasets
We would like to have:
an official SEQ specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
ImagePro Workspace
Extensions: .ipw
Owner: Media Cybernetics
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: IPWReader (Source Code, Supported Metadata Fields)
We currently have:
the Image-Pro Plus software
a few IPW datasets
the ability to produce more datasets
We would like to have:
an official IPW specification document
more IPW datasets:
multiple datasets in one file
2+ GB files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats uses a modified version of the Apache Jakarta POI library to read IPW files.
IMAGIC
Extensions: .hed, .img
Developer: Image Science
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: ImagicReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
one example dataset
official file format documentation
We would like to have:
more example datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
See also
IMOD
Extensions: .mod
Developer: Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells
Owner: Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: IMODReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a few sample datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Improvision Openlab LIFF
Extensions: .liff
Developer: Improvision, now PerkinElmer
Owner: PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions: 2.0, 5.0
Reader: OpenlabReader (Source Code, Supported Metadata Fields)
We currently have:
an Openlab specification document (from 2000 February 8, in DOC)
Improvision’s XLIFFFileImporter code for reading Openlab LIFF v5 files (from 2006, in C++)
several Openlab datasets
We would like to have:
more Openlab datasets (preferably with 32-bit integer data)
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Improvision Openlab Raw
Extensions: .raw
Developer: Improvision, now PerkinElmer
Owner: PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: OpenlabRawReader (Source Code, Supported Metadata Fields)
We currently have:
an Openlab Raw specification document (from 2004 November 09, in HTML)
a few Openlab Raw datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Improvision TIFF
Extensions: .tif
Developer: Improvision, now PerkinElmer
Owner: PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: ImprovisionTiffReader (Source Code, Supported Metadata Fields)
We currently have:
an Improvision TIFF specification document
a few Improvision TIFF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Imspector OBF
Extensions: .obf, .msr
Developer: Department of NanoBiophotonics, MPI-BPC
Owner: MPI-BPC
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: OBFReader (Source Code, Supported Metadata Fields)
We currently have:
a few OBF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
InCell 1000/2000
Extensions: .xdce, .tif
Developer: GE Healthcare
Owner: Cytiva
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: InCellReader (Source Code, Supported Metadata Fields)
We currently have:
a few InCell 1000 datasets
We would like to have:
an InCell 1000 specification document
more InCell 1000 datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
InCell 3000
Extensions: .frm
Developer: GE Healthcare
Owner: Cytiva
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: InCell3000Reader (Source Code, Supported Metadata Fields)
We currently have:
a few example datasets
We would like to have:
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
INR
Extensions: .inr
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: INRReader (Source Code, Supported Metadata Fields)
We currently have:
several sample .inr datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Inveon
Extensions: .hdr
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: InveonReader (Source Code, Supported Metadata Fields)
We currently have:
a few Inveon datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Ionpath MIBI
Extensions: .tif, .tiff
Developer: IonPath
Owner: IonPath
Support
BSD-licensed:
Export:
Officially Supported Versions: 0.1
Reader: IonpathMIBITiffReader (Source Code, Supported Metadata Fields)
We currently have:
a few sample datasets
a specification document
We would like to have:
more sample datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
IPLab
Extensions: .ipl
Developer: Scanalytics
Owner: was BD Biosystems, now BioVision Technologies
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: IPLabReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
an IPLab specification document (v3.6.5, from 2004 December 1, in PDF)
several IPLab datasets
We would like to have:
more IPLab datasets (preferably with 32-bit integer or floating point data)
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Commercial applications that support IPLab include:
See also
IVision
Extensions: .ipm
Owner: BioVision Technologies
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: IvisionReader (Source Code, Supported Metadata Fields)
We currently have:
a few iVision-Mac datasets
a specification document
We would like to have:
more iVision-Mac datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
iVision-Mac was formerly called IPLab for Macintosh.
JEOL
Extensions: .dat, .img, .par
Owner: JEOL
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: JEOLReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that reads JEOL files (from ImageSXM)
a few JEOL files
We would like to have:
an official specification document
more JEOL files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
JPEG
Extensions: .jpg
Developer: Independent JPEG Group
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: JPEGReader (Source Code, Supported Metadata Fields)
Writer: JPEGWriter (Source Code)
We currently have:
a JPEG specification document (v1.04, from 1992 September 1, in PDF)
numerous JPEG datasets
the ability to produce more datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats can save individual planes as JPEG. Bio-Formats uses the Java Image I/O API to read and write JPEG files. JPEG stands for “Joint Photographic Experts Group”.
See also
JPEG 2000
Extensions: .jp2, .j2k, .jpf
Developer: Independent JPEG Group
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: JPEG2000Reader (Source Code, Supported Metadata Fields)
Writer: JPEG2000Writer (Source Code)
Freely Available Software:
We currently have:
a JPEG 2000 specification document (free draft from 2000, no longer available online)
a few .jp2 files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats uses the JAI Image I/O Tools library to read JP2 files. Conflicting versions of this no-longer-maintained library may cause errors, see JAI ImageIO component for details.
JPEG stands for “Joint Photographic Experts Group”.
JPK
Extensions: .jpk
Developer: JPK Instruments
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: JPKReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read JPK files (from ImageSXM)
a few JPK files
We would like to have:
an official specification document
more JPK files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
JPX
Extensions: .jpx
Developer: JPEG Committee
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: JPXReader (Source Code, Supported Metadata Fields)
We currently have:
a few .jpx files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Keller Lab Block
Extensions: .klb
Developer: Keller Lab (Janelia Research Campus)
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: KLBReader (Source Code, Supported Metadata Fields)
We currently have:
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Khoros VIFF (Visualization Image File Format) Bitmap
Extensions: .xv
Developer: Khoral
Owner: AccuSoft
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: KhorosReader (Source Code, Supported Metadata Fields)
Sample Datasets:
We currently have:
several VIFF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Kodak BIP
Extensions: .bip
Developer: Kodak/Carestream
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: KodakReader (Source Code, Supported Metadata Fields)
We currently have:
a few .bip datasets
We would like to have:
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Lambert Instruments FLIM
Extensions: .fli
Developer: Lambert Instruments
Support
BSD-licensed:
Export:
Officially Supported Versions: 1.0, 2.0
Reader: LiFlimReader (Source Code, Supported Metadata Fields)
We currently have:
an LI-FLIM specification document
several example LI-FLIM datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
LaVision Imspector
Extensions: .msr
Developer: LaVision BioTec
Support
BSD-licensed:
Export:
Officially Supported Versions: 4.0, 4.1
Reader: ImspectorReader (Source Code, Supported Metadata Fields)
We currently have:
a few .msr files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Leica LCS LEI
Extensions: .lei, .tif
Developer: Leica Microsystems CMS GmbH
Owner: Leica Microsystems
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: LeicaReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
an LEI specification document (beta 2.000, from no later than 2004 February 17, in PDF)
many LEI datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
LCS stands for “Leica Confocal Software”. LEI presumably stands for “Leica Experimental Information”.
Commercial applications that support LEI include:
Leica LAS AF LIF (Leica Image File Format)
Extensions: .lif
Developer: Leica Microsystems CMS GmbH
Owner: Leica Microsystems
Support
BSD-licensed:
Export:
Officially Supported Versions: 1.0, 2.0
Reader: LIFReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a LIF/XLLF/XLEF/LOF specification document (version 3.2, from no later than 2016 December 15, in PDF)
a LIF specification document (version 2, from no later than 2007 July 26, in PDF)
a LIF specification document (version 1, from no later than 2006 April 3, in PDF)
numerous LIF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Additional options are available for reading or writing this format type, see Additional reader and writer options for information.
LAS stands for “Leica Application Suite”. AF stands for “Advanced Fluorescence”.
Commercial applications that support LIF include:
Versions of Bio-Formats prior to 5.3.3 incorrectly calculated the physical
pixel width and height. The physical image width and height were divided by
the number of pixels, which was inconsistent with the official Leica LIF
specification documents. Versions 5.3.3 and later correctly calculate
physical pixel sizes by dividing the physical image size by the number of
pixels minus one. To revert to the old method of physical pixel size
calculation in 5.3.3 and later, set the leicalif.old_physical_size option
to true as described in Additional reader and writer options.
Leica LOF
Extensions: .lof
Developer: Leica Microsystems CMS GmbH
Owner: Leica Microsystems
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: LOFReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
numerous LOF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Leica SCN
Extensions: .scn
Developer: Leica Microsystems
Support
BSD-licensed:
Export:
Officially Supported Versions: 2012-03-10
Reader: LeicaSCNReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a few sample datasets
We would like to have:
an official specification document
sample datasets that cannot be opened
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Leica XLEF
Extensions: .xlef
Developer: Leica Microsystems CMS GmbH
Owner: Leica Microsystems
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: XLEFReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
numerous XLEF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
LEO
Extensions: .sxm, .tif, .tiff
Owner: ZEISS International
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: LEOReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read LEO files (from ImageSXM)
a few LEO files
We would like to have:
an official specification document
more LEO files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Li-Cor L2D
Extensions: .l2d, .tif, .scn
Owner: LiCor Biosciences
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: L2DReader (Source Code, Supported Metadata Fields)
We currently have:
a few L2D datasets
We would like to have:
an official specification document
more L2D datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
L2D datasets cannot be imported into OME using server-side import. They can, however, be imported from ImageJ, or using the omeul utility.
LIM (Laboratory Imaging/Nikon)
Extensions: .lim
Owner: Laboratory Imaging
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: LIMReader (Source Code, Supported Metadata Fields)
We currently have:
several LIM files
the ability to produce more LIM files
We would like to have:
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats only supports uncompressed LIM files.
Commercial applications that support LIM include:
MetaMorph 7.5 TIFF
Extensions: .tiff
Owner: Molecular Devices
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: MetamorphTiffReader (Source Code, Supported Metadata Fields)
We currently have:
a few Metamorph 7.5 TIFF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
MetaMorph Stack (STK)
Extensions: .stk, .nd
Owner: Molecular Devices
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: MetamorphReader (Source Code, Supported Metadata Fields)
We currently have:
an STK specification document (from 2006 November 21, in DOC)
an older STK specification document (from 2005 March 25, in DOC)
an ND specification document (from 2002 January 24, in PDF)
a large number of datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Commercial applications that support STK include:
See also
MetaXpress
Extensions: .htd, .tif, .tiff
Owner: Molecular Devices
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: CellWorxReader (Source Code, Supported Metadata Fields)
We currently have:
several MetaXpress datasets
We would like to have:
a MetaXpress specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
MIAS (Maia Scientific)
Extensions: .tif
Developer: Maia Scientific
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: MIASReader (Source Code, Supported Metadata Fields)
We currently have:
several MIAS datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Micro-Manager
Extensions: .tif, .txt, .xml
Developer: Vale Lab
Support
BSD-licensed:
Export:
Officially Supported Versions: Up to 1.4.22
Reader: MicromanagerReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
many Micro-manager datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats will recognize a
*metadata.txtfile as part of a Micro-Manager fileset if pointed at it and will load the fileset including the companion TIFF files.If pointed at a companion
.ome.tiffile, Bio-Formats will recognize an OME-TIFF format instead. This means it may load the fileset if there are multiple .ome.tif but it will not include*metadata.txtin this fileset and therefore the extended Micro-Manager metadata will be skipped.See Micro-Manager for more information.
Mikroscan TIFF
Extensions: .tif, .tiff
Owner: Mikroscan
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: MikroscanTiffReader (Source Code, Supported Metadata Fields)
We currently have:
some Mikroscan datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
MINC MRI
Extensions: .mnc
Developer: McGill University
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: MINCReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a few MINC files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Minolta MRW
Extensions: .mrw
Developer: Minolta
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: MRWReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
several .mrw files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
MNG (Multiple-image Network Graphics)
Extensions: .mng
Developer: MNG Development Group
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: MNGReader (Source Code, Supported Metadata Fields)
Freely Available Software:
Sample Datasets:
We currently have:
the libmng-testsuites package (from 2003 March 05, in C)
a large number of MNG datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
See also
Molecular Imaging
Extensions: .stp
Owner: Molecular Imaging Corp, San Diego CA (closed)
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: MolecularImagingReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that reads Molecular Imaging files (from ImageSXM)
a few Molecular Imaging files
We would like to have:
an official specification document
more Molecular Imaging files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
MRC (Medical Research Council)
Extensions: .mrc, .st, .ali, .map, .rec, .mrcs
Developers:
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: MRCReader (Source Code, Supported Metadata Fields)
Sample Datasets:
We currently have:
an IMOD-specific MRC specification document (in TXT)
a few MRC datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Commercial applications that support MRC include:
Bio-Formats provides support for the base MRC2000/MRC2014 specifications. Limited support is provided for vendor-specific extended headers, as described in the MRC2014 specification. IMOD extended metadata is perhaps the best-supported variant.
See also
NEF (Nikon Electronic Format)
Extensions: .nef, .tif
Developer: Nikon
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: NikonReader (Source Code, Supported Metadata Fields)
Sample Datasets:
We currently have:
a NEF specification document (v0.1, from 2003, in PDF)
several NEF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
See also
NIfTI
Extensions: .img, .hdr, .nii, .nii.gz
Developer: National Institutes of Health
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: NiftiReader (Source Code, Supported Metadata Fields)
We currently have:
several NIfTI datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Nikon Elements TIFF
Extensions: .tiff
Developer: Nikon
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: NikonElementsTiffReader (Source Code, Supported Metadata Fields)
We currently have:
a few Nikon Elements TIFF files
We would like to have:
more Nikon Elements TIFF files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Nikon EZ-C1 TIFF
Extensions: .tiff
Developer: Nikon
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: NikonTiffReader (Source Code, Supported Metadata Fields)
We currently have:
a few Nikon EZ-C1 TIFF files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Nikon NIS-Elements ND2
Extensions: .nd2
Developer: Nikon USA
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: ND2Reader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
many ND2 datasets
We would like to have:
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Additional options are available for reading or writing this format type, see Additional reader and writer options for information.
There are two distinct versions of ND2: an old version, which uses JPEG-2000 compression, and a new version which is either uncompressed or Zip-compressed. We are not aware of the version number or release date for either format.
Bio-Formats uses the JAI Image I/O Tools library to read ND2 files compressed with JPEG-2000.
NRRD (Nearly Raw Raster Data)
Extensions: .nrrd, .nhdr, .raw, .txt
Developer: Teem developers
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: NRRDReader (Source Code, Supported Metadata Fields)
Freely Available Software:
Sample Datasets:
We currently have:
an nrrd specification document (v1.9, from 2005 December 24, in HTML)
a few nrrd datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Olympus CellR/APL
Extensions: .apl, .mtb, .tnb, .tif, .obsep
Owner: Olympus
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: APLReader (Source Code, Supported Metadata Fields)
We currently have:
a few CellR datasets
We would like to have:
more Cellr datasets
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Olympus FluoView FV1000
Extensions: .oib, .oif
Owner: Olympus
Support
BSD-licensed:
Export:
Officially Supported Versions: 1.0, 2.0
Reader: FV1000Reader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
an OIF specification document (v2.0.0.0, from 2008, in PDF)
an FV1000 specification document (v1.0.0.0, from 2004 June 22, in PDF)
older FV1000 specification documents (draft, in DOC and XLS)
many FV1000 datasets
We would like to have:
more OIB datasets (especially 2+ GB files)
more FV1000 version 2 datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Bio-Formats uses a modified version of the Apache POI library to read OIB files. OIF stands for “Original Imaging Format”. OIB stands for “Olympus Image Binary”. OIF is a multi-file format that includes an .oif file and a directory of .tif, .roi, .pty, .lut, and .bmp files. OIB is a single file format.
Commercial applications that support this format include:
See also
Olympus FluoView TIFF
Extensions: .tif
Owner: Olympus
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: FluoviewReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a FluoView specification document (from 2002 November 14, in DOC)
Olympus’ FluoView Image File Reference Suite (from 2002 March 1, in DOC)
several FluoView datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Commercial applications that support this format include:
Olympus OIR
Extensions: .oir
Owner: Olympus
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: OIRReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
several OIR datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Support for this format was added in partnership with OLYMPUS EUROPA SE & Co. KG
Olympus OMP2INFO
Extensions: .omp2info
Owner: Olympus
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: OlympusTileReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
several OMP2INFO datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Support for this format was added in partnership with OLYMPUS EUROPA SE & Co. KG
Olympus ScanR
Extensions: .xml, .dat, .tif
Developer: Olympus
Owner: Olympus
Support
BSD-licensed:
Export:
Officially Supported Versions: Up to 2.5.1
Reader: ScanrReader (Source Code, Supported Metadata Fields)
We currently have:
several ScanR datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Olympus SIS TIFF
Extensions: .tiff
Developer: Olympus
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: SISReader (Source Code, Supported Metadata Fields)
We currently have:
a few example SIS TIFF files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
OME-TIFF
Extensions: .ome.tiff, .ome.tif, .ome.tf2, .ome.tf8, .ome.btf
Developer: Open Microscopy Environment
Support
BSD-licensed:
Export:
Officially Supported Versions: 2003FC, 2007-06, 2008-02, 2008-09, 2009-09, 2010-04, 2010-06, 2011-06, 2012-06, 2013-06, 2015-01, 2016-06
Reader: OMETiffReader (Source Code, Supported Metadata Fields)
Writer: OMETiffWriter (Source Code)
We currently have:
many OME-TIFF datasets
the ability to produce additional datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Additional options are available for reading or writing this format type, see Additional reader and writer options for information.
Bio-Formats can save image stacks as OME-TIFF.
Commercial applications that support OME-TIFF are listed on our commercial partners page
See also
OME-XML
Extensions: .ome, .ome.xml
Developer: Open Microscopy Environment
Support
BSD-licensed:
Export:
Officially Supported Versions: 2003FC, 2007-06, 2008-02, 2008-09, 2009-09, 2010-04, 2010-06, 2011-06, 2012-06, 2013-06, 2015-01, 2016-06
Reader: OMEXMLReader (Source Code, Supported Metadata Fields)
Writer: OMEXMLWriter (Source Code)
We currently have:
many OME-XML datasets
the ability to produce more datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats uses the OME-XML Java library to read OME-XML files.
Commercial applications that support OME-XML include:
OMERO Pyramid
Developer: Open Microscopy Environment
Support
BSD-licensed:
Export:
Officially Supported Versions: 1.0.0
Reader: TiffReader (Source Code, Supported Metadata Fields)
We currently have:
several OMERO Pyramid datasets
the ability to produce additional datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Oxford Instruments
Extensions: .top
Owner: Oxford Instruments
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: OxfordInstrumentsReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read Oxford Instruments files (from ImageSXM)
a few Oxford Instruments files
We would like to have:
an official specification document
more Oxford Instruments files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
PCORAW
Extensions: .pcoraw, .rec
Developer: PCO
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: PCORAWReader (Source Code, Supported Metadata Fields)
We currently have:
a few example datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
PCX (PC Paintbrush)
Extensions: .pcx
Developer: ZSoft Corporation
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: PCXReader (Source Code, Supported Metadata Fields)
We currently have:
several .pcx files
the ability to generate additional .pcx files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Commercial applications that support PCX include Zeiss LSM Image Browser.
Perkin Elmer Densitometer
Extensions: .pds
Developer: Perkin Elmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: PDSReader (Source Code, Supported Metadata Fields)
We currently have:
a few PDS datasets
We would like to have:
an official specification document
more PDS datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
PerkinElmer Columbus
Extensions: .xml, .csv, .tif
Owner: PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: ColumbusReader (Source Code, Supported Metadata Fields)
We currently have:
a few example datasets
We would like to have:
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
PerkinElmer Nuance
Extensions: .im3
Developer: PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: IM3Reader (Source Code, Supported Metadata Fields)
We currently have:
a few sample datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
PerkinElmer Operetta
Extensions: .tiff, .xml
Developer: PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: OperettaReader (Source Code, Supported Metadata Fields)
We currently have:
a few sample datasets
We would like to have:
an official specification document
more sample datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
PerkinElmer UltraVIEW
Extensions: .tif, .2, .3, .4, etc.
Owner: PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: PerkinElmerReader (Source Code, Supported Metadata Fields)
We currently have:
several UltraVIEW datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Other associated extensions include: .tim, .zpo, .csv, .htm, .cfg, .ano, .rec
Commercial applications that support this format include:
Portable Any Map
Extensions: .pbm, .pgm, .ppm
Developer: Netpbm developers
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: PGMReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a PGM specification document (from 2003 October 3, in HTML)
a few PBM, PPM and PGM files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Adobe Photoshop PSD
Extensions: .psd
Developer: Adobe
Support
BSD-licensed:
Export:
Officially Supported Versions: 1.0
Reader: PSDReader (Source Code, Supported Metadata Fields)
We currently have:
a PSD specification document (v3.0.4, 16 July 1995)
a few PSD files
We would like to have:
more PSD files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Photoshop TIFF
Extensions: .tif, .tiff
Developer: Adobe
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: PhotoshopTiffReader (Source Code, Supported Metadata Fields)
We currently have:
a Photoshop TIFF specification document
a few Photoshop TIFF files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
PicoQuant Bin
Extensions: .bin
Developer: PicoQuant
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: PQBinReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a few example datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
PICT (Macintosh Picture)
Extensions: .pict
Developer: Apple Computer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: PictReader (Source Code, Supported Metadata Fields)
We currently have:
many PICT datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
PNG (Portable Network Graphics)
Extensions: .png
Developer: PNG Development Group
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: APNGReader (Source Code, Supported Metadata Fields)
Writer: APNGWriter (Source Code)
Freely Available Software:
We currently have:
a PNG specification document (W3C/ISO/IEC version, from 2003 November 10, in HTML)
several PNG datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats uses the Java Image I/O API to read and write PNG files.
See also
Prairie Technologies TIFF
Extensions: .tif, .xml, .cfg
Developer: Prairie Technologies
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: PrairieReader (Source Code, Supported Metadata Fields)
We currently have:
many Prairie datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Princeton Instruments SPE
Extensions: .spe
Developer: Princeton Instruments
Support
BSD-licensed:
Export:
Officially Supported Versions: 3.0
Reader: SPEReader (Source Code, Supported Metadata Fields)
We currently have:
two SPE files
We would like to have:
more SPE files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Quesant
Extensions: .afm
Developer: Quesant Instrument Corporation
Owner: KLA-Tencor Corporation
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: QuesantReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read Quesant files (from ImageSXM)
several Quesant files
We would like to have:
an official specification document
more Quesant files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
QuickTime Movie
Extensions: .mov
Owner: Apple Computer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: QTReader (Source Code, Supported Metadata Fields)
Writer: QTWriter (Source Code)
Freely Available Software:
We currently have:
several QuickTime datasets
the ability to produce more datasets
We would like to have:
more QuickTime datasets, including:
files compressed with a common, unsupported codec
files with audio tracks and/or multiple video tracks
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats can save image stacks as QuickTime movies. The following table shows supported codecs:
Codec |
Description |
Native |
|---|---|---|
raw |
Full Frames (Uncompressed) |
read & write |
iraw |
Intel YUV Uncompressed |
read only |
rle |
Animation (run length encoded RGB) |
read only |
jpeg |
Still Image JPEG DIB |
read only |
rpza |
Apple Video 16 bit “road pizza” |
read only (partial) |
mjpb |
Motion JPEG codec |
read only |
See also
RHK
Extensions: .sm2, .sm3
Owner: RHK Technologies
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: RHKReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read RHK files (from ImageSXM)
a few RHK files
We would like to have:
an official specification document
more RHK files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
SBIG
Owner: Diffraction Limited (formerly Santa Barbara Instrument Group)
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: SBIGReader (Source Code, Supported Metadata Fields)
We currently have:
a few SBIG files
We would like to have:
more SBIG files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Seiko
Extensions: .xqd, .xqf
Owner: Seiko
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: SeikoReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read Seiko files (from ImageSXM)
a few Seiko files
We would like to have:
an official specification document
more Seiko files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
SimplePCI & HCImage
Extensions: .cxd
Developer: Compix
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: PCIReader (Source Code, Supported Metadata Fields)
We currently have:
several SimplePCI files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats uses a modified version of the Apache POI library to read CXD files.
See also
SimplePCI & HCImage TIFF
Extensions: .tiff
Developer: Hamamatsu
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: SimplePCITiffReader (Source Code, Supported Metadata Fields)
We currently have:
a few SimplePCI TIFF datasets
We would like to have:
more SimplePCI TIFF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
SM Camera
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: SMCameraReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read SM-Camera files (from ImageSXM)
a few SM-Camera files
We would like to have:
an official specification document
more SM-Camera files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
SPIDER
Extensions: .spi, .stk
Developer: Wadsworth Center
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: SpiderReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a few example datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Targa
Extensions: .tga
Developer: Truevision
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: TargaReader (Source Code, Supported Metadata Fields)
We currently have:
a Targa specification document
a few Targa files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Tecan Spark Cyto Workspace
Extensions: .db, .tif
Owner: Tecan Trading
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: TecanReader (Source Code, Supported Metadata Fields)
We currently have:
a few Tecan Spark Cyto workspaces
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Fiji users will need to enable the “Tissue Analyzer” update site and install “sqlite-jdbc.jar”
Text
Extensions: .txt
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: TextReader (Source Code, Supported Metadata Fields)
We currently have:
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Reads tabular pixel data produced by a variety of software.
TIFF (Tagged Image File Format)
Extensions: .tiff, .tif, .tf2, .tf8, .btf
Developer: Aldus and Microsoft
Owner: Adobe
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: TiffReader (Source Code, Supported Metadata Fields)
Writer: TiffWriter (Source Code)
Sample Datasets:
We currently have:
many TIFF datasets
a few BigTIFF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Bio-Formats can also read BigTIFF files (TIFF files larger than 4 GB). Bio-Formats can save image stacks as TIFF or BigTIFF.
TIFF files written by ImageJ are also supported, including ImageJ TIFFs larger than 4GB. ImageJ TIFFs are detected based upon the text in the first IFD’s “ImageDescription” tag; this tag’s value is then used to determine Z, C, and T sizes as well as physical sizes and timestamps. For ImageJ TIFFs larger than 4GB, a single IFD is expected (instead of one IFD per image plane). The “ImageDescription” is used to determine the number of images, the pixel data for which are expected to be stored contiguously at the offset indicated in the sole IFD. This differs from standard TIFF and BigTIFF; if the “ImageDescription” tag is missing or invalid, only the first image will be read.
TillPhotonics TillVision
Extensions: .vws
Developer: TILL Photonics
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: TillVisionReader (Source Code, Supported Metadata Fields)
We currently have:
several TillVision datasets
We would like to have:
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Topometrix
Extensions: .tfr, .ffr, .zfr, .zfp, .2fl
Owner: TopoMetrix (now Veeco)
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: TopometrixReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that reads Topometrix files (from ImageSXM)
a few Topometrix files
We would like to have:
an official specification document
more Topometrix files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Trestle
Extensions: .tif, .sld, .jpg
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: TrestleReader (Source Code, Supported Metadata Fields)
Sample Datasets:
We currently have:
a few example datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
UBM
Extensions: .pr3
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: UBMReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read UBM files (from ImageSXM)
one UBM file
We would like to have:
an official specification document
more UBM files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Unisoku
Extensions: .dat, .hdr
Owner: Unisoku
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: UnisokuReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read Unisoku files (from ImageSXM)
a few Unisoku files
We would like to have:
an official specification document
more Unisoku files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Varian FDF
Extensions: .fdf
Developer: Varian, Inc.
Owner: Agilent Technologies
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: VarianFDFReader (Source Code, Supported Metadata Fields)
We currently have:
a few Varian FDF datasets
We would like to have:
an official specification document
more Varian FDF datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Vectra QPTIFF
Extensions: .tif, .qptiff
Owner: Akoya Biosciences, formerly owned by PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: VectraReader (Source Code, Supported Metadata Fields)
We currently have:
several datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Support for this format was added in partnership with PerkinElmer and updated in partnership with Akoya Biosciences
Veeco AFM
Extensions: .hdf
Developer: Veeco
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: VeecoReader (Source Code, Supported Metadata Fields)
We currently have:
a few sample datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Ventana BIF
Extensions: .bif
Owner: Roche Digital Diagnostics
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: VentanaReader (Source Code, Supported Metadata Fields)
We currently have:
some Ventana datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
VG SAM
Extensions: .dti
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: VGSAMReader (Source Code, Supported Metadata Fields)
We currently have:
a few VG-SAM files
We would like to have:
an official specification document
more VG-SAM files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
VisiTech XYS
Extensions: .xys, .html
Developer: VisiTech International
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: VisitechReader (Source Code, Supported Metadata Fields)
We currently have:
several VisiTech datasets
We would like to have:
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Volocity
Extensions: .mvd2
Developer: PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: VolocityReader (Source Code, Supported Metadata Fields)
Sample Datasets:
We currently have:
many example Volocity datasets
We would like to have:
an official specification document
any Volocity datasets that do not open correctly
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
.mvd2 files are Metakit database files.
Volocity Library Clipping
Extensions: .acff
Developer: PerkinElmer
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: VolocityClippingReader (Source Code, Supported Metadata Fields)
We currently have:
several Volocity library clipping datasets
We would like to have:
any datasets that do not open correctly
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
RGB .acff files are not yet supported. See #6413.
WA-TOP
Extensions: .wat
Developer: WA Technology
Owner: Oxford Instruments
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: WATOPReader (Source Code, Supported Metadata Fields)
We currently have:
Pascal code that can read WA-TOP files (from ImageSXM)
a few WA-TOP files
We would like to have:
an official specification document
more WA-TOP files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Windows Bitmap
Extensions: .bmp
Developer: Microsoft and IBM
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: BMPReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
many BMP datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Compressed BMP files are currently not supported.
See also
Zeiss Axio CSM
Extensions: .lms
Developer: ZEISS International
Owner: ZEISS International
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: ZeissLMSReader (Source Code, Supported Metadata Fields)
We currently have:
one example dataset
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
This should not be confused with the more common Zeiss LSM format, which has a similar extension. As far as we know, the Axio CSM 700 system is the only one which saves files in the .lms format.
Zeiss AxioVision TIFF
Extensions: .xml, .tif
Developer: ZEISS International
Owner: ZEISS International
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: ZeissTIFFReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
many example datasets
We would like to have:
an official specification document
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Zeiss AxioVision ZVI (Zeiss Vision Image)
Extensions: .zvi
Developer: Carl Zeiss Microscopy GmbH
Owner: ZEISS International
Support
BSD-licensed:
Export:
Officially Supported Versions: 1.0, 2.0
Reader: ZeissZVIReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
a ZVI specification document (v2.0.5, from 2010 August, in PDF)
an older ZVI specification document (v2.0.2, from 2006 August 23, in PDF)
an older ZVI specification document (v2.0.1, from 2005 April 21, in PDF)
an older ZVI specification document (v1.0.26.01.01, from 2001 January 29, in DOC)
Zeiss’ ZvImageReader code (v1.0, from 2001 January 25, in C++)
many ZVI datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Bio-Formats uses a modified version of the Apache POI library to read ZVI files. ImageJ/FIJI will use the ZVI reader plugin in preference to Bio-Formats if both are installed. If you have a problem which is solved by opening the file using the Bio-Formats Importer plugin, you can just remove the ZVI_Reader.class from the plugins folder.
Commercial applications that support ZVI include Bitplane Imaris.
As of May 2021, the proprietary ZEISS AxioVision software is classed as End of Support. Zeiss ZEN is the successor programme to AxioVision.
Zeiss CZI
Extensions: .czi
Developer: ZEISS International
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: ZeissCZIReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
many example datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Additional options are available for reading or writing this format type, see Additional reader and writer options for information.
JPEG-XR compressed CZI files are supported on the following 64-bit platforms:
Windows 7 and above with Visual Studio 2015 C++ Redistributable
CentOS 6 and above, Ubuntu 12.04 and above
OS X 10.10 and above
Zeiss LSM (Laser Scanning Microscope) 510/710
Extensions: .lsm, .mdb
Owner: ZEISS International
Support
BSD-licensed:
Export:
Officially Supported Versions:
Reader: ZeissLSMReader (Source Code, Supported Metadata Fields)
Freely Available Software:
We currently have:
LSM specification v3.2, from 2003 March 12, in PDF
LSM specification v5.5, from 2009 November 23, in PDF
LSM specification v6.0, from 2010 September 28, in PDF
many LSM datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Please note that while we have specification documents for this format, we are not able to distribute them to third parties.
Bio-Formats uses the MDB Tools Java port
Commercial applications that support this format include:
Summary of supported metadata fields
Format readers
Reader |
Supported |
Unsupported |
Partial |
Unknown/Missing |
|---|---|---|---|---|
31 |
0 |
0 |
445 |
|
22 |
0 |
0 |
454 |
|
21 |
0 |
0 |
455 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
33 |
0 |
0 |
443 |
|
22 |
0 |
0 |
454 |
|
24 |
0 |
0 |
452 |
|
59 |
0 |
0 |
417 |
|
37 |
0 |
0 |
439 |
|
19 |
0 |
0 |
457 |
|
21 |
0 |
0 |
455 |
|
28 |
0 |
0 |
448 |
|
84 |
0 |
0 |
392 |
|
21 |
0 |
0 |
455 |
|
40 |
0 |
0 |
436 |
|
29 |
0 |
0 |
447 |
|
23 |
0 |
0 |
453 |
|
22 |
0 |
0 |
454 |
|
57 |
0 |
0 |
419 |
|
19 |
0 |
0 |
457 |
|
41 |
0 |
0 |
435 |
|
48 |
0 |
0 |
428 |
|
39 |
0 |
0 |
437 |
|
50 |
0 |
0 |
426 |
|
36 |
0 |
0 |
440 |
|
43 |
0 |
0 |
433 |
|
19 |
0 |
0 |
457 |
|
51 |
0 |
0 |
425 |
|
27 |
0 |
0 |
449 |
|
19 |
0 |
0 |
457 |
|
23 |
0 |
0 |
453 |
|
19 |
0 |
0 |
457 |
|
39 |
0 |
0 |
437 |
|
113 |
0 |
0 |
363 |
|
91 |
0 |
0 |
385 |
|
20 |
0 |
0 |
456 |
|
19 |
0 |
0 |
457 |
|
71 |
0 |
0 |
405 |
|
20 |
0 |
0 |
456 |
|
49 |
0 |
0 |
427 |
|
23 |
0 |
0 |
453 |
|
19 |
0 |
0 |
457 |
|
30 |
0 |
0 |
446 |
|
69 |
0 |
0 |
407 |
|
21 |
0 |
0 |
455 |
|
27 |
0 |
0 |
449 |
|
21 |
0 |
0 |
455 |
|
26 |
0 |
0 |
450 |
|
31 |
0 |
0 |
445 |
|
19 |
0 |
0 |
457 |
|
72 |
0 |
0 |
404 |
|
19 |
0 |
0 |
457 |
|
44 |
0 |
0 |
432 |
|
22 |
0 |
0 |
454 |
|
31 |
0 |
0 |
445 |
|
20 |
0 |
0 |
456 |
|
23 |
0 |
0 |
453 |
|
19 |
0 |
0 |
457 |
|
22 |
0 |
0 |
454 |
|
24 |
0 |
0 |
452 |
|
32 |
0 |
0 |
444 |
|
23 |
0 |
0 |
453 |
|
26 |
0 |
0 |
450 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
69 |
0 |
0 |
407 |
|
30 |
0 |
0 |
446 |
|
22 |
0 |
0 |
454 |
|
34 |
0 |
0 |
442 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
22 |
0 |
0 |
454 |
|
19 |
0 |
0 |
457 |
|
26 |
0 |
0 |
450 |
|
29 |
0 |
0 |
447 |
|
27 |
0 |
0 |
449 |
|
85 |
0 |
0 |
391 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
56 |
0 |
0 |
420 |
|
33 |
0 |
0 |
443 |
|
25 |
0 |
0 |
451 |
|
67 |
0 |
0 |
409 |
|
26 |
0 |
0 |
450 |
|
19 |
0 |
0 |
457 |
|
22 |
0 |
0 |
454 |
|
19 |
0 |
0 |
457 |
|
59 |
0 |
0 |
417 |
|
43 |
0 |
0 |
433 |
|
19 |
0 |
0 |
457 |
|
24 |
0 |
0 |
452 |
|
42 |
0 |
0 |
434 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
21 |
0 |
0 |
455 |
|
19 |
0 |
0 |
457 |
|
52 |
0 |
0 |
424 |
|
32 |
0 |
0 |
444 |
|
22 |
0 |
0 |
454 |
|
22 |
0 |
0 |
454 |
|
24 |
0 |
0 |
452 |
|
50 |
0 |
0 |
426 |
|
19 |
0 |
0 |
457 |
|
47 |
0 |
0 |
429 |
|
19 |
0 |
0 |
457 |
|
48 |
0 |
0 |
428 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
32 |
0 |
0 |
444 |
|
60 |
0 |
0 |
416 |
|
22 |
0 |
0 |
454 |
|
29 |
0 |
0 |
447 |
|
26 |
0 |
0 |
450 |
|
19 |
0 |
0 |
457 |
|
23 |
0 |
0 |
453 |
|
19 |
0 |
0 |
457 |
|
21 |
0 |
0 |
455 |
|
19 |
0 |
0 |
457 |
|
30 |
0 |
0 |
446 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
46 |
0 |
0 |
430 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
22 |
0 |
0 |
454 |
|
25 |
0 |
0 |
451 |
|
22 |
0 |
0 |
454 |
|
22 |
0 |
0 |
454 |
|
19 |
0 |
0 |
457 |
|
20 |
0 |
0 |
456 |
|
20 |
0 |
0 |
456 |
|
33 |
0 |
0 |
443 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
30 |
0 |
0 |
446 |
|
33 |
0 |
0 |
443 |
|
43 |
0 |
0 |
433 |
|
22 |
0 |
0 |
454 |
|
33 |
0 |
0 |
443 |
|
37 |
0 |
0 |
439 |
|
34 |
0 |
0 |
442 |
|
30 |
0 |
0 |
446 |
|
21 |
0 |
0 |
455 |
|
22 |
0 |
0 |
454 |
|
20 |
0 |
0 |
456 |
|
36 |
0 |
0 |
440 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
22 |
0 |
0 |
454 |
|
19 |
0 |
0 |
457 |
|
22 |
0 |
0 |
454 |
|
22 |
0 |
0 |
454 |
|
27 |
0 |
0 |
449 |
|
19 |
0 |
0 |
457 |
|
22 |
0 |
0 |
454 |
|
19 |
0 |
0 |
457 |
|
25 |
0 |
0 |
451 |
|
43 |
0 |
0 |
433 |
|
19 |
0 |
0 |
457 |
|
28 |
0 |
0 |
448 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
38 |
0 |
0 |
438 |
|
22 |
0 |
0 |
454 |
|
19 |
0 |
0 |
457 |
|
175 |
0 |
0 |
301 |
|
23 |
0 |
0 |
453 |
|
101 |
0 |
0 |
375 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
|
19 |
0 |
0 |
457 |
Metadata fields
Field |
Supported |
Unsupported |
Partial |
Unknown/Missing |
|---|---|---|---|---|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
5 |
0 |
0 |
175 |
|
0 |
0 |
0 |
180 |
|
20 |
0 |
0 |
160 |
|
1 |
0 |
0 |
179 |
|
24 |
0 |
0 |
156 |
|
21 |
0 |
0 |
159 |
|
1 |
0 |
0 |
179 |
|
3 |
0 |
0 |
177 |
|
180 |
0 |
0 |
0 |
|
3 |
0 |
0 |
177 |
|
1 |
0 |
0 |
179 |
|
7 |
0 |
0 |
173 |
|
2 |
0 |
0 |
178 |
|
2 |
0 |
0 |
178 |
|
49 |
0 |
0 |
131 |
|
11 |
0 |
0 |
169 |
|
0 |
0 |
0 |
180 |
|
180 |
0 |
0 |
0 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
2 |
0 |
0 |
178 |
|
0 |
0 |
0 |
180 |
|
7 |
0 |
0 |
173 |
|
37 |
0 |
0 |
143 |
|
1 |
0 |
0 |
179 |
|
5 |
0 |
0 |
175 |
|
15 |
0 |
0 |
165 |
|
7 |
0 |
0 |
173 |
|
4 |
0 |
0 |
176 |
|
28 |
0 |
0 |
152 |
|
3 |
0 |
0 |
177 |
|
4 |
0 |
0 |
176 |
|
19 |
0 |
0 |
161 |
|
21 |
0 |
0 |
159 |
|
35 |
0 |
0 |
145 |
|
9 |
0 |
0 |
171 |
|
5 |
0 |
0 |
175 |
|
6 |
0 |
0 |
174 |
|
0 |
0 |
0 |
180 |
|
6 |
0 |
0 |
174 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
6 |
0 |
0 |
174 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
3 |
0 |
0 |
177 |
|
0 |
0 |
0 |
180 |
|
7 |
0 |
0 |
173 |
|
0 |
0 |
0 |
180 |
|
7 |
0 |
0 |
173 |
|
7 |
0 |
0 |
173 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
2 |
0 |
0 |
178 |
|
4 |
0 |
0 |
176 |
|
0 |
0 |
0 |
180 |
|
2 |
0 |
0 |
178 |
|
2 |
0 |
0 |
178 |
|
2 |
0 |
0 |
178 |
|
7 |
0 |
0 |
173 |
|
7 |
0 |
0 |
173 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
5 |
0 |
0 |
175 |
|
5 |
0 |
0 |
175 |
|
0 |
0 |
0 |
180 |
|
2 |
0 |
0 |
178 |
|
5 |
0 |
0 |
175 |
|
12 |
0 |
0 |
168 |
|
4 |
0 |
0 |
176 |
|
9 |
0 |
0 |
171 |
|
1 |
0 |
0 |
179 |
|
4 |
0 |
0 |
176 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
2 |
0 |
0 |
178 |
|
8 |
0 |
0 |
172 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
8 |
0 |
0 |
172 |
|
1 |
0 |
0 |
179 |
|
2 |
0 |
0 |
178 |
|
2 |
0 |
0 |
178 |
|
2 |
0 |
0 |
178 |
|
2 |
0 |
0 |
178 |
|
2 |
0 |
0 |
178 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
2 |
0 |
0 |
178 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
180 |
0 |
0 |
0 |
|
1 |
0 |
0 |
179 |
|
48 |
0 |
0 |
132 |
|
2 |
0 |
0 |
178 |
|
0 |
0 |
0 |
180 |
|
7 |
0 |
0 |
173 |
|
180 |
0 |
0 |
0 |
|
52 |
0 |
0 |
128 |
|
0 |
0 |
0 |
180 |
|
180 |
0 |
0 |
0 |
|
16 |
0 |
0 |
164 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
10 |
0 |
0 |
170 |
|
0 |
0 |
0 |
180 |
|
58 |
0 |
0 |
122 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
3 |
0 |
0 |
177 |
|
0 |
0 |
0 |
180 |
|
6 |
0 |
0 |
174 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
2 |
0 |
0 |
178 |
|
6 |
0 |
0 |
174 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
6 |
0 |
0 |
174 |
|
6 |
0 |
0 |
174 |
|
0 |
0 |
0 |
180 |
|
11 |
0 |
0 |
169 |
|
8 |
0 |
0 |
172 |
|
1 |
0 |
0 |
179 |
|
2 |
0 |
0 |
178 |
|
5 |
0 |
0 |
175 |
|
0 |
0 |
0 |
180 |
|
4 |
0 |
0 |
176 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
8 |
0 |
0 |
172 |
|
9 |
0 |
0 |
171 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
3 |
0 |
0 |
177 |
|
5 |
0 |
0 |
175 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
3 |
0 |
0 |
177 |
|
0 |
0 |
0 |
180 |
|
7 |
0 |
0 |
173 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
2 |
0 |
0 |
178 |
|
3 |
0 |
0 |
177 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
7 |
0 |
0 |
173 |
|
7 |
0 |
0 |
173 |
|
7 |
0 |
0 |
173 |
|
7 |
0 |
0 |
173 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
3 |
0 |
0 |
177 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
3 |
0 |
0 |
177 |
|
3 |
0 |
0 |
177 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
3 |
0 |
0 |
177 |
|
3 |
0 |
0 |
177 |
|
3 |
0 |
0 |
177 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
2 |
0 |
0 |
178 |
|
13 |
0 |
0 |
167 |
|
4 |
0 |
0 |
176 |
|
3 |
0 |
0 |
177 |
|
0 |
0 |
0 |
180 |
|
8 |
0 |
0 |
172 |
|
27 |
0 |
0 |
153 |
|
43 |
0 |
0 |
137 |
|
29 |
0 |
0 |
151 |
|
2 |
0 |
0 |
178 |
|
24 |
0 |
0 |
156 |
|
1 |
0 |
0 |
179 |
|
6 |
0 |
0 |
174 |
|
17 |
0 |
0 |
163 |
|
35 |
0 |
0 |
145 |
|
3 |
0 |
0 |
177 |
|
12 |
0 |
0 |
168 |
|
1 |
0 |
0 |
179 |
|
38 |
0 |
0 |
142 |
|
1 |
0 |
0 |
179 |
|
10 |
0 |
0 |
170 |
|
0 |
0 |
0 |
180 |
|
180 |
0 |
0 |
0 |
|
180 |
0 |
0 |
0 |
|
180 |
0 |
0 |
0 |
|
180 |
0 |
0 |
0 |
|
96 |
0 |
0 |
84 |
|
96 |
0 |
0 |
84 |
|
49 |
0 |
0 |
131 |
|
180 |
0 |
0 |
0 |
|
180 |
0 |
0 |
0 |
|
180 |
0 |
0 |
0 |
|
180 |
0 |
0 |
0 |
|
180 |
0 |
0 |
0 |
|
180 |
0 |
0 |
0 |
|
17 |
0 |
0 |
163 |
|
180 |
0 |
0 |
0 |
|
0 |
0 |
0 |
180 |
|
29 |
0 |
0 |
151 |
|
38 |
0 |
0 |
142 |
|
0 |
0 |
0 |
180 |
|
40 |
0 |
0 |
140 |
|
40 |
0 |
0 |
140 |
|
33 |
0 |
0 |
147 |
|
180 |
0 |
0 |
0 |
|
180 |
0 |
0 |
0 |
|
180 |
0 |
0 |
0 |
|
0 |
0 |
0 |
180 |
|
8 |
0 |
0 |
172 |
|
15 |
0 |
0 |
165 |
|
3 |
0 |
0 |
177 |
|
4 |
0 |
0 |
176 |
|
15 |
0 |
0 |
165 |
|
13 |
0 |
0 |
167 |
|
8 |
0 |
0 |
172 |
|
15 |
0 |
0 |
165 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
3 |
0 |
0 |
177 |
|
11 |
0 |
0 |
169 |
|
10 |
0 |
0 |
170 |
|
0 |
0 |
0 |
180 |
|
5 |
0 |
0 |
175 |
|
11 |
0 |
0 |
169 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
5 |
0 |
0 |
175 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
2 |
0 |
0 |
178 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
2 |
0 |
0 |
178 |
|
0 |
0 |
0 |
180 |
|
5 |
0 |
0 |
175 |
|
5 |
0 |
0 |
175 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
2 |
0 |
0 |
178 |
|
0 |
0 |
0 |
180 |
|
8 |
0 |
0 |
172 |
|
0 |
0 |
0 |
180 |
|
8 |
0 |
0 |
172 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
3 |
0 |
0 |
177 |
|
2 |
0 |
0 |
178 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
2 |
0 |
0 |
178 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
2 |
0 |
0 |
178 |
|
0 |
0 |
0 |
180 |
|
6 |
0 |
0 |
174 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
6 |
0 |
0 |
174 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
3 |
0 |
0 |
177 |
|
2 |
0 |
0 |
178 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
2 |
0 |
0 |
178 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
16 |
0 |
0 |
164 |
|
5 |
0 |
0 |
175 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
3 |
0 |
0 |
177 |
|
0 |
0 |
0 |
180 |
|
12 |
0 |
0 |
168 |
|
12 |
0 |
0 |
168 |
|
0 |
0 |
0 |
180 |
|
3 |
0 |
0 |
177 |
|
0 |
0 |
0 |
180 |
|
2 |
0 |
0 |
178 |
|
5 |
0 |
0 |
175 |
|
2 |
0 |
0 |
178 |
|
3 |
0 |
0 |
177 |
|
3 |
0 |
0 |
177 |
|
1 |
0 |
0 |
179 |
|
12 |
0 |
0 |
168 |
|
12 |
0 |
0 |
168 |
|
12 |
0 |
0 |
168 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
3 |
0 |
0 |
177 |
|
2 |
0 |
0 |
178 |
|
2 |
0 |
0 |
178 |
|
3 |
0 |
0 |
177 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
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1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
5 |
0 |
0 |
175 |
|
1 |
0 |
0 |
179 |
|
5 |
0 |
0 |
175 |
|
1 |
0 |
0 |
179 |
|
1 |
0 |
0 |
179 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
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0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
16 |
0 |
0 |
164 |
|
0 |
0 |
0 |
180 |
|
1 |
0 |
0 |
179 |
|
16 |
0 |
0 |
164 |
|
0 |
0 |
0 |
180 |
|
16 |
0 |
0 |
164 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
|
16 |
0 |
0 |
164 |
|
16 |
0 |
0 |
164 |
|
16 |
0 |
0 |
164 |
|
9 |
0 |
0 |
171 |
|
9 |
0 |
0 |
171 |
|
0 |
0 |
0 |
180 |
|
0 |
0 |
0 |
180 |
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2 |
0 |
0 |
178 |
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1 |
0 |
0 |
179 |
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2 |
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178 |
AFIReader
This page lists supported metadata fields for the Bio-Formats Aperio AFI format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 31 of them (6%).
Of those, Bio-Formats fully or partially converts 31 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Aperio AFI format reader:
Total supported: 31
Total unknown or missing: 445
AIMReader
This page lists supported metadata fields for the Bio-Formats AIM format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats AIM format reader:
Total supported: 22
Total unknown or missing: 454
APLReader
This page lists supported metadata fields for the Bio-Formats Olympus APL format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 21 of them (4%).
Of those, Bio-Formats fully or partially converts 21 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Olympus APL format reader:
Total supported: 21
Total unknown or missing: 455
APNGReader
This page lists supported metadata fields for the Bio-Formats Animated PNG format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Animated PNG format reader:
Total supported: 19
Total unknown or missing: 457
ARFReader
This page lists supported metadata fields for the Bio-Formats ARF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats ARF format reader:
Total supported: 19
Total unknown or missing: 457
AVIReader
This page lists supported metadata fields for the Bio-Formats Audio Video Interleave format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Audio Video Interleave format reader:
Total supported: 19
Total unknown or missing: 457
AliconaReader
This page lists supported metadata fields for the Bio-Formats Alicona AL3D format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 33 of them (6%).
Of those, Bio-Formats fully or partially converts 33 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Alicona AL3D format reader:
Total supported: 33
Total unknown or missing: 443
AmiraReader
This page lists supported metadata fields for the Bio-Formats Amira format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Amira format reader:
Total supported: 22
Total unknown or missing: 454
AnalyzeReader
This page lists supported metadata fields for the Bio-Formats Analyze 7.5 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 24 of them (5%).
Of those, Bio-Formats fully or partially converts 24 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Analyze 7.5 format reader:
Total supported: 24
Total unknown or missing: 452
BDReader
This page lists supported metadata fields for the Bio-Formats BD Pathway format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 59 of them (12%).
Of those, Bio-Formats fully or partially converts 59 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats BD Pathway format reader:
Total supported: 59
Total unknown or missing: 417
BDVReader
This page lists supported metadata fields for the Bio-Formats BDV format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 37 of them (7%).
Of those, Bio-Formats fully or partially converts 37 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats BDV format reader:
Total supported: 37
Total unknown or missing: 439
BIFormatReader
This page lists supported metadata fields for the Bio-Formats BIFormatReader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats BIFormatReader:
Total supported: 19
Total unknown or missing: 457
BMPReader
This page lists supported metadata fields for the Bio-Formats Windows Bitmap format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 21 of them (4%).
Of those, Bio-Formats fully or partially converts 21 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Windows Bitmap format reader:
Total supported: 21
Total unknown or missing: 455
BaseTiffReader
This page lists supported metadata fields for the Bio-Formats BaseTiffReader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 28 of them (5%).
Of those, Bio-Formats fully or partially converts 28 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats BaseTiffReader:
Total supported: 28
Total unknown or missing: 448
BaseZeissReader
This page lists supported metadata fields for the Bio-Formats BaseZeissReader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 84 of them (17%).
Of those, Bio-Formats fully or partially converts 84 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats BaseZeissReader:
Total supported: 84
Total unknown or missing: 392
BioRadGelReader
This page lists supported metadata fields for the Bio-Formats Bio-Rad GEL format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 21 of them (4%).
Of those, Bio-Formats fully or partially converts 21 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Bio-Rad GEL format reader:
Total supported: 21
Total unknown or missing: 455
BioRadReader
This page lists supported metadata fields for the Bio-Formats Bio-Rad PIC format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 40 of them (8%).
Of those, Bio-Formats fully or partially converts 40 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Bio-Rad PIC format reader:
Total supported: 40
Total unknown or missing: 436
BioRadSCNReader
This page lists supported metadata fields for the Bio-Formats Bio-Rad SCN format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 29 of them (6%).
Of those, Bio-Formats fully or partially converts 29 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Bio-Rad SCN format reader:
Total supported: 29
Total unknown or missing: 447
BrukerReader
This page lists supported metadata fields for the Bio-Formats Bruker format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 23 of them (4%).
Of those, Bio-Formats fully or partially converts 23 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Bruker format reader:
Total supported: 23
Total unknown or missing: 453
BurleighReader
This page lists supported metadata fields for the Bio-Formats Burleigh format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Burleigh format reader:
Total supported: 22
Total unknown or missing: 454
CV7000Reader
This page lists supported metadata fields for the Bio-Formats Yokogawa CV7000 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 57 of them (11%).
Of those, Bio-Formats fully or partially converts 57 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Yokogawa CV7000 format reader:
Total supported: 57
Total unknown or missing: 419
CanonRawReader
This page lists supported metadata fields for the Bio-Formats Canon RAW format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Canon RAW format reader:
Total supported: 19
Total unknown or missing: 457
CellH5Reader
This page lists supported metadata fields for the Bio-Formats CellH5 (HDF) format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 41 of them (8%).
Of those, Bio-Formats fully or partially converts 41 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats CellH5 (HDF) format reader:
Total supported: 41
Total unknown or missing: 435
CellSensReader
This page lists supported metadata fields for the Bio-Formats CellSens VSI format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 48 of them (10%).
Of those, Bio-Formats fully or partially converts 48 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats CellSens VSI format reader:
Total supported: 48
Total unknown or missing: 428
CellVoyagerReader
This page lists supported metadata fields for the Bio-Formats CellVoyager format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 39 of them (8%).
Of those, Bio-Formats fully or partially converts 39 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats CellVoyager format reader:
Total supported: 39
Total unknown or missing: 437
CellWorxReader
This page lists supported metadata fields for the Bio-Formats CellWorx format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 50 of them (10%).
Of those, Bio-Formats fully or partially converts 50 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats CellWorx format reader:
Total supported: 50
Total unknown or missing: 426
CellomicsReader
This page lists supported metadata fields for the Bio-Formats Cellomics C01 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 36 of them (7%).
Of those, Bio-Formats fully or partially converts 36 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Cellomics C01 format reader:
Total supported: 36
Total unknown or missing: 440
ColumbusReader
This page lists supported metadata fields for the Bio-Formats PerkinElmer Columbus format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 43 of them (9%).
Of those, Bio-Formats fully or partially converts 43 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats PerkinElmer Columbus format reader:
Total supported: 43
Total unknown or missing: 433
DNGReader
This page lists supported metadata fields for the Bio-Formats DNG format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats DNG format reader:
Total supported: 19
Total unknown or missing: 457
DeltavisionReader
This page lists supported metadata fields for the Bio-Formats Deltavision format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 51 of them (10%).
Of those, Bio-Formats fully or partially converts 51 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Deltavision format reader:
Total supported: 51
Total unknown or missing: 425
DicomReader
This page lists supported metadata fields for the Bio-Formats DICOM format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 27 of them (5%).
Of those, Bio-Formats fully or partially converts 27 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats DICOM format reader:
Total supported: 27
Total unknown or missing: 449
EPSReader
This page lists supported metadata fields for the Bio-Formats Encapsulated PostScript format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Encapsulated PostScript format reader:
Total supported: 19
Total unknown or missing: 457
Ecat7Reader
This page lists supported metadata fields for the Bio-Formats ECAT7 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 23 of them (4%).
Of those, Bio-Formats fully or partially converts 23 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats ECAT7 format reader:
Total supported: 23
Total unknown or missing: 453
FEIReader
This page lists supported metadata fields for the Bio-Formats FEI/Philips format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats FEI/Philips format reader:
Total supported: 19
Total unknown or missing: 457
FEITiffReader
This page lists supported metadata fields for the Bio-Formats FEI TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 39 of them (8%).
Of those, Bio-Formats fully or partially converts 39 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats FEI TIFF format reader:
Total supported: 39
Total unknown or missing: 437
FV1000Reader
This page lists supported metadata fields for the Bio-Formats Olympus FV1000 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 113 of them (23%).
Of those, Bio-Formats fully or partially converts 113 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Olympus FV1000 format reader:
Total supported: 113
Total unknown or missing: 363
FakeReader
This page lists supported metadata fields for the Bio-Formats Simulated data format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 91 of them (19%).
Of those, Bio-Formats fully or partially converts 91 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Simulated data format reader:
Total supported: 91
Total unknown or missing: 385
FilePatternReader
This page lists supported metadata fields for the Bio-Formats File pattern format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 20 of them (4%).
Of those, Bio-Formats fully or partially converts 20 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats File pattern format reader:
Total supported: 20
Total unknown or missing: 456
FitsReader
This page lists supported metadata fields for the Bio-Formats Flexible Image Transport System format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Flexible Image Transport System format reader:
Total supported: 19
Total unknown or missing: 457
FlexReader
This page lists supported metadata fields for the Bio-Formats Evotec Flex format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 71 of them (14%).
Of those, Bio-Formats fully or partially converts 71 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Evotec Flex format reader:
Total supported: 71
Total unknown or missing: 405
FlowSightReader
This page lists supported metadata fields for the Bio-Formats FlowSight format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 20 of them (4%).
Of those, Bio-Formats fully or partially converts 20 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats FlowSight format reader:
Total supported: 20
Total unknown or missing: 456
FluoviewReader
This page lists supported metadata fields for the Bio-Formats Olympus Fluoview/ABD TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 49 of them (10%).
Of those, Bio-Formats fully or partially converts 49 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Olympus Fluoview/ABD TIFF format reader:
Total supported: 49
Total unknown or missing: 427
FujiReader
This page lists supported metadata fields for the Bio-Formats Fuji LAS 3000 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 23 of them (4%).
Of those, Bio-Formats fully or partially converts 23 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Fuji LAS 3000 format reader:
Total supported: 23
Total unknown or missing: 453
GIFReader
This page lists supported metadata fields for the Bio-Formats Graphics Interchange Format format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Graphics Interchange Format format reader:
Total supported: 19
Total unknown or missing: 457
GatanDM2Reader
This page lists supported metadata fields for the Bio-Formats Gatan DM2 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 30 of them (6%).
Of those, Bio-Formats fully or partially converts 30 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Gatan DM2 format reader:
Total supported: 30
Total unknown or missing: 446
GatanReader
This page lists supported metadata fields for the Bio-Formats Gatan Digital Micrograph format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 69 of them (14%).
Of those, Bio-Formats fully or partially converts 69 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Gatan Digital Micrograph format reader:
Total supported: 69
Total unknown or missing: 407
GelReader
This page lists supported metadata fields for the Bio-Formats Amersham Biosciences GEL format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 21 of them (4%).
Of those, Bio-Formats fully or partially converts 21 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Amersham Biosciences GEL format reader:
Total supported: 21
Total unknown or missing: 455
HISReader
This page lists supported metadata fields for the Bio-Formats Hamamatsu HIS format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 27 of them (5%).
Of those, Bio-Formats fully or partially converts 27 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Hamamatsu HIS format reader:
Total supported: 27
Total unknown or missing: 449
HRDGDFReader
This page lists supported metadata fields for the Bio-Formats NOAA-HRD Gridded Data Format format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 21 of them (4%).
Of those, Bio-Formats fully or partially converts 21 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats NOAA-HRD Gridded Data Format format reader:
Total supported: 21
Total unknown or missing: 455
HamamatsuVMSReader
This page lists supported metadata fields for the Bio-Formats Hamamatsu VMS format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 26 of them (5%).
Of those, Bio-Formats fully or partially converts 26 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Hamamatsu VMS format reader:
Total supported: 26
Total unknown or missing: 450
HitachiReader
This page lists supported metadata fields for the Bio-Formats Hitachi format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 31 of them (6%).
Of those, Bio-Formats fully or partially converts 31 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Hitachi format reader:
Total supported: 31
Total unknown or missing: 445
I2IReader
This page lists supported metadata fields for the Bio-Formats I2I format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats I2I format reader:
Total supported: 19
Total unknown or missing: 457
ICSReader
This page lists supported metadata fields for the Bio-Formats Image Cytometry Standard format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 72 of them (15%).
Of those, Bio-Formats fully or partially converts 72 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Image Cytometry Standard format reader:
Total supported: 72
Total unknown or missing: 404
IM3Reader
This page lists supported metadata fields for the Bio-Formats Perkin-Elmer Nuance IM3 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Perkin-Elmer Nuance IM3 format reader:
Total supported: 19
Total unknown or missing: 457
IMODReader
This page lists supported metadata fields for the Bio-Formats IMOD format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 44 of them (9%).
Of those, Bio-Formats fully or partially converts 44 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats IMOD format reader:
Total supported: 44
Total unknown or missing: 432
INRReader
This page lists supported metadata fields for the Bio-Formats INR format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats INR format reader:
Total supported: 22
Total unknown or missing: 454
IPLabReader
This page lists supported metadata fields for the Bio-Formats IPLab format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 31 of them (6%).
Of those, Bio-Formats fully or partially converts 31 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats IPLab format reader:
Total supported: 31
Total unknown or missing: 445
IPWReader
This page lists supported metadata fields for the Bio-Formats Image-Pro Workspace format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 20 of them (4%).
Of those, Bio-Formats fully or partially converts 20 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Image-Pro Workspace format reader:
Total supported: 20
Total unknown or missing: 456
ImaconReader
This page lists supported metadata fields for the Bio-Formats Imacon format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 23 of them (4%).
Of those, Bio-Formats fully or partially converts 23 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Imacon format reader:
Total supported: 23
Total unknown or missing: 453
ImageIOReader
This page lists supported metadata fields for the Bio-Formats ImageIOReader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats ImageIOReader:
Total supported: 19
Total unknown or missing: 457
ImagicReader
This page lists supported metadata fields for the Bio-Formats IMAGIC format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats IMAGIC format reader:
Total supported: 22
Total unknown or missing: 454
ImarisHDFReader
This page lists supported metadata fields for the Bio-Formats Bitplane Imaris 5.5 (HDF) format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 24 of them (5%).
Of those, Bio-Formats fully or partially converts 24 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Bitplane Imaris 5.5 (HDF) format reader:
Total supported: 24
Total unknown or missing: 452
ImarisReader
This page lists supported metadata fields for the Bio-Formats Bitplane Imaris format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 32 of them (6%).
Of those, Bio-Formats fully or partially converts 32 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Bitplane Imaris format reader:
Total supported: 32
Total unknown or missing: 444
ImarisTiffReader
This page lists supported metadata fields for the Bio-Formats Bitplane Imaris 3 (TIFF) format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 23 of them (4%).
Of those, Bio-Formats fully or partially converts 23 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Bitplane Imaris 3 (TIFF) format reader:
Total supported: 23
Total unknown or missing: 453
ImprovisionTiffReader
This page lists supported metadata fields for the Bio-Formats Improvision TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 26 of them (5%).
Of those, Bio-Formats fully or partially converts 26 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Improvision TIFF format reader:
Total supported: 26
Total unknown or missing: 450
ImspectorReader
This page lists supported metadata fields for the Bio-Formats Lavision Imspector format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Lavision Imspector format reader:
Total supported: 19
Total unknown or missing: 457
InCell3000Reader
This page lists supported metadata fields for the Bio-Formats InCell 3000 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats InCell 3000 format reader:
Total supported: 19
Total unknown or missing: 457
InCellReader
This page lists supported metadata fields for the Bio-Formats InCell 1000/2000 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 69 of them (14%).
Of those, Bio-Formats fully or partially converts 69 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats InCell 1000/2000 format reader:
Total supported: 69
Total unknown or missing: 407
InveonReader
This page lists supported metadata fields for the Bio-Formats Inveon format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 30 of them (6%).
Of those, Bio-Formats fully or partially converts 30 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Inveon format reader:
Total supported: 30
Total unknown or missing: 446
IonpathMIBITiffReader
This page lists supported metadata fields for the Bio-Formats Ionpath MIBI format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Ionpath MIBI format reader:
Total supported: 22
Total unknown or missing: 454
IvisionReader
This page lists supported metadata fields for the Bio-Formats IVision format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 34 of them (7%).
Of those, Bio-Formats fully or partially converts 34 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats IVision format reader:
Total supported: 34
Total unknown or missing: 442
JEOLReader
This page lists supported metadata fields for the Bio-Formats JEOL format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats JEOL format reader:
Total supported: 19
Total unknown or missing: 457
JPEG2000Reader
This page lists supported metadata fields for the Bio-Formats JPEG-2000 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats JPEG-2000 format reader:
Total supported: 19
Total unknown or missing: 457
JPEGReader
This page lists supported metadata fields for the Bio-Formats JPEG format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats JPEG format reader:
Total supported: 19
Total unknown or missing: 457
JPKReader
This page lists supported metadata fields for the Bio-Formats JPK Instruments format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats JPK Instruments format reader:
Total supported: 19
Total unknown or missing: 457
JPXReader
This page lists supported metadata fields for the Bio-Formats JPX format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats JPX format reader:
Total supported: 19
Total unknown or missing: 457
KLBReader
This page lists supported metadata fields for the Bio-Formats KLB format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats KLB format reader:
Total supported: 22
Total unknown or missing: 454
KhorosReader
This page lists supported metadata fields for the Bio-Formats Khoros XV format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Khoros XV format reader:
Total supported: 19
Total unknown or missing: 457
KodakReader
This page lists supported metadata fields for the Bio-Formats Kodak Molecular Imaging format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 26 of them (5%).
Of those, Bio-Formats fully or partially converts 26 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Kodak Molecular Imaging format reader:
Total supported: 26
Total unknown or missing: 450
L2DReader
This page lists supported metadata fields for the Bio-Formats Li-Cor L2D format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 29 of them (6%).
Of those, Bio-Formats fully or partially converts 29 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Li-Cor L2D format reader:
Total supported: 29
Total unknown or missing: 447
LEOReader
This page lists supported metadata fields for the Bio-Formats LEO format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 27 of them (5%).
Of those, Bio-Formats fully or partially converts 27 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats LEO format reader:
Total supported: 27
Total unknown or missing: 449
LIFReader
This page lists supported metadata fields for the Bio-Formats Leica Image File Format format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 85 of them (17%).
Of those, Bio-Formats fully or partially converts 85 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Leica Image File Format format reader:
Total supported: 85
Total unknown or missing: 391
LIMReader
This page lists supported metadata fields for the Bio-Formats Laboratory Imaging format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Laboratory Imaging format reader:
Total supported: 19
Total unknown or missing: 457
LOFReader
This page lists supported metadata fields for the Bio-Formats Leica Object Format format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Leica Object Format format reader:
Total supported: 19
Total unknown or missing: 457
LeicaReader
This page lists supported metadata fields for the Bio-Formats Leica format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 56 of them (11%).
Of those, Bio-Formats fully or partially converts 56 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Leica format reader:
Total supported: 56
Total unknown or missing: 420
LeicaSCNReader
This page lists supported metadata fields for the Bio-Formats Leica SCN format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 33 of them (6%).
Of those, Bio-Formats fully or partially converts 33 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Leica SCN format reader:
Total supported: 33
Total unknown or missing: 443
LiFlimReader
This page lists supported metadata fields for the Bio-Formats LI-FLIM format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 25 of them (5%).
Of those, Bio-Formats fully or partially converts 25 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats LI-FLIM format reader:
Total supported: 25
Total unknown or missing: 451
MIASReader
This page lists supported metadata fields for the Bio-Formats MIAS format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 67 of them (14%).
Of those, Bio-Formats fully or partially converts 67 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats MIAS format reader:
Total supported: 67
Total unknown or missing: 409
MINCReader
This page lists supported metadata fields for the Bio-Formats MINC MRI format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 26 of them (5%).
Of those, Bio-Formats fully or partially converts 26 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats MINC MRI format reader:
Total supported: 26
Total unknown or missing: 450
MNGReader
This page lists supported metadata fields for the Bio-Formats Multiple-image Network Graphics format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Multiple-image Network Graphics format reader:
Total supported: 19
Total unknown or missing: 457
MRCReader
This page lists supported metadata fields for the Bio-Formats Medical Research Council format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Medical Research Council format reader:
Total supported: 22
Total unknown or missing: 454
MRWReader
This page lists supported metadata fields for the Bio-Formats Minolta MRW format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Minolta MRW format reader:
Total supported: 19
Total unknown or missing: 457
MetamorphReader
This page lists supported metadata fields for the Bio-Formats Metamorph STK format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 59 of them (12%).
Of those, Bio-Formats fully or partially converts 59 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Metamorph STK format reader:
Total supported: 59
Total unknown or missing: 417
MetamorphTiffReader
This page lists supported metadata fields for the Bio-Formats Metamorph TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 43 of them (9%).
Of those, Bio-Formats fully or partially converts 43 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Metamorph TIFF format reader:
Total supported: 43
Total unknown or missing: 433
MetaxpressTiffReader
This page lists supported metadata fields for the Bio-Formats MetaXpress TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats MetaXpress TIFF format reader:
Total supported: 19
Total unknown or missing: 457
MicroCTReader
This page lists supported metadata fields for the Bio-Formats MicroCT format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 24 of them (5%).
Of those, Bio-Formats fully or partially converts 24 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats MicroCT format reader:
Total supported: 24
Total unknown or missing: 452
MicromanagerReader
This page lists supported metadata fields for the Bio-Formats Micro-Manager format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 42 of them (8%).
Of those, Bio-Formats fully or partially converts 42 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Micro-Manager format reader:
Total supported: 42
Total unknown or missing: 434
MikroscanTiffReader
This page lists supported metadata fields for the Bio-Formats Mikroscan TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Mikroscan TIFF format reader:
Total supported: 19
Total unknown or missing: 457
MinimalTiffReader
This page lists supported metadata fields for the Bio-Formats Minimal TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Minimal TIFF format reader:
Total supported: 19
Total unknown or missing: 457
MolecularImagingReader
This page lists supported metadata fields for the Bio-Formats Molecular Imaging format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 21 of them (4%).
Of those, Bio-Formats fully or partially converts 21 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Molecular Imaging format reader:
Total supported: 21
Total unknown or missing: 455
NAFReader
This page lists supported metadata fields for the Bio-Formats Hamamatsu Aquacosmos format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Hamamatsu Aquacosmos format reader:
Total supported: 19
Total unknown or missing: 457
ND2Reader
This page lists supported metadata fields for the Bio-Formats Nikon ND2 format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 52 of them (10%).
Of those, Bio-Formats fully or partially converts 52 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Nikon ND2 format reader:
Total supported: 52
Total unknown or missing: 424
NDPIReader
This page lists supported metadata fields for the Bio-Formats Hamamatsu NDPI format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 32 of them (6%).
Of those, Bio-Formats fully or partially converts 32 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Hamamatsu NDPI format reader:
Total supported: 32
Total unknown or missing: 444
NDPISReader
This page lists supported metadata fields for the Bio-Formats Hamamatsu NDPIS format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Hamamatsu NDPIS format reader:
Total supported: 22
Total unknown or missing: 454
NRRDReader
This page lists supported metadata fields for the Bio-Formats NRRD format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats NRRD format reader:
Total supported: 22
Total unknown or missing: 454
NiftiReader
This page lists supported metadata fields for the Bio-Formats NIfTI format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 24 of them (5%).
Of those, Bio-Formats fully or partially converts 24 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats NIfTI format reader:
Total supported: 24
Total unknown or missing: 452
NikonElementsTiffReader
This page lists supported metadata fields for the Bio-Formats Nikon Elements TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 50 of them (10%).
Of those, Bio-Formats fully or partially converts 50 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Nikon Elements TIFF format reader:
Total supported: 50
Total unknown or missing: 426
NikonReader
This page lists supported metadata fields for the Bio-Formats Nikon NEF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Nikon NEF format reader:
Total supported: 19
Total unknown or missing: 457
NikonTiffReader
This page lists supported metadata fields for the Bio-Formats Nikon TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 47 of them (9%).
Of those, Bio-Formats fully or partially converts 47 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Nikon TIFF format reader:
Total supported: 47
Total unknown or missing: 429
OBFReader
This page lists supported metadata fields for the Bio-Formats OBF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats OBF format reader:
Total supported: 19
Total unknown or missing: 457
OIRReader
This page lists supported metadata fields for the Bio-Formats Olympus OIR format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 48 of them (10%).
Of those, Bio-Formats fully or partially converts 48 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Olympus OIR format reader:
Total supported: 48
Total unknown or missing: 428
OMETiffReader
This page lists supported metadata fields for the Bio-Formats OME-TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats OME-TIFF format reader:
Total supported: 19
Total unknown or missing: 457
OMEXMLReader
This page lists supported metadata fields for the Bio-Formats OME-XML format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats OME-XML format reader:
Total supported: 19
Total unknown or missing: 457
OlympusTileReader
This page lists supported metadata fields for the Bio-Formats Olympus .omp2info format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Olympus .omp2info format reader:
Total supported: 19
Total unknown or missing: 457
OpenlabRawReader
This page lists supported metadata fields for the Bio-Formats Openlab RAW format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Openlab RAW format reader:
Total supported: 19
Total unknown or missing: 457
OpenlabReader
This page lists supported metadata fields for the Bio-Formats Openlab LIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 32 of them (6%).
Of those, Bio-Formats fully or partially converts 32 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Openlab LIFF format reader:
Total supported: 32
Total unknown or missing: 444
OperettaReader
This page lists supported metadata fields for the Bio-Formats PerkinElmer Operetta format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 60 of them (12%).
Of those, Bio-Formats fully or partially converts 60 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats PerkinElmer Operetta format reader:
Total supported: 60
Total unknown or missing: 416
OxfordInstrumentsReader
This page lists supported metadata fields for the Bio-Formats Oxford Instruments format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Oxford Instruments format reader:
Total supported: 22
Total unknown or missing: 454
PCIReader
This page lists supported metadata fields for the Bio-Formats Compix Simple-PCI format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 29 of them (6%).
Of those, Bio-Formats fully or partially converts 29 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Compix Simple-PCI format reader:
Total supported: 29
Total unknown or missing: 447
PCORAWReader
This page lists supported metadata fields for the Bio-Formats PCO-RAW format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 26 of them (5%).
Of those, Bio-Formats fully or partially converts 26 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats PCO-RAW format reader:
Total supported: 26
Total unknown or missing: 450
PCXReader
This page lists supported metadata fields for the Bio-Formats PCX format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats PCX format reader:
Total supported: 19
Total unknown or missing: 457
PDSReader
This page lists supported metadata fields for the Bio-Formats Perkin Elmer Densitometer format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 23 of them (4%).
Of those, Bio-Formats fully or partially converts 23 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Perkin Elmer Densitometer format reader:
Total supported: 23
Total unknown or missing: 453
PGMReader
This page lists supported metadata fields for the Bio-Formats Portable Any Map format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Portable Any Map format reader:
Total supported: 19
Total unknown or missing: 457
PQBinReader
This page lists supported metadata fields for the Bio-Formats PicoQuant Bin format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 21 of them (4%).
Of those, Bio-Formats fully or partially converts 21 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats PicoQuant Bin format reader:
Total supported: 21
Total unknown or missing: 455
PSDReader
This page lists supported metadata fields for the Bio-Formats Adobe Photoshop format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Adobe Photoshop format reader:
Total supported: 19
Total unknown or missing: 457
PerkinElmerReader
This page lists supported metadata fields for the Bio-Formats PerkinElmer format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 30 of them (6%).
Of those, Bio-Formats fully or partially converts 30 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats PerkinElmer format reader:
Total supported: 30
Total unknown or missing: 446
PhotoshopTiffReader
This page lists supported metadata fields for the Bio-Formats Adobe Photoshop TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Adobe Photoshop TIFF format reader:
Total supported: 19
Total unknown or missing: 457
PictReader
This page lists supported metadata fields for the Bio-Formats PICT format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats PICT format reader:
Total supported: 19
Total unknown or missing: 457
PovrayReader
This page lists supported metadata fields for the Bio-Formats POV-Ray format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats POV-Ray format reader:
Total supported: 19
Total unknown or missing: 457
PrairieReader
This page lists supported metadata fields for the Bio-Formats Prairie TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 46 of them (9%).
Of those, Bio-Formats fully or partially converts 46 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Prairie TIFF format reader:
Total supported: 46
Total unknown or missing: 430
PyramidTiffReader
This page lists supported metadata fields for the Bio-Formats Pyramid TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Pyramid TIFF format reader:
Total supported: 19
Total unknown or missing: 457
QTReader
This page lists supported metadata fields for the Bio-Formats QuickTime format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats QuickTime format reader:
Total supported: 19
Total unknown or missing: 457
QuesantReader
This page lists supported metadata fields for the Bio-Formats Quesant AFM format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Quesant AFM format reader:
Total supported: 22
Total unknown or missing: 454
RCPNLReader
This page lists supported metadata fields for the Bio-Formats RCPNL format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 25 of them (5%).
Of those, Bio-Formats fully or partially converts 25 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats RCPNL format reader:
Total supported: 25
Total unknown or missing: 451
RHKReader
This page lists supported metadata fields for the Bio-Formats RHK Technologies format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats RHK Technologies format reader:
Total supported: 22
Total unknown or missing: 454
SBIGReader
This page lists supported metadata fields for the Bio-Formats SBIG format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats SBIG format reader:
Total supported: 22
Total unknown or missing: 454
SDTReader
This page lists supported metadata fields for the Bio-Formats SPCImage Data format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats SPCImage Data format reader:
Total supported: 19
Total unknown or missing: 457
SEQReader
This page lists supported metadata fields for the Bio-Formats Image-Pro Sequence format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 20 of them (4%).
Of those, Bio-Formats fully or partially converts 20 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Image-Pro Sequence format reader:
Total supported: 20
Total unknown or missing: 456
SIFReader
This page lists supported metadata fields for the Bio-Formats Andor SIF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 20 of them (4%).
Of those, Bio-Formats fully or partially converts 20 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Andor SIF format reader:
Total supported: 20
Total unknown or missing: 456
SISReader
This page lists supported metadata fields for the Bio-Formats Olympus SIS TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 33 of them (6%).
Of those, Bio-Formats fully or partially converts 33 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Olympus SIS TIFF format reader:
Total supported: 33
Total unknown or missing: 443
SMCameraReader
This page lists supported metadata fields for the Bio-Formats SM Camera format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats SM Camera format reader:
Total supported: 19
Total unknown or missing: 457
SPCReader
This page lists supported metadata fields for the Bio-Formats SPC FIFO Data format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats SPC FIFO Data format reader:
Total supported: 19
Total unknown or missing: 457
SPEReader
This page lists supported metadata fields for the Bio-Formats Princeton Instruments SPE format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 30 of them (6%).
Of those, Bio-Formats fully or partially converts 30 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Princeton Instruments SPE format reader:
Total supported: 30
Total unknown or missing: 446
SVSReader
This page lists supported metadata fields for the Bio-Formats Aperio SVS format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 33 of them (6%).
Of those, Bio-Formats fully or partially converts 33 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Aperio SVS format reader:
Total supported: 33
Total unknown or missing: 443
ScanrReader
This page lists supported metadata fields for the Bio-Formats Olympus ScanR format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 43 of them (9%).
Of those, Bio-Formats fully or partially converts 43 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Olympus ScanR format reader:
Total supported: 43
Total unknown or missing: 433
SeikoReader
This page lists supported metadata fields for the Bio-Formats Seiko format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Seiko format reader:
Total supported: 22
Total unknown or missing: 454
SimplePCITiffReader
This page lists supported metadata fields for the Bio-Formats SimplePCI TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 33 of them (6%).
Of those, Bio-Formats fully or partially converts 33 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats SimplePCI TIFF format reader:
Total supported: 33
Total unknown or missing: 443
SlideBook7Reader
This page lists supported metadata fields for the Bio-Formats SlideBook 7 SLD (native) format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 37 of them (7%).
Of those, Bio-Formats fully or partially converts 37 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats SlideBook 7 SLD (native) format reader:
Total supported: 37
Total unknown or missing: 439
SlidebookReader
This page lists supported metadata fields for the Bio-Formats Olympus Slidebook format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 34 of them (7%).
Of those, Bio-Formats fully or partially converts 34 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Olympus Slidebook format reader:
Total supported: 34
Total unknown or missing: 442
SlidebookTiffReader
This page lists supported metadata fields for the Bio-Formats Slidebook TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 30 of them (6%).
Of those, Bio-Formats fully or partially converts 30 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Slidebook TIFF format reader:
Total supported: 30
Total unknown or missing: 446
SpiderReader
This page lists supported metadata fields for the Bio-Formats SPIDER format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 21 of them (4%).
Of those, Bio-Formats fully or partially converts 21 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats SPIDER format reader:
Total supported: 21
Total unknown or missing: 455
TCSReader
This page lists supported metadata fields for the Bio-Formats Leica TCS TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Leica TCS TIFF format reader:
Total supported: 22
Total unknown or missing: 454
TargaReader
This page lists supported metadata fields for the Bio-Formats Truevision Targa format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 20 of them (4%).
Of those, Bio-Formats fully or partially converts 20 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Truevision Targa format reader:
Total supported: 20
Total unknown or missing: 456
TecanReader
This page lists supported metadata fields for the Bio-Formats Tecan Spark Cyto format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 36 of them (7%).
Of those, Bio-Formats fully or partially converts 36 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Tecan Spark Cyto format reader:
Total supported: 36
Total unknown or missing: 440
TextReader
This page lists supported metadata fields for the Bio-Formats Text format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Text format reader:
Total supported: 19
Total unknown or missing: 457
TiffDelegateReader
This page lists supported metadata fields for the Bio-Formats Tagged Image File Format format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Tagged Image File Format format reader:
Total supported: 19
Total unknown or missing: 457
TiffJAIReader
This page lists supported metadata fields for the Bio-Formats Tagged Image File Format format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Tagged Image File Format format reader:
Total supported: 19
Total unknown or missing: 457
TiffReader
This page lists supported metadata fields for the Bio-Formats Tagged Image File Format format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Tagged Image File Format format reader:
Total supported: 22
Total unknown or missing: 454
TileJPEGReader
This page lists supported metadata fields for the Bio-Formats Tile JPEG format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Tile JPEG format reader:
Total supported: 19
Total unknown or missing: 457
TillVisionReader
This page lists supported metadata fields for the Bio-Formats TillVision format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats TillVision format reader:
Total supported: 22
Total unknown or missing: 454
TopometrixReader
This page lists supported metadata fields for the Bio-Formats TopoMetrix format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats TopoMetrix format reader:
Total supported: 22
Total unknown or missing: 454
TrestleReader
This page lists supported metadata fields for the Bio-Formats Trestle format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 27 of them (5%).
Of those, Bio-Formats fully or partially converts 27 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Trestle format reader:
Total supported: 27
Total unknown or missing: 449
UBMReader
This page lists supported metadata fields for the Bio-Formats UBM format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats UBM format reader:
Total supported: 19
Total unknown or missing: 457
UnisokuReader
This page lists supported metadata fields for the Bio-Formats Unisoku STM format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Unisoku STM format reader:
Total supported: 22
Total unknown or missing: 454
VGSAMReader
This page lists supported metadata fields for the Bio-Formats VG SAM format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats VG SAM format reader:
Total supported: 19
Total unknown or missing: 457
VarianFDFReader
This page lists supported metadata fields for the Bio-Formats Varian FDF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 25 of them (5%).
Of those, Bio-Formats fully or partially converts 25 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Varian FDF format reader:
Total supported: 25
Total unknown or missing: 451
VectraReader
This page lists supported metadata fields for the Bio-Formats PerkinElmer Vectra/QPTIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 43 of them (9%).
Of those, Bio-Formats fully or partially converts 43 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats PerkinElmer Vectra/QPTIFF format reader:
Total supported: 43
Total unknown or missing: 433
VeecoReader
This page lists supported metadata fields for the Bio-Formats Veeco format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Veeco format reader:
Total supported: 19
Total unknown or missing: 457
VentanaReader
This page lists supported metadata fields for the Bio-Formats Ventana .bif format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 28 of them (5%).
Of those, Bio-Formats fully or partially converts 28 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Ventana .bif format reader:
Total supported: 28
Total unknown or missing: 448
VisitechReader
This page lists supported metadata fields for the Bio-Formats Visitech XYS format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Visitech XYS format reader:
Total supported: 19
Total unknown or missing: 457
VolocityClippingReader
This page lists supported metadata fields for the Bio-Formats Volocity Library Clipping format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Volocity Library Clipping format reader:
Total supported: 19
Total unknown or missing: 457
VolocityReader
This page lists supported metadata fields for the Bio-Formats Volocity Library format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 38 of them (7%).
Of those, Bio-Formats fully or partially converts 38 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Volocity Library format reader:
Total supported: 38
Total unknown or missing: 438
WATOPReader
This page lists supported metadata fields for the Bio-Formats WA Technology TOP format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 22 of them (4%).
Of those, Bio-Formats fully or partially converts 22 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats WA Technology TOP format reader:
Total supported: 22
Total unknown or missing: 454
XLEFReader
This page lists supported metadata fields for the Bio-Formats Extended leica file format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Extended leica file format reader:
Total supported: 19
Total unknown or missing: 457
ZeissCZIReader
This page lists supported metadata fields for the Bio-Formats Zeiss CZI format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 175 of them (36%).
Of those, Bio-Formats fully or partially converts 175 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Zeiss CZI format reader:
Total supported: 175
Total unknown or missing: 301
ZeissLMSReader
This page lists supported metadata fields for the Bio-Formats Zeiss LMS format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 23 of them (4%).
Of those, Bio-Formats fully or partially converts 23 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Zeiss LMS format reader:
Total supported: 23
Total unknown or missing: 453
ZeissLSMReader
This page lists supported metadata fields for the Bio-Formats Zeiss Laser-Scanning Microscopy format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 101 of them (21%).
Of those, Bio-Formats fully or partially converts 101 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Zeiss Laser-Scanning Microscopy format reader:
Total supported: 101
Total unknown or missing: 375
ZeissTIFFReader
This page lists supported metadata fields for the Bio-Formats Zeiss AxioVision TIFF format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Zeiss AxioVision TIFF format reader:
Total supported: 19
Total unknown or missing: 457
ZeissZVIReader
This page lists supported metadata fields for the Bio-Formats Zeiss Vision Image (ZVI) format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Zeiss Vision Image (ZVI) format reader:
Total supported: 19
Total unknown or missing: 457
ZipReader
This page lists supported metadata fields for the Bio-Formats Zip format reader.
These fields are from the OME data model. Bio-Formats standardizes each format’s original metadata to and from the OME data model so that you can work with a particular piece of metadata (e.g. physical width of the image in microns) in a format-independent way.
- Of the 476 fields documented in the metadata summary table:
The file format itself supports 19 of them (3%).
Of those, Bio-Formats fully or partially converts 19 (100%).
Supported fields
- These fields are fully supported by the Bio-Formats Zip format reader:
Total supported: 19
Total unknown or missing: 457
Grouping files using a pattern file
Individual files can be grouped together into a single fileset using a pattern file. This works for any single-file format that Bio-Formats supports, as long as all files are in the same format. It is most useful for sets of TIFF, JPEG, PNG, etc. files that do not have any associated metadata.
All files to be grouped together should be in the same folder. The pattern
file should be in the same folder as the other files; it can have any name,
but must have the .pattern extension. The pattern file is what must be
opened or imported, so it may be helpful to give it a descriptive or
easily-recognizable name.
The pattern file contains a single line of text that is specially formatted to describe how the files should be grouped. The file can be created in any text editor.
The text in the pattern file can take one of several forms. To illustrate, consider a folder with the following file names:
red.tiff
green.tiff
blue.tiff
test_Z0_C0.png
test_Z1_C0.png
test_Z0_C1.png
test_Z1_C1.png
test_Z0_C2.png
test_Z1_C2.png
test_Z00.tiff
test_Z01.tiff
A pattern file that groups red.tiff, green.tiff, and blue.tiff
in that order would look like:
<red,green,blue>.tiff
A pattern that groups test_Z0_C0.png, test_Z1_C0.png,
test_Z0_C2.png, and test_Z1_C2.png:
test_Z<0-1>_C<0-2:2>.png
The <> notation in general can accept a single literal value, a
comma-separated list of literal values, a range of integer values, or a range
of integer values with a step value greater than 1 (the range and step are
separated by :). Note that inverting the values in a range (e.g. <2-0>) is not
supported and will cause an exception to be thrown.
The characters immediately preceding the < can affect
which dimension is assigned to the specified values. The values will be
interpreted as:
channels, if
c,ch,w, orwavelengthprecede<timepoints, if
t,tl,tp, ortimepointprecede<Z sections, if
z,zs,sec,fp,focal, orfocalplaneprecede<series, if
s,sp, orseriesprecede<
Note that the listed dimension specifier characters are case insensitive. A separator character (underscore or space) must precede the dimension specifier if it is not at the beginning of the filename. In the above example, 2 Z sections and 2 out of 3 channels would be detected according to the dimension specifiers.
Leading zeros in the integer values must be specified. To group
test_Z00.tiff and test_Z01.tiff:
test_Z<00-01>.tiff
or:
test_Z0<0-1>.tiff
Note that this pattern would not group the files correctly:
test_Z<0-1>.tiff
A pattern file that groups all PNG files beginning with test_ would look like:
test_.*.png
This and most other Java-style regular expressions can be used in place of the
<> notation above. See the java.util.regex.Pattern Javadoc
for more information on constructing regular expressions.
Additional reader and writer options
Some readers and writers have additional options which can be used to inform how Bio-Formats reads or writes files in that format.
Reader options
Format name |
Option |
Default |
Description |
|---|---|---|---|
|
false |
Throw an exception if an expected associated .ets file is missing |
|
|
true |
Split montage image tiles across multiple planes |
|
|
false |
Ensure physical pixel sizes are compatible with versions <= 5.3.2 |
|
|
true |
Use chunkmap table to read image offsets |
|
|
true |
Ignore missing wells |
|
|
true |
Fail if a missing file is detected in a partial dataset |
|
|
false |
Report each tile as a separate series |
|
|
true |
Include attachment images |
|
|
true |
Automatically stitch tiled images |
|
|
false |
Trim XY dimensions to match those in ZEN |
|
|
false |
Use pixel position instead of the physical stage position |
|
|
true |
If set any missing planes will be replaced by the first plane in the channel. When set to false a blank plane will be returned. |
|
|
true |
If set the thumbnail image (if present) will not be available, and in particular will not be included in the pyramid. When set to false, the thumbnail image will be available for compatibility with versions <= 7.1.0. |
Usage
Reader options can be used via the command line with
showinf -option, in ImageJ via the
configuration window, or via the API using the
DynamicMetadataOptions class.
Writer options
Format name |
Option |
Default |
Description |
|---|---|---|---|
|
None |
If set, OME-XML will be written to a companion file with a name determined by the option value |
|
|
false |
If set to false, the OME-XML Creator attribute will be updated to include the current Bio-Formats version. This will overwrite any existing Creator in the input metadata. If set to true, the Creator attribute will only be updated if it wasn’t previously set; any existing value will be preserved. |
|
|
false |
If set to false, the OME-XML Creator attribute will be updated to include the current Bio-Formats version. This will overwrite any existing Creator in the input metadata. If set to true, the Creator attribute will only be updated if it wasn’t previously set; any existing value will be preserved. |
|
|
true |
If set to true, DICOM files will be written as dual-personality DICOM/TIFF files which include TIFF metadata as described in Clunie DA. Dual-Personality DICOM-TIFF for Whole Slide Images: A Migration Technique for Legacy Software. J Pathol Inform. 2019 Apr 3;10:12. doi: 10.4103/jpi.jpi_93_18. PMID: 31057981; PMCID: PMC6489422.. If set to false, the writing of DICOM files will revert back to the original plain DICOM files |
Usage
Writer options can be used via the command line using
bfconvert -option, or via the API using the
DynamicMetadataOptions class.
Version history
7.3.0 (2024 April)
File format fixes and improvements:
- CellSens VSI
fixed an exception in CellSens 4.1 data by updating the handling of orphaned ets files (thanks to Edward Scanlon)
- DICOM
updated handling of nested sequences that include pixel data
removed a duplicate enum check in the DICOM writer
- OME-XML
reading an OME-XML file now populates the original metadata table
- PerkinElmer Columbus
added support for reading data with Z stacks (thanks to Tim Blackmore)
- Prairie Technologies TIFF
improved type checking for Prairie files
- SimplePCI
fixed handling of Z position metadata
Bio-Formats improvements:
Bio-Formats is now compatible with Java 21 builds
added a new quality option to bfconvert which enables the setting of the compression quality to be used.
when using the channel option in bfconvert, the unselected channels are now correctly removed from the OME-XML metadata
added coverage of Apple M1 as part of the CI process
added coverage of Java 21 builds as part of the CI process
Component updates:
ome-jai was upgraded to 0.1.4
ome-stubs was upgraded to 6.0.2
ome-mdbtools was upgraded to 5.3.3
ome-common was upgraded to 6.0.22
ome-poi was upgraded to 5.3.9
ome-metakit was upgraded to 5.3.7
ome-codecs was upgraded to 1.0.3
ome-xml was upgraded to 6.3.6
specification was upgraded to 6.3.6
Documentation improvements:
fixed a number of broken external links
documented the new quality option in bfconvert
7.2.0 (2024 February)
File format fixes and improvements:
- Aperio SVS
improved detection of label and macro images
thumbnails are now removed by default
added a new reader option svs.remove_thumbnail to control the thumbnail behaviour. By default the option is true and thumbnails are removed. Setting the option to false will restore the previous behavior and include thumbnails
- Imaris HDF
channel names are now correctly populated
- Olympus OIR
fixed an issue with channel ordering
prevent certain pixel blocks from being incorrectly skipped
- TIFF
dimension order is now marked as certain if metadata is read from ImageJ tag
- Zeiss CZI
improved well column indexing by using alternate sources for well identifiers when available
improved image naming, particularly for attachments
fixed a bug so that opening CZI compressed with ZSTD now allows access to pyramid levels (thanks to Stephan Wagner-Conrad)
fixed an integer arithmetic problem when calculating pyramid scales (thanks to Stephan Wagner-Conrad)
Bio-Formats improvements:
JPEG handling no longer fails for non 4:4:4 JPEG (thanks to Can Gokhan Dogan)
fixed a bug in the Bio-Formats Plugins configuration window when toggling the Nikon ND2 chunkmap option
updated testing to add an additional check for image names when resolutions are not flattened
Documentation improvements:
fixed a number of broken external links
7.1.0 (2023 December)
API Additions
- ICompressedTileReader
a new interface allowing for the reading of compressed bytes without decompression. Currently only implemented by the SVSReader
- ICompressedTileWriter
a new interface allowing for the writing of precompressed bytes. Currently only implemented by the DICOM Writer
- IExtraMetadataWriter
a new interface enabling extra supplemental metadata to be set for inclusion in a writer. Currently only implemented by the DICOM Writer
File format fixes and improvements:
- Aperio SVS
added implementation for the reading of compressed data without decompression using the new ICompressedTileReader interface
- cellSens VSI
fixed handling of uncompressed BGR data
- CV7000
action index is now included in the channel name
Fluor will now be set on Channel when possible
for missing planes the default behavior has switched from returning a blank plane to returning the first plane in the channel
added a new reader option cv7000.duplicate_missing_planes to control the behavior for missing planes
- DICOM
added implementation for the writing of precompressed data using the new ICompressedTileWriter interface
added implementation for the writing of extra supplemental metadata data using the new IExtraMetadataWriter interface. Extra metadata can be provided in the form of a .json file
This functionality was implemented through collaboration between Glencoe Software and NCI Imaging Data Commons, and has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN2612015000031.
- Photoshop TIFF
fixed plane reading with memoization
Bio-Formats improvements:
fixed handling of JPEG Turbo service when the native library cannot be loaded, most notably for Apple Silicon instances. An IOException will now be thrown by readers that require the library but the RunTimeException introduced in 7.0.1 will no longer be thrown when the library is not required
prevented unnecessary Lurawave debug error being printed (thanks to Can Gokhan Dogan)
updated license headers for all Java sources of the OME-XML library
added a new codec option disableChromaSubsampling along with implementation for the JPEG Codec (thanks to Peter Haub)
updated github actions checkout version to v4 and build release on ubuntu 22.04
json dependency moved from formats-gpl to formats-bsd
TiffSaver now generates valid 4-channel RGBA images (thanks to Can Gokhan Dogan)
added a new ` precompressed` option to the bfconvert tool, enabling the conversion of precompressed tiles. Currently only supported for converting from SVS to DICOM.
added a new ` extra-metadata` option to the bfconvert tool for providing supplemental metadata during conversion. Currently only supported for writing to DICOM
Component updates:
slf4j-api was upgraded to 2.0.9
logback-classic was upgraded to 1.3.14
logback-core was upgraded to 1.3.14
xalan was upgraded to 2.7.3
com.google.guava was upgraded to 32.0.0-jre
json was upgraded to 20230227
ome-common was upgraded to 6.0.21
ome-model was upgraded to 6.3.4
ome-codecs was upgraded to 1.0.1
ome-poi was upgraded to 5.3.8
ome-metakit was upgraded to 5.3.6
Documentation improvements:
fixed a number of broken external links
updated the bfconvert instructions to document new options
added a new link for the external Bioformats.NET project
7.0.1 (2023 October)
File format fixes and improvements:
- Amersham Biosciences Gel
improved format detection
- Aperio SVS
fixed a NullPointerException when attempting to read the magnification metadata
physical sizes and positions are now calculated for full resolution label and macro images
fixed a regression from Bio-Formats 6.8.0 which saw label and macro images incorrectly indexed
- DICOM
the DICOM writer will now throw an exception if the provided tiles don’t match the expected tile size
- Gatan DM3
fixed a StringIndexOutOfBoundsException when parsing acquisition mode
- Hamamatsu NDPI
corrected for potential integer overflow in stored restart marker tag
- IVision
improved the version and data type checks in isThisType
- Leica LIF
improved the exception handling if no images are found
- Olympus OIR
fixed issue with XML block reading that resulted in missing pixel blocks
- OME-TIFF
reader will now fail fast and throw a FormatException if an invalid file is found
- TIFF
a FormatException is now thrown for unsupported 64-bit int data
for all TIFF based formats the IFD entry offset is now checked before seeking
- TillVision
improved metadata parsing and detection of .pst files
- Ventana
fixed tile arithmetic for smallest resolutions
- Zeiss CZI
unified channel color parsing so that retrieving lookup tables now allows RGB and ARGB colors
Bio-Formats improvements:
URLHandle will fall back to resetting stream if resetting to a mark fails
an exception will now be thrown if the TurboJPEG library fails to load (thanks to Can Gokhan Dogan)
fixed a Bio-Formats plugin bug when attempting to export a file after reducing the range of channels
reviewed and updated a number of file headers
updated GitHub Actions from checkout v2 to v3
Component updates:
ome-common was upgraded to 6.0.20
Documentation improvements:
fixed a number of broken external links
updated the link to OME Model documentation
migrated readthedocs configuration to version 2
7.0.0 (2023 August)
Removal of deprecated components:
- Legacy ND2 Reader
The LegacyND2Reader and underlying components have been removed. This reader depended on an outdated DLL which had not been built in years, was untested and fully superseded by the new NativeND2Reader. The existing NativeND2Reader has been renamed as ND2Reader and now acts as the sole reader for the format. Support for the ND2 format will be unaffected and continue via this newly renamed reader.
- Legacy QuickTime
The LegacyQT Reader, Writer and Tools have been removed. These classes depended on the external QuickTime for Java library which is long obsolete. The existing NativeQTReader has been renamed as QTReader and support for QuickTime is now limited to non legacy readers and writers.
- LuraWave Codec
The LuraWave Codec along with the LuraWaveService and associated components have been removed and are no longer supported. This codec was dependent on a third-party proprietary library with a license code. This may impact LuraWave compressed files for the Opera Flex format.
- Woolz
The Woolz Reader, Writer and Service have been removed and are no longer supported. The reader and writer are untested and rely on an underlying library which has an unclear maintenance status.
File format fixes and improvements:
- DICOM
support has been added for the writing dual-personality of DICOM/TIFF. The DICOM writer will now, by default, include TIFF metadata as described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6489422/. These new dual-personality files can be read either by the DICOM reader or can also be recognised as TIFF. A new option named dicom.dual_personality has been added to the DicomWriter. Setting this new option to false will revert writing of DICOM files back to the original plain DICOM files. This functionality was implemented through collaboration with NCI Imaging Data Commons, and has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN2612015000031.
- PerkinElmer Opera Flex
reader will now ignore files in which the compression cannot be identified
- PerkinElmer Operetta
fixed an exception when reading null planes (thanks to Nicolas Chiaruttini)
Component updates:
ome-common was upgraded to 6.0.19
ome-stubs was upgraded to 6.0.1
ome-codecs was upgraded to 1.0.0
native-lib-loader was upgraded to 2.4.0 (thanks to Can Gokhan Dogan)
Documentation improvements:
fixed a number of broken links
6.14.0 (2023 July)
Deprecation warnings:
- Legacy ND2 Reader
The LegacyND2Reader and underlying components have been marked as deprecated in preparation for removal in the upcoming 7.0.0 major release of Bio-Formats. This reader depends on an outdated DLL which has not been built in years, is untested and fully superseded by the new NativeND2Reader. From Bio-Formats 7.0.0 onwards the existing NativeND2Reader will be renamed as ND2Reader and act as the sole reader for the format. Support for the ND2 format will be unaffected and continue via this newly renamed reader
- Legacy QuickTime
The LegacyQT Reader, Writer and Tools have been marked as deprecated in preparation for removal in the upcoming 7.0.0 major release of Bio-Formats. These classes depended on the external QuickTime for Java library which is long obsolete. From Bio-Formats 7.0.0 onwards the existing NativeQTReader will be renamed as QTReader and support for QuickTime will be limited to non legacy readers and writers.
- LuraWave Codec
The LuraWave Codec along with the LuraWaveService and associated components have been marked as deprecated in preparation for removal in the upcoming 7.0.0 major release of Bio-Formats. This codec depends on a third-party proprietary library with a license code. Opera Flex is the format that is most likely to be impacted by this change.
- Woolz
The Woolz Reader, Writer and Service have been marked as deprecated in preparation for removal in the upcoming 7.0.0 major release of Bio-Formats. The reader and writer are untested and rely on an underlying library which maintenance status is unclear
File format fixes and improvements:
- CV7000/CV8000
updated CV7000 isThisType test to improve performance by skipping extended type checking
reader now handles the use case where wells are recorded, but all files were removed
fixed channel indexing in scenarios where more channels are defined than acquired
- ICS (Image Cytometry Standard)
fixed an Illegal group reference exception when constructing slice label
- KLB (Keller Lab Block)
fixed a bug with the reading of image planes in Z stacks
- MicroManager
updated handling of truncated files to prevent possible infinite loop and throw an exception
Bio-Formats improvements:
updated handling of exceptions in Bio-Formats plugins to ensure readers are closed
updated list of external readers to include new external ZeissQuickStartCZIReader (thanks to Nicolas Chiaruttini)
updated top-level Git mailmap to normalize commit author variants
added a new bf-unconfigured tool to the Bio-Formats toolbox. The new tool lists classes which are not configured for testing as part of format reader tests
replaced use tt tag in java docs with code tag
Documentation improvements:
fixed a number of broken links
migrated OME-Model documentation to Read the Docs
added deprecation warnings to format pages of the affected components
Component updates:
ome-common was upgraded to 6.0.17
6.13.0 (2023 April)
File format fixes and improvements:
- Aperio SVS
removed broken special case path when there is only one (pyramidal) image (thanks to Alexandr Virodov)
- Bio-Rad Gel
fixed pixel data offsets for cropped images
- cellSens VSI
improved tile decoding to fail faster on invalid tiles
- CellWorX/MetaXpress
fixed a bug when retrieving channel metadata when the files for the entire first field are missing
- CV7000
extra folders mixed in with the plate data will now be ignored
corrected channel indexing if a subset of channels was acquired
- Lambert Instruments FLIM
added support for Fli 2.0 (thanks to Shaquille Louisa - Lambert Instruments)
- MetaMorph
prevented an exception when attempting to read metadata keys that don’t exist
- MetaMorph TIFF
fixed a NullPointerException when there are missing stage positions
- MRC
the IMOD flag is now used to determine int8 or uint8 pixel type
- NIFTI
improved the performance for gzip-compressed files by reducing the number of backwards seeks
- Nikon ND2
fixed an exception when reading blocks greater than 2GB
- OME-TIFF
file paths are now normalized rather than resolving symlinks
- Perkin Elmer Operetta
fixed series validation for single plane images (thanks to Alex Herbert)
- Zeiss CZI
improved the tile stitching when a pyramid does not exist
Bio-Formats improvements:
added a new writer option preserve_creator for OME-TIFF and OME-XML writers. When set to true the original OME/Creator attribute will be preserved by the writer. If set to false, the OME Creator attribute will be updated to include the current Bio-Formats version. Attribute is set to false by default.
enabled the configuration of the fill value for undefined pixel values through new API additions to IFormatReader. Two new methods (along with default implementations) have been added for setFillColor(Byte color) and Byte getFillColor(), the default value if undefined is 0.
added a new -fill option to the command line tools, allowing a byte value to be configured for use with undefined pixels (0-255)
enabled the configuration of JPEG quality in the JPEGCodec using the existing quality setting on CodecOptions (thanks to Peter Haub)
improved JPEG performance by using in-memory cache in JPEGCodec (thanks to Pete Bankhead)
made minor API updates to Memoizer to allow a null reader to be specified in the constructors, in which case a new ImageReader will be wrapped
prevented file leaks in FileStitcher by closing readers when setting the class list
fixed exceptions in FileStitcher when a no-op file pattern is encountered
updated GitHub Actions release process
Documentation improvements:
updated the format page for MRC to clarify list of developers and add links to latest specifications
added new developer documentation pages for Bioconductor RBioFormats
corrected one of the examples in the OME-TIFF specification page (thanks to Tom Boissonnet)
updated the list of writer options to add documentation for new preserve_creator options
updated the list of command line tools options to add documentation for new fill option
version history and bug reporting are now linked from the main documentation page
fixed a number of broken links
updated the Li-Flim format page to add supported versions
Component updates:
ome-common was upgraded to 6.0.16
ome-model was upgraded to 6.3.3
ome-codecs was upgraded to 0.4.5
imagej1 was upgraded to 1.54c
json was upgraded to 20230227
kryo was upgraded to 5.4.0
snakeyaml was upgraded to 2.0
joda-time was upgraded to 2.12.2
guava was upgraded to 31.1-jre
jackson-annotations was upgraded to 12.14.2
jackson-databind was upgraded to 12.14.2
6.12.0 (2023 February)
File format fixes and improvements:
- Lambert Instruments FLIM
added support for MSB 12 to 16 bit conversion (thanks to Shaquille Louisa - Lambert Instruments)
- Olympus cellSens VSI
corrected tile handling to respect tile origin metadata
pixel data will now only be read from ets files with the prefix frame_ (funded by a partnership between Glencoe Software and Evident Scientific)
- Perkin Elmer Operetta/Harmony
plates containing 32-bit TIFF files will now return blank planes
- Zeiss CZI
fixed pyramid dimension calculation
Bio-Formats improvements:
implemented full Java 17 support for Bio-Formats
- logback dependencies are now optional as per the SLF4J best practices (thanks to Curtis Rueden)
downstream consumers must now declare the specific SLF4J binding they wish to use
CI build matrix updated to use Java versions 8, 11 and 17
ant tasks switched to use Maven Artifact Resolver
fixed a bug when decompressing using the Base64Codec
added a new ImageJ macro example to Bio-Formats examples
FakeReader now ensures correct dimension order for RGB image
added new unit tests for FakeReader
fixed min/max calculation for RGB data
artifacts from the GitHub Actions build are now uploaded and archived for 30 days
release artifacts are now generated via GitHub Actions
fixed a number of small issues in OME-Model (thanks to Roger Leigh)
Documentation improvements:
migrated Bio-Formats documentation to Read the Docs
fixed and updated a number of links in documentation
updated OME-Model links to comply with Sphinx 5 deprecation warnings
updated GitHub Actions set-output to comply with deprecation warnings
updated OME-TIFF documentation to add links to new sample dataset BBBC017
Component updates:
ome-metakit was upgraded to 5.3.5
ome-common was upgraded to 6.0.14
ome-codecs was upgraded to 0.4.4
ome-model was upgraded to 6.3.2
jackson-annotations was upgraded to 12.14.1
jackson-databind was upgraded to 12.14.1
aircompressor was upgraded to 0.21
6.11.1 (2022 December)
File format fixes and improvements:
- 3i SlideBook 7
refactored code to remove a false positive threat report in Fortinet
- DICOM
fixed handling of some datasets with multiple optical paths
- Leica SCN
fixed colour correction for datasets from SCN 400 models
- Olympus cellSens VSI
corrected the handling of exposure times
- TIFF
handle REFERENCE_BLACK_WHITE tag as an array of floats or ints
- Vectra QPTIFF
biomarker data in channel name will now be preserved
- Zeiss CZI
added support for plates with multiple fields
Bio-Formats improvements:
updated the output command for GitHub actions
Documentation improvements:
fixed a number of broken links
added a link to public sample files for Olympus-FluoView
Component updates:
snakeyaml was upgraded to 1.3.2
6.11.0 (2022 October)
File format fixes and improvements:
- Amira Mesh
fixed handling of files with empty key values
- InCell 1000/2000
improved calculation of plane count
- Nikon NIS-Elements ND2
fixed handling of chunk map skipping logic
- Olympus FluoView FV1000
fixed an exception when parsing double values in the metadata
- OME-TIFF
improved initialization performance for files with a large number of planes
enabled individual file reading for datasets with one file per series
- SimplePCI & HCImage
fixed physical size calculation to make use of magnification value
- TIFF
implemented Zstandard decompression for Tiff formats (thanks to Willem Pomp)
Bio-Formats improvements:
updated pattern file handling to support a single file wrapped in a pattern file
Bio-Formats plugin now closes underlying readers after an exception
contrast will be retained when using VirtualImagePlus in the Bio-Formats plugin (thanks to Tomas Farago)
fixed overwrite checking in bfconvert tool when output path is a pattern
Documentation improvements:
fixed a number of broken links
updated test image documentation to add note on on setting fake file channel colors
added new public sample files for Olympus-FluoView
updated OME-TIFF sample files for BBBC017
Component updates:
ome-codecs was upgraded to 0.4.1
snakeyaml was upgraded to 1.3.1
6.10.1 (2022 August)
File format fixes and improvements:
- Hamamatsu NDPI
fixed handling of non number tags for files greater than 4GB in size
- OME-TIFF
improved performance of initializing a single file OME-TIFF datasets with a larger number of series
- TIFF (Tagged Image File Format)
fixed a ClassCastException when the SubfileType tag has the wrong type
- Zeiss CZI
scene names will now be taken into account when generating image names
Documentation improvements:
fixed a number of broken links
Component updates:
ome-common was upgraded to 6.0.13
ome-poi was upgraded to 5.3.7
slf4j was upgraded to 1.7.30
metadata-extractor was upgraded to 2.18.0
6.10.0 (2022 May)
New file formats:
- Slidebook 7
added support for reading SlideBook Format 7 from SlideBook 2021 This functionality was implemented and contributed by Intelligent Imaging Innovations
File format fixes and improvements:
- CellWorX / MetaXpress
channel metadata will now be preserved for all channels by reading from each file
- Cellomics
marked the private Pattern field as transient to fix memo file generation with JDK17
- DeltaVision
fixed detection of incorrect XY tile counts
- Hitachi S-4800
enhanced format recognition and identification of datasets
corrected the units for physical sizes to nanometers instead of micrometers
- Nikon NIS-Elements ND2
improved metadata parsing, especially for objective data, timestamps, and exposure times
- PerkinElmer Operetta
improved checks for invalid TIFFs and supplemental metadata files
updated image names to make well names more readable
- TIFF (Tagged Image File Format)
fixed incorrect SampleValue metadata values
- Vectra QPTIFF
reader has been updated to support schema version 4
funded by a partnership between Glencoe Software and Akoya Biosciences.
Bio-Formats improvements:
updated automated testing to ensure files are initialized before all tests
Documentation improvements:
fixed broken link in MIPAV documentation
updated logback component version in developer docs
updated link to View5D software
added a new format page for Slidebook 7
Component updates:
ome-metakit was upgraded to 5.3.4
ome-common was upgraded to 6.0.9
ome-model was upgraded to 6.3.1
ome-poi was upgraded to 5.3.6
ome-codecs was upgraded to 0.3.2
logback-core was upgraded to 1.2.9
logback-classic was upgraded to 1.2.9
xercesImpl was upgraded to 2.12.2
xml-apis was upgraded to 1.4.01
snakeyaml 1.29 was added as a dependency
6.9.1 (2022 April)
File format fixes and improvements:
- DeltaVision
allowed partial planes to be read from truncated files
- MetaMorph
fixed a NumberFormatException when parsing double values in metdata
- OME-TIFF
performance improvements to reduce the number of open file handles during initialization
- PerkinElmer Operetta
performance improvements to speed up the reading of datasets (thanks to Nicolas Chiaruttini)
- Zeiss CZI
switched to a white background for brightfield data to better match Zeiss Zen software
- Zeiss LSM
fixed a bug that resulted in an incorrect pixel type for some floating point data
Bio-Formats improvements:
removed the maven deploy step from workflows in forked repositories
upgraded cdm dependency from 4.6.13 to cdm-core 5.3.3
configurable sleep time in FakeReader moved to the end of initialization
Documentation improvements:
DICOM format page updated with improved links for sample datasets, software, and specification
updated guidelines for submitting sample datasets
6.9.0 (2022 February)
New file formats:
- Leica LOF
added support for reading Leica LOF files. This functionality was implemented and contributed by Leica Microsystems
- Leica XLEF
added support for reading Leica XLEF files. This functionality was implemented and contributed by Leica Microsystems
File format fixes and improvements:
- FEI TIFF
fixed parsing of physical pixel sizes for Phenom data
- Imspector OBF
improved handling of deflate errors when opening older OBF files (thanks to Nils Gladitz)
- JPEG
performance improvements to reduce memory required to read tiles from large JPEGs
- Leica LIF
improved parsing of channel metadata (thanks to Zach Marin)
- Nikon NIS-Elements ND2
-improved parsing of metadata tables with invalid characters
- OME-TIFF
performance improvements of tile read speeds for some pyramid OME-TIFFs
- PerkinElmer Operetta
enabled support for handling sparse planes
Bio-Formats improvements:
added new API methods to FormatTools for creating well names
added a swap option to bfconvert to override input dimension order (thanks to Roberto Calabrese)
Documentation improvements:
new public sample files for Leica XLEF (thanks to Leica Microsystems)
added documentation for using the swap option with the command line tools
updated the process for contributing sample files via Zenodo
updated the link to NDP.view2 software on the Hamamatsu ndpi format page
6.8.1 (2022 January)
File format fixes and improvements:
- Aperio SVS / Aperio AFI
improved handling of macro and label images when no image description is present
- cellSens VSI
added support for physicalSizeZ metadata
- Gatan Digital Micrograph DM4
fixed a FormatException when encountering null values in the metadata
Bio-Formats improvements:
fixed a bug in TiffSaver which could result in an invalid TIFF when saving a file with tiling and compression (thanks to Pete Bankhead)
made performance improvements to TIFF reading and writing (thanks to Pete Bankhead)
Security improvements:
Updated use of the git:// protocol in POM as it has now been deprecated. See the GitHub blog post for further details
Removed the loci_tools from Bio-Formats builds due to log4j vulnerability, users should instead use bioformats_package. See the OME security advisory for further details
6.8.0 (2021 December)
New file formats:
- DICOM
added support for reading and writing DICOM whole slide images (DICOM WSI format). This functionality was implemented through collaboration with NCI Imaging Data Commons, and has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Task Order No. HHSN26110071 under Contract No. HHSN2612015000031
- Olympus omp2info
Added a new reader for the Olympus tile format provided through a partnership with Glencoe Software and OLYMPUS EUROPA SE & Co. KG
File format fixes and improvements:
- Amira Mesh
added support for Amira 3.0 keys
- Aperio SVS / Aperio AFI
improved handling of macro and label images
- AVI (Audio Video Interleave)
set fps from Pixels Time Increment when writing AVI files
- Nikon NIS-Elements ND2
updated parsing of newer ND2 files to resolve issues with incorrect dimensions(thanks to Ilya Parmon)
- Olympus OIR
fixed a Null Pointer Exception for Laser Data ID
- OME-TIFF
fixed handling of partial datasets
added a new reader option ometiff.fail_on_missing_tiff to configure behaviour of partial dataset
- PerkinElmer Operetta
added support for Phenix v6 data
- TIFF
fixed non-sequential offset correction for TIFF files between 2 and 4 GB
- Zeiss CZI
added support for zstd compression. This feature will require FIJI users to additionally download the dependency io.airlift.aircompressor 0.18. (funded by a partnership between Glencoe Software and ZEISS)
Bio-Formats improvements:
updated the ordering of reader.txt
bfconvert tool updated to use multiple of tile size granularity when writing (thanks to Jeremy Muhlich)
added a new no-sequential option to enable writing in non sequential order
Component updates:
jhdf5 was upgraded to 19.04.0
commons-lang 2.6 was added as a dependency
aircompressor 0.18 was added as a dependency
Documentation improvements:
updated page for using Bio-Formats in Python to add links for AICSImageIO and PyImageJ (thanks to Curtis Rueden)
6.7.0 (2021 August)
File format fixes and improvements:
- cellSens VSI
corrected offset checking to prevent seeking beyond EOF
- Deltavision
fixed a bug which resulted in an IndexOutOfBoundsException
- Hamamatsu ndpis
added support for channel names from NDP Shading Data
- Nikon NIS-Elements ND2
improved parsing of timestamp values (thanks to Ilya Parmon)
improved parsing of channel names and colors
- Olympus FluoView FV1000
fixed a bug with the handling of filter indexes
- OME-TIFF
resolution annotations now removed when resolutions are flattened
fixed handling of filesets with BinaryOnly across multiple folders
- PerkinElmer Operetta
channel colors now populated using emission wavelength
- TIFF
added support for Deflate compressed tiles/strips with lsb2msb order
prioritised units from TIFF tag over those from ImageJ comment
- Zeiss CZI
plates will now be correctly detected
added a new reader option
zeissczi.relative_positionswhich when set to true will change the PositionX and PositionY values stored in OME-XML to the pixel position instead of the absolute physical stage positionadded a new reader option
zeissczi.trim_dimensionswhich when set to true will use the pixel block metadata to trim XY dimensions to match those reported in ZEN
Bio-Formats improvements:
the pattern reader now supports populating channel names from pattern tokens
the channel filler will correctly reset bits per pixel if a lookup table is applied
existing reader options are now registered in getAvailableOptions command
improved performance of OME-XML validation (thanks to Nils Gladitz)
added unit tests for the upgrade of custom attributes in OME-XML transforms
Documentation improvements:
updated link to a 2005 publication about the OME data model
bumped low level components logback-core and logback-classic to 1.2.0
updated the licensing for BDV, KLB and CellH5 readers to BSD
added documentation for additional reader options
fixed a number of broken links
The below have been relicensed under the more permissive BSD-2 clause:
Big Data Viewer reader
Keller Lab Block reader
CellH5 reader
JHDF service
Bio-Formats GNU Octave package
Bio-Formats MATLAB functions
Component updates:
ome-model was upgraded to 6.2.3
ome-common was upgraded to 6.0.7
ome-poi was upgraded to 5.3.4
ome-codecs was upgraded to 0.3.1
ome-metakit was upgraded to 5.3.3
logback was upgraded to 1.2.0
6.6.1 (2021 March)
File format fixes and improvements:
- CV7000
fixed the channel-wise ordering of planes. The implementation changes to channel mapping will require existing memo files to be regenerated for CV7000 datasets
- Hamamatsu NDPIS
transmittance values will now be used to pick valid channels if no wavelength present
- Leica SCN
updated position units from reference frame to nm
original metadata now populated correctly for all series
- MetaMorph Stack
support added for parsing NDInfoFile Version to determined correct file suffix
improved detection of companion binary files
- MetaXpress
improved detection of thumbnail paths
- Nikon NIS-Elements ND2
made performance improvements to reduce memory usage when reading large datasets
- Olympus OIR
fixed a bug which resulted in blank planes when XML blocks end with CRLF
Documentation improvements:
updated bfconvert documentation for using pattern string on Windows (thanks to Nathanael Reveal)
added a Fiji usage note to the Tecan Spark Cyto Workspace format page
added references to the public Imaris IMS format specification page
Bio-Formats improvements:
added support for ChannelName in Fake series tables
6.6.0 (2020 December)
New file formats:
- Tecan Spark Cyto Workspace
Added a new reader for Tecan Spark Cyto workspace files, provided through a collaboration between Tecan Trading and Glencoe Software
File format fixes and improvements:
- Applied Precision CellWorX / MetaXpress
support for CellWorX and MetaXpress has now been split into separate readers
- BD Pathway
plate row and column dimensions now being populated
- Bitmap
fixed offset calculation for files larger than 2 GB
- Cellomics
channel data now being parsed from companion .mdb file
corrected Plate/Well/Image mappings for sparse plates
plate size now calculated using the maximum row/column index
plate row and column dimensions now being populated
- Gatan Digital Micrograph DM4
fixed support for montages with single Z dimensions
- MetaMorph Stack
corrected laser indexes for multi series datasets
- MIAS (Maia Scientific)
plate row and column dimensions now being populated
- Nikon NIS-Elements ND2
fixed a null pointer exception when parsing metadata key value pairs
- Olympus ScanR
added functionality to handle missing wells through a new option
scanr.skip_missing_wells. By default the option is set to true and missing wells are skipped
- Olympus SIS TIFF
corrected parsing of pixel size values (thanks to Stephan Wagner-Conrad)
removed trailing null byte from imageName and channelName
improved formatting of the image reader
- PerkinElmer Opera Flex
plate row and column dimensions now being populated
- PerkinElmer Operetta
updated metadata files logic to skip plate folders
- PNG (Portable Network Graphics)
fixed an issue which resulted in a hanging call to openBytes
- Zeiss CZI
scene number is now correctly padded and indexes begin at 1
- Zeiss LSM
improved handling of cached plane variables
Documentation improvements:
added new OME-TIFF plate companion sample files
references to image index in the API documentation have been updated to plane index
updated various links to follow the LOCI site migration
fixed broken Javadoc links
removed outdated references to mailing lists
Component updates:
ome-model was upgraded to 6.2.2
ome-common was upgraded to 6.0.6
Memoizer version has been incremented meaning previous memo files are invalidated and will be regenerated
kryo dependency updated to 4.0.2
Added new sqlite-jdbc version 3.28.0 dependency for the Tecan Spark Cyto Workspace format
Bio-Formats improvements:
removed automatic file stitching from format reader tests
improved stringency of ChannelName and ImageName testing
improved reader detection for image conversion testing
reviewed all instances of whitelist/blacklist
introduced support for GitHub Actions
improved handling of DynamicMetadataOptions on Windows
introduced the ability to set metadata options using a .bfoptions file
test-suite updated to handle new .bfoptions file
6.5.1 (2020 July)
File format fixes and improvements:
- Aperio SVS / Aperio AFI
fixed a Null Pointer Exception when exposure time is not defined
- Big Data Viewer
corrected series indexes for non flattened multi resolution images
- Cellomics
physical sizes are now set for all series rather than just the first
- Imspector OBF
file format version and stack version are now recorded as part of global metadata
- MetaMorph
improved wavelength parsing using Metamorph XML or original metadata
- Mikroscan TIFF
stricter format recognition now used to prevent erroneous use of the reader
- Ventana BIF
added support for LEFT overlap direction (thanks to Joan Gibert)
- Zeiss CZI
fixed a bug to ensure Channel Illumination Type is not overridden by display settings
Documentation improvements:
added link from OME-TIFF page to commercial partners page
updated links for Biplane to now use Oxford Instruments
fixed a number of broken hyperlinks in documentation
Component updates:
jxrlib was upgraded to 0.2.4
Bio-Formats improvements:
fixed a bug in bfconvert for multi-series files with varying image sizes
removed the logging OMERO IDs passed to FormatReader and ImageReader
6.5.0 (2020 April)
File format fixes and improvements:
- Big Data Viewer
improved performance of tiled reading
- DeltaVision
implemented additional sanity check to header to ensure correct panel count
- DICOM
improved performance of initialization of multi-file datasets. Files spread across multiple directories are now handled by a DICOMDIR file that groups the dataset
- Imspector OBF
added support for OBF Version 6 stacks (thanks to Nils Gladitz)
added support for OBF Version 4 stack flush points (thanks to Nils Gladitz)
- MetaMorph
ensured dimension metadata read from tags and/or .nd file rather than allowing the underlying TIFF reader to treat each IFD as a series
- MetaXpress
added support for single site HCS variant
- Zeiss CZI
fixed the position count when only one position is present and the starting index is greater than 0
- Various Readers
reviewed and updated readers to prevent potential cases of integer overflow
OME-Model updates:
version of
OME-Modelhas been updated to 6.1.0added support for Python 3.8 and make code-generation Python 3 only (thanks to Roger Leigh)
added getters and setters for OME@Creator attribute for ome.xml metadata interfaces and implementations (thanks to Nils Gladitz)
removed unmaintained C++ OME-XML implementation (thanks to Roger Leigh)
updated code-generation for building on Python 3.6, 3.7 (thanks to Roger Leigh)
uncapped the Sphinx version for OME-Model documentation
Documentation improvements:
fixed a number of broken links within the documentation
added a new format page for MetaXpress
added a reference to public OBF sample images in the format page
6.4.0 (2020 March)
File format fixes and improvements:
- Applied Precision CellWorX
added support for multiple Z sections
- DeltaVision
added and updated objective metadata based on values from softWoRx 7.2.0 (thanks to David Pinto)
- Hamamatsu NDPI
added support for JPEG-XR compression
added full support for files larger than 4 GB
improved support for a number of additional metadata tags
the Hamamatsu NDPI reader improvements are provided via work from Glencoe Software Inc.
- InCell
inverted Y coordinate in plane/field positions to correct stitching of tiles
- PerkinElmer Vectra QPTIFF
plane position values will now be populated on OME-XML
- TIFF
values for XPosition and YPosition in original metadata will now be more accurately stored as doubles
implemented a fix to prevent integer overflow when reading from a large tile greater than 2 GB
- Ventana BIF
improved handling of physical sizes for pre-stitched TIFFs
- Zeiss CZI
added a fix for uncompressed pixels incorrectly flagged as JPEG-XR
fixed a bug so that line-scans are now read correctly (thanks to Stephan Wagner-Conrad)
improved parsing of detector metadata
Bio-Formats tools improvements:
added a new
nobigtiffoption tobfconvertto disable automatic switching to BigTiff based upon the number of pixel bytes (TIFF files larger than 4GB). This may be useful when converting using a compression codec so that the output file size is less than 4GBfixed a bug in
xmlvalidtool to properly handle lowercasing of file namesadded new bfGetPlaneAtZCT function to MATLAB toolbox to retrieve a particular plane at a ZCT coordinate (thanks to Mark Kittisopikul)
added a new bfTestInRange helper function to MATLAB toolbox with improved performance and error handling (thanks to Mark Kittisopikul)
fixed a bug when using
bfconverton multi-series files with only a single timepoint, channel or Z slice selected
Bio-Formats API updates:
version of
jxrlibhas been updated to 0.2.2version of
ome-codecshas been updated to 0.3.0 which includes performance upgrades for LZW compression (thanks to Alexander Popiel)moved JPEG-XR codec and service from
formats-gpltoformats-bsdcomponentTiffParser and TiffSaver have now been updated to implement Closeable
added a documentation note to use one IFD instance per plane with
saveBytesinTiffWriterFormatWriter will now create output file’s parent directory if needed
FakeReader now allows for DeltaT to be set in INI file
FakeReader now handles INI files in plates created by
mkfakefixed a number of deprecation warnings in various readers
6.3.1 (2019 December)
File format fixes and improvements:
- ICS (Image Cytometry Standard)
prevented a potential error when writing ICS files with physical units which could not be converted
- Imspector OBF
fixed a bug with incorrect dimensions being parsed for some Imspector OBF files
- Leica LAS AF LIF (Leica Image File Format)
fixed a NullPointerException in some variants of the LIF file format
- TIFF
improved the performance of tiled writing
- Zeiss CZI
fixed issues with tile stitching and position size
Bio-Formats tools improvements:
fixed a potential NullPointerException in SpringUtilities for Bio-Formats plugins (thanks to July Chen)
updated URL for fetching ImageJ upgrades in
ijviewfixed the XY coordinates for cropped images in
bfconvertfixed a bug when using a cropped multi-series file in
bfconvert(thanks to Matthieu Moisse)fixed issues in
bfconvertwhen writing separate tiles with additional optionsadded documentation of tile output patterns to utility help in
bfconvert
6.3.0 (2019 October)
File format fixes and improvements:
- Big Data Viewer
added support for parsing of physical sizes
- DeltaVision
added a new RCPNL reader which is a variant and split out of the DeltaVision format
- Hamamatsu NDPI
fixed population of the nominal magnification from the SourceLens TIFF tag
- ICS (Image Cytometry Standard)
fixed a bug when using tiles to read files from SVI-Huygens
- Imspector OBF
fixed an IndexOutOfBoundsException exception when using DummyMetadata (thanks to Nils Gladitz)
- JPEG 2000
added support for sub-resolutions
- Leica LIF
updated to parse attachments to determine if XY positions should be flipped or swapped
- MetaMorph
improved file name construction and plate detection logic
- Nikon ND2
updated to use floating point for 32 bit values
- OME-TIFF
reduced memory usage when reading files and memo file size for cached files
- PerkinElmer Operetta
improved handling of empty fields to prevent series from having X or Y set to 0
API updates:
added overwriteIFDValue signature that takes an IFD offset to TiffSaver
added a new getRequiredDirectories method to FormatTools
new FakeReader keys added for sleepOpenBytes and sleepInitFile
Build updates:
updated deployment mechanism for SNAPSHOT and Release to use Travis CI
increased the strictness of AcquisitionDate checks in FormatReaderTest
improved test coverage of companion file datasets
Component updates:
ome-common was upgraded to 6.0.4
updated DateTools to attempt to parse invalid dates with Locale.US
DateTools documentation updated to clarify expected units for timestamp passed to convertDate
Documentation improvements:
added documentation for sleep options when generating test images
fixed broken external links in documentation
corrected suffixes used for JPEG 2000
6.2.1 (2019 August)
File format fixes and improvements:
- Applied Precision CellWorX
corrected plane positions for series index > 0 rather than reusing positions from the first series
- DeltaVision
added objective info for new Applied Precision 100X/1.4 lensID
updated so that date from dv file will override log file date to avoid locale-dependent dates
- Leica LAS AF LIF (Leica Image File Format)
fixed units and indexing for tile-based plane positions
- TIFF
fixed a potential exception in MinimalTiffReader when the TIFF is stored using very large tile/strip dimensions
- Zeiss CZI
fixed a potential index out of bounds exception when populating positions
Bug fixes and improvements:
bfconvert has been updated so that when the dimensions of a sub-resolution are smaller than the requested tile size then they default to the size of the sub-resolution
fixed a bug in the execution of bfsave in the GNU Octave environment
Codec updates:
ome-codecs was upgraded to 0.2.5
JPEG codec updated to reduce decompression time for 8-bit RGB images
Huffman codec updated to allow the decoding tree to go all the way down to the 16-bit depth required by the standard (thanks to Aaron Avery)
Lossless JPEG codec updated to provide better compliance with the LJPEG standard (thanks to Aaron Avery)
Documentation improvements:
added instructions for building Bio-Formats with IntelliJ IDEA
corrected command-line tools documentation for the novalid and noncore options
updated broken links to Barre’s Medical Imaging Samples
updated the imagej.net link for Zeiss LSM toolbox plugin
- added links to public sample files for the following formats:
6.2.0 (2019 July)
New file formats:
- Mikroscan TIFF
a new reader for Mikroscan TIFF files has been contributed with thanks to Jim Crowe, Mikroscan Technologies, Inc.
- Ventana BIF
added a new reader for Ventana BIF files which has been commissioned via Glencoe Software
File format fixes and improvements:
- Cellomics
fixed indexing for plates with a single well or missing fields
- DeltaVision
added support for the reading of the new panel count field (provided through a collaboration between GE Healthcare and Glencoe Software Inc.)
- PerkinElmer Operetta
images with smaller XY dimensions than all other TIFF files in dataset will now be padded
- TIFF
updated functionality for overwriting IFD values to ensure that previous value is completely overwritten and no orphaned tags are left
- Zeiss CZI
expanded support for auto-stitching of tiles
Bug fixes and improvements:
added
-cache,-cache-dirand-no-sasoptions tobfconverttooldeprecated broken TRUNK and DAILY builds from upgrade checker
disabled Oracle JDK from Travis CI checks
Documentation improvements:
fixed broken link for discontinued Dcraw software
updated links for Zeiss formats
6.1.1 (2019 June)
File format fixes and improvements:
- DeltaVision
added new lens definitions associated with rcpnl files
- Gatan Digital Micrograph (DM3/DM4)
now parsing the Montage tag to determine if tiles are present
- Leica LAS AF LIF (Leica Image File Format)
added fix to correctly read scale from polygon regions of interest (thanks to Sean Warren)
- PerkinElmer Columbus
improved handling of truncated TIFF files to return blank planes
- PerkinElmer Opera Flex
plate barcodes are now used to improve grouping and handling of truncated files
- TIFF (Tagged Image File Format)
improved parsing times for images stored as uncompressed contiguous strips
- Zeiss CZI
improved plane position metadata for many CZI datasets
Automated test changes:
format reader tests have been updated to handle PerkinElmer Columbus datasets with flex files
Documentation improvements:
added help for missing options in
bfconvertcommand line tool
6.1.0 (2019 May)
New file formats:
- BDV
added a new reader for Big Data Viewer files
File format fixes and improvements:
- Applied Precision CellWorX
improved handling of thumbnail files
- DeltaVision
updated handling of rcpnl files to treat each file as a single timepoint
- FakeReader
removed header key from original metadata
- Hamamatsu VMS
removed header key from original metadata
- Hitachi S-4800
removed header key from original metadata
- ICS (Image Cytometry Standard)
fixed an issue reading .ics/.ids files written by SVI Huygens (thanks to Jan Eglinger)
- Imaris IMS
fixed issues with newer files which had been failing due to older netcdf version
- JPEG
improved the reading of EXIF data
- Lambert Instruments FLIM
added support for packed UINT12 datatype (thanks to Johan Herz)
- LEO
fixed a bug with the parsing of physical sizes
improved support for additional global metadata fields
- Olympus OIR
fixed a bug which would show empty pixels when more than 1000 timepoints
Automated test changes:
added additional tests for HCS/SPW datasets to ensure Plate, PlateAcquisition, Well, WellSample, and WellSample position values are configured where present
added a new file-leak-detector test to flag potential memory leaks
Bio-Formats API changes:
ImageConverteras used inbfconvertcommand line tool is now publicmade
ImageReadermore defensive against exceptions thrown when determining reader typefixed an issue when performing a non-sequential write for multi-resolution TIFF files
Component changes:
ome-common was upgraded to 6.0.3
perf4j was upgraded to 0.9.16
removed Guava dependency which will be pulled transitively from the upstream ome-common dependency
jhdf5 was upgraded to 14.12.6
metadata-extractor was upgraded to 2.11.0
xercesImpl version 2.8.1 was added as it is no longer a dependency of metadata-extractor
netcdf was upgraded to 4.6.13
6.0.1 (2019 March)
File format fixes and improvements:
- cellSens VSI
improved tag parsing resulting in fixes for missing or incorrect metadata
- Hamamatsu ndpi
improved handling of variants where a constituent NDPI has no wavelength
- LaVision Imspector
fixed a potential NullPointerException when ‘xyz-Table Z Resolution’ is false
- NRRD (Nearly Raw Raster Data)
added support for raw GZIP-compressed data files
- Olympus OIR
fix to ensure file path is normalized which fixes detection on Windows
- TIFF
improved handling of direct tile copying to prevent invalid images
improved handling of tiles in scenarios of an invalid offset or byte count of 0
- Documentation improvements:
added documentation for -noflat option to the showinf and bfconvert users pages
updated recommended minimal MATLAB version to R2017b
documented support for MATLAB versions prior to R2017b
links to MicroCT public datasets now point to the public archive rather than directly to the zip file
6.0.0 (2019 February)
Bio-Formats API changes:
Java 8 is now the minimum supported version
Sub-resolution reading:
added
MetadataListandCoreMetadataListclassesadded a new
SubResolutionFormatReaderabstract class for handling pyramidal format readersupdated all pyramid format readers to use
SubResolutionFormatReaderdeprecated
getCoreMetadataList,seriesToCoreIndex,coreIndexToSeries,getCoreIndexandsetCoreIndexinIFormatWriter
Added a new
IPyramidHandlerinterface with the resolution getter methodsSub-resolution writing changes:
IFormatWriternow extendsIPyramidHandler(breaking)added
setResolutionsandgetResolutionsmethods toIFormatWriter(breaking)added examples of using the sub-resolution writing API
Tiled writing API changes:
updated
IFormatWriterto usesetTileSizeX(0)andsetTileSizeY(0)as a way to disable tiling (breaking)updated
FormatWriterset 0 as the default values ofgetTileSizeX()andgetTileSizeY(breaking)
IFormatWriter.getCompressionTypesnow returns the types for the selected writer onlyMetadata handling:
added getter methods to
MetadataToolsfor retrieving OME enumerations by valuedeprecated OME enumeration getter methods in
FormatReader
Refactor
FilePatternReaderlogic in a newWrappedReaderabstract class
New file formats:
KLB
added a new reader for Keller Lab Block (KLB) files
CV7000
added a new reader for Yokogawa CV7000 datasets
GE MicroCT
added a new reader for GE MicroCT datasets
File format fixes and improvements:
Aperio SVS/AFI
removed pyramidal resolutions of mismatching pixel types
fixed exposure times, improved image naming of AFI datasets
displayed original metadata keys for each channel of AFI datasets
added support for multiple Z sections
DICOM
improved file grouping and file-to-series mapping for multi-file datasets
Fake
added support for multi-resolution test images
now populating WellSample positions when present using Plane data
Gatan Digital Micrograph
adjusted endianness and record byte count for long values
allowed ROIs to be stored in DocumentObjectList groups
no longer creating an empty ROI when an unsupported shape type is encountered
Image Pro
added support for Image Pro Plus .ips set
GE InCell
added support for parsing minimum and maximum pixel values
Lambert Instruments FLIM
fixed an integer overflow error with large files (thanks to Rolf Harkes)
Leica LIF
unified metadata parsing to use
DataTools.parseDouble
Leica SCN
improved support for Versa datasets
Micro-Manager
improved handling of very large
*_metadata.txtfilesprevented
NumberFormatExceptionfor invalid double valuesadd support for parsing ChannelColor from
*_metadata.txtfiles
Metamorph
added support for multi-dimensional .scan dataset created from Scan Slide (thanks to Jeremy Muhlich)
MRC (Medical Research Council)
fixed endian detection for old-style headers
Nikon ND2
prevented integer overflow when reading chunkmaps from files larger than 2GB
fixed handling of duplicate and incomplete exposure time lists
fixed chunk map handling when CustomData blocks are between ImageDataSeqs
OME-TIFF
added support for reading OME-TIFF with pyramidal resolutions stored as SubIFDs
added support for writing OME-TIFF with pyramidal resolutions
added support for companion OME-TIFF filesets where TIFF does not link back to the metadata file
improved handling of missing planes in TiffData
PerkinElmer Operetta
improved support to handle datasets generated by the Harmony software
TIFF
split IFDs into separate series if the dimensions or pixel type mismatch
restricted use case for legacy TIFF JAI reader
fixed a bug with FillOrder which resulted in 0 pixel values
Zeiss CZI
reduced duplicate original metadata when reading a pyramid file
Zeiss TIFF
added support for AVI files acquired with Keyence software
Zeiss ZVI
reuse stream for sequential calls to
openByteson the same plane
updated all pyramidal format readers to consume
SubResolutionReaderupdated all readers to consume
MetadataToolsgetter to retrieve enumerationsreviewed all readers and plugins to close open instances of
RandomAccessInputStreamfixed some deprecation warnings in a number of readers
for RGB images using
ChannelSeparatorall channel metadata is now copied instead of just names
ImageJ plugin improvements:
updated the updater message in the Fiji plugin (thanks to Jan Eglinger)
disabled LUT writing for any plane that has a default grayscale lookup table
added macro option to always skip LUT writing
MATLAB toolbox improvements:
improved performance of bfGetPlane by removing an unnecessary data copy (thanks to Cris Luengo)
Command-line tools improvements:
bfconvertutilityadded
-no-flatoption to the command-line tools to convert files with sub-resolutionsadded
-pyramid-scaleand-pyramid-resolutionsoptions to generate sub-resolutions during conversionremoved
Plateelements when-seriesis passed as an optionextended usage to describe available formats, extensions and compressions
xmlvalidutilityadded new
validatemethods toloci.formats.tools.XMLValidatereturning the validation statusadded a return code to
xmlvalid
Component changes:
ome-common was upgraded to 6.0.0
ome-codecs was upgraded to 0.2.3
ome-model was upgraded to 6.0.0
Automated test changes:
added
testng.allow-missingproperty allowing to skip unconfigured filesetsadded
testUnflattenedSaneOMEXMLto compare series count to OME-XML images count when resolution flattening is disabledadded
test-equivalenttarget to compare pixel data between two filesadded support for storing resolution index and resolution count in the configuration files used for automated testing
tests now fail when a configured file throws UnknownFormatException
Documentation improvements:
fixed the xmlvalid documentation page (thanks to Kouichi C. Nakamura)
improved the memory section of the MATLAB documentation page (thanks to Kouichi C. Nakamura)
extended
IFormatReaderJavadocs to reflect the reader guideadded reference to current Adobe TIFF specification
switched to image.sc as the reference location for public feedback
5.9.2 (2018 September 03)
File format fixes and improvements:
- AVI
added support for AVI files acquired with Keyence software
- Gatan
fixed a bug when reading a file with an empty tag of type 23
- Deltavision
extended the objective metadata support (thanks to David Pinto)
- MRC
fixed the reading of MRC files generated with FEI EPU software
- Zeiss LSM
improved the channel color detection for SIM data
Component changes:
All OME dependencies were upgraded mostly with build changes and documentation improvements:
ome-common was upgraded from 5.3.2 to 5.3.6
ome-poi was upgraded from 5.3.1 to 5.3.3
ome-mdbtools was upgraded from 5.3.1 to 5.3.3
ome-jai was upgraded from 0.1.0 to 0.1.3
ome-codecs was upgraded from 0.2.0 to 0.2.2
ome-stubs was upgraded from 5.3.0 to 5.3.2
ome-model was upgraded from 5.5.4 to 5.6.3
Documentation improvements:
added links to public sample files for Imaris IMS, DICOM, Leica-SCN, LEO, MRC, PNG, TIFF and Trestle formats
5.9.1 (2018 August 14)
File format fixes and improvements:
- Olympus OIR
fixed a bug to prevent incorrect files from being read when multiple datasets are in the same location
- LEO
updated parsing of metadata values for image pixel size, working distance, filament, EHT and date (thanks to David Mankus)
- DeltaVision
reader can now detect up to 12 channels
- Micro-Manager
now logs a warning when an image is acquired with an unsupported version
Documentation improvements:
added QuPath to the list of visualization and analysis applications
updated the link to the i3dcore library
updated the link to Slidebook
improved MATLAB documentation with information on Java heap memory preferences (thanks to Kouichi C. Nakamura)
corrected a number of permanently redirected URLs in the component and format pages
5.9.0 (2018 July 3)
File format fixes and improvements:
- MetaMorph
fixed a
NullPointerExceptionwhen a stage label is not presentensured that reported domain is now consistent with the existence of a Plate in OME-XML
fixed Metamorph RGB series channel count (thanks to Jeremy Muhlich)
- Leica LIF
improved handling of dimension order for non-RGB channels
- Imspector OBF
added support for FLIM datasets
- Inveon
updated to attempt to locate renamed data files
- Volocity
expanded image names to include the stack parent names
- Olympus OIR
added a fix for slow tag reading and a potential infinite loop
- TIFF
added support in
TiffWriterfor the writing of DEFLATE (zlib) compressiondeprecated
getIFDs()inTiffParserand addedgetMainIFDs()andgetSubIFDs()
- Zeiss CZI
fixed an issue with big images when tiling is present but a pyramid is not
- Nikon NIS-Elements ND2
prevented integer overflow exception when reading a tile from a large image
- Amersham Biosciences Gel
prevented overflow issue when reading unsigned integer values
- Cellomics
fixed indexing when the field counts are variable
- Trestle
updated to ensure consistent ordering of used files
Bug fixes and improvements:
enabled building and testing with Java 9 and 10
added CI testing with Java 10 on AppVeyor and Travis
removed Java 7 from Appveyor matrix
updated a number of Maven plugins to current versions
corrected warnings in Maven configuration in sub-components
added a warning to clarify the behavior when passing metadata with
dimensionOrderinbfsaveas part of the Bio-Formats MATLAB toolbox (thanks to Jonathan Armond)improved robustness in the detection of patterns as part of the file stitching
fixed a bug relating to dimension order in the Bio-Formats plugins Exporter
fixed download URLs in Bio-Formats command-line tools
updated use of
static finalto match Oracle’s recommendations and conventiondisabled upgrade checker when running unit tests
added support to data repo test suite for unconfigured tests
Documentation improvements:
fixed unstable links flagged by automated link checking
begun adding testing for breakages to memo files
clarified ordering expectation in
getUsedFilesJavadocsadded documentation for dimensionOrder in bfsave with the MATLAB toolbox
fixed broken links in previous release notes
expanded documentation for command-line tools to cover undocumented options and environment variables
added a new license/copyright section to the About Bio-Formats page
updated the public format page for the Vectra QPTIFF format
5.8.2 (2018 April 23)
File format fixes and improvements:
- JPEG
large images with no restart markers now revert to using
DefaultJPEGReaderfor improved decoding
- Micro-Manager
when available
PositionNamewill be parsed and used as the image name
- Hamamatsu ndpi
updated image names to be more meaningful when resolutions are not flattened
- InCell 2000/6000
fixed an
IllegalArgumentExceptionand improved well and field indexing
- AVI
fixed a bug with padding for RGB images
- NIfTI
the
nDimensionsfield is now used to read additional dimensions when size is greater than 4
- PerkinElmer Opera Flex
fixed a bug which resulted in an incorrect field count
- Zeiss CZI
improved handling of files with no extension
Bug fixes and improvements:
an error message is now logged by
ImageReaderwhen finding a reader for an empty fileadded a new protected helper method to
Memoizerto check if a directory is writableimproved the rounding of
PlanePositionvalues for data repo configuration testingprevented a null pointer exception when retrieving plane exposure time using Bio-Formats ImageJ macro extensions
updated
MinMaxCalculatorto account for unflattened multi resolution images
Documentation improvements:
decoupled the Bio-Formats documentation to the new ome/bio-formats-documentation GitHub repository
updated Adding format/reader documentation for the new decoupled workflow
improved link checking in automated builds
5.8.1 (2018 March 22)
File format fixes and improvements:
- TIFF
updated TiffWriter so that planes will no longer be split when using non-standard SamplesPerPixel e.g. images with 2 or 4 samples per pixel. This will ensure the
TiffDataelements represent the structure specified by the user. If users wish to split planes theChannelSeparatorandbfconvertprovide the means to do this explicitlyupdated TiffWriter to use the correct logic for index checking when writing tiled images
fixed a
ClassCastExceptionwhen theNEW_SUBFILE_TYPEtag has a non-standard type or count such that the value is not inlinedupdated to also check the last IFD for an ImageJ comment in the scenario that the image has been processed by other software
- NRRD (Nearly Raw Raster Data)
added support for
space directionsandspace unitsfields added in version 4
- Evotec/PerkinElmer Opera Flex
updated to read rather than calculate image offsets when a single tile is used
Bug fixes and improvements:
limited the number of exceptions in the Bio-Formats plugins exporter when an unsupported pixel type is found
fake test images now allow for per-plane ExposureTime{X,Y,Z} and Position{X,Y,Z} keys in the INI file (for further details see the documentation for Generating test images)
file patterns now have expanded support for multi-channel pyramids, allowing for the matching of at least two channels rather than three, and the stitching of files containing a pyramid has also been fixed
Documentation improvements:
improved testing of external links
5.8.0 (2018 February 21)
New file formats:
- Ionpath MIBI
added a new reader to support the reading of Ionpath Multiplexed Ion Beam Imaging (MIBI) files (thanks to Rachel Finck)
- PerkinElmer Vectra QPTIFF
added support for PerkinElmer Vectra QPTIFF files (The QPTIFF Bio-Formats reader is provided through a collaboration between PerkinElmer, Inc and Glencoe Software Inc.)
File format fixes and improvements:
- cellSens VSI
added support for lossless JPEG compression
- Imspector OBF
improved the parsing of OBF files with embedded OME-XML metadata (thanks to Bjoern Thiel)
- Leica LIF
companion metadata files are now attached if present
- Micro-Manager
fixed a bug related to the parsing of the metadata closing block
- NRRD (Nearly Raw Raster Data)
added support for GZIP pixel stream contained within a .nrrd file
- Olympus OIR
added support for multi-file datasets
- OME-TIFF
when files are ungrouped the dimensions are corrected by checking the indexes for each associated TiffData
- PerkinElmer Operetta
added support for additional metadata fields such as
Instrument,WavelengthandExposure time
- TIFF
fixed a bug when printing IFD values of type
OnDemandLongArrayfixed a bug when writing tile sizes for multi-series images
- Zeiss CZI
when Z positions are not enumerated then values are calculated from a Z step
metadata for DisplaySetting will now be preserved in the original metadata table
Bug fixes and improvements:
removed unused ScreenReader in preparation for migrating it to be an external reader
fixed a bug with the generation of thumbnails in Bio-Formats plugins
updated the Maven POM to unify component version property names
tile size is now reported in the core metadata when using the showinf tool
added
setFilePatternIdstoImporterOptionsfor use with Bio-Formats pluginsimproved the precision of format identification for MRC, I2I, and Zeiss LSM
Documentation improvements:
fixed and updated a number of external documentation links
added links to public NRRD samples
5.7.3 (2018 January 11)
File format fixes and improvements:
- TIFF
fixed a NullPointerException when reading a TIFF file from the root system directory
improved support for large images that are stored as a single uncompressed tile with multiple interleaved channels
- MRC (Medical Research Council)
added support in original metadata for the fields
ISPGandIs data cube
- TillPhotonics TillVision
directory listings for .pst files are now sorted
- MetaMorph
directory listings are now sorted during file initialization
- Amira Mesh
now supports
Avizoin the file header in addition to the existing support forAmiraMesh
- Becker & Hickl SPCImage
added a fix for IllegalArgumentException when reading files with compressed data
- Zeiss CZI
fixed an IndexOutOfBoundsException when creating ROI objects
Bug fixes and improvements:
removed unused target utils-formats-api from ant build
automated Memoizer tests updated to use UUID for generating unique memo file directories
detect and fix Findbugs’
SBSC_USE_STRINGBUFFER_CONCATENATIONusing StringBuilderconfiguration files for the automated test suite now use raw physical size rather than formatted size
added first version of Dockerfile for running the automated test suite standalone
Documentation improvements:
added a support page to the Bio-Formats project
updated reference URLs for the Aperio ImageScope and Micro-Manager
documented issues with conflicts in the JAI ImageIO component
clarified the default values of HCS keys for fake images in the documentation for Generating test images
corrected external links which failed automatic link checking
5.7.2 (2017 November 21)
File format fixes and improvements:
Nikon ND2 - fixed a bug which would use the incorrect channel count for small-sized single channel images
- MetaMorph TIFF
changed the reader’s behaviour to populate exposure times for all planes when only a single exposure time is defined
- DeltaVision
improved parsing of the associated log files to add additional key value pairs to global metadata
- EPS (Encapsulated PostScript)
fixed an exception when reading pixel data in cases with embedded TIFF
- GIF
fixed a bug to display the correct data when reading planes out of order
Bug fixes and improvements:
fixed failures with Ant build from a clean Maven repository by updating Maven repositories to use HTTPS rather than HTTP
now using safe version checking for Bio-Formats plugins to prevent a bug with Java 9
updated the JPEG-XR codec to allow either interleaved or non-interleaved data to be returned
Documentation improvements:
added clarification regarding Bio-Formats version requirements for using Java 7 or above
updated download links to latest Bio-Formats release version
updated the link to the most active fork of JAI ImageIO
fixed a number of external broken links
added a Trello link for contributing external developers
added a link to the page Adding format/reader documentation pages to help those contributing to the documentation or supported formats pages
the Bio-Rad Gel page has been updated to add a link to biorad1sc_reader, an external python implementation (thanks to Matthew Clapp)
5.7.1 (2017 September 20)
File format fixes and improvements:
- Nikon NIS-Elements ND2
improved parsing of Z position values
- LaVision Imspector
corrected the value of time per FLIM channel
fixed a bug which saw the Z and T dimensions swapped
fixed a divide by zero exception
added a fix for incorrect time-base and number of channels
- TIFF
added support for handling files with a FillOrder of 2 in which the bits in each byte are reversed
improved support for multi-channel ImageJ TIFF files greater than 4GB in size
Performance improvements:
improved TIFF performance by using non-regexp String replacement (thanks to Thushara Wijeratna)
improved TIFF handling of Strings for large metadata (thanks to T. Alexander Popiel)
Documentation improvements:
updated documentation to reference support for ImageJ TIFFs
added links to format options page to user and developer index pages
5.7.0 (2017 September 4)
File format fixes and improvements:
- Imaris HDF
fixed resolution problems in which dimensions and resolution order were incorrectly calculated (thanks to Eliana Andreica)
- Nikon NIS-Elements ND2
fixed a bug in offset calculation when native chunk map is being used
- MetaMorph
corrected delta T and position Z values for multi-channel images when channels are split across multiple files
- Amnis FlowSight
better handling of exceptions in isThisType method (thanks to Claire McQuin)
- PicoQuant Bin
better handling of exceptions in isThisType method (thanks to Claire McQuin)
Bug fixes and improvements:
reviewed and corrected URLs throughout the Bio-Formats source code
updated Bio-Formats Macro Extensions list with a missing function
added a new option in Bio-Formats plugins to configure the slice label display using patterns
Documentation improvements:
added new format page for OMERO Pyramid
updated the developer page for Working with whole slide images
added new page for configuring options in Bio-Formats plugins
updated documentation sidebar to enable navigation of previous versions
5.6.0 (2017 August 14)
File format fixes and improvements:
- Zeiss CZI
added support for images from Elyra PALM system
prevented a potential infinite loop when a scene with a pyramid is missing
- cellSens VSI
a new option has been added to throw an exception rather than logging a warning if .ets file is missing. The option,
cellsens.fail_on_missing_ets, can be used via the MetadataOptions API, as a parameter in the command line tools or via the Bio-Formats configuration dialog in ImageJ
- MetaMorph Stack (STK)
fixed an error with HCS style datasets always returning the first plane regardless of the requested index
updated to use stage labels starting with
Scanto detect when a whole plate is saved in a single .stk filefixed a bug for
ArrayIndexOutOfBoundsExceptionwhen an image contains a single Z plane
- Gatan Digital Micrograph
added support for Z stacks and ROIs
fixed several bugs in tag parsing
- PerkinElmer Operetta
ensure TIFF files exist before reading
- JPEG
support added for images with more than
Integer.MAX_VALUEpixels
Bug fixes and improvements:
- JPEGTileDecoder
class now implements AutoCloseable to prevent resource leaks
- Bio-Formats Plugin
improved performance when using options to concatenate multiple series together
- TiffSaver
made performance improvements to prevent the writing of a new IFD for each tile, resulting in significant file size reductions for images with a large quantity of tiles
Documentation improvements:
updated website and URL links for new OME Website website
added missing Andor SIF to supported formats page
added a new page Working with whole slide images outlining the API support for pyramids/resolutions
fixed broken documentation links for external resources which are no longer available
updated the style of Sphinx documentation
Component architecture changes/decoupling:
decoupled image encoding and decoding routines to the new ome/ome-codecs GitHub repository and consumed as ‘org.openmicroscopy:ome-codecs’ artifact from Maven Central
removed components/forks/jai - decoupled to the new ome/ome-jai GitHub repository and consumed as part of ‘org.openmicroscopy:ome-jai’ artifact from Maven Central
replaced components/formats-api/codecs classes with wrappers around ‘org.openmicroscopy:ome-codecs’
replaced components/formats-bsd/codecs classes with wrappers around ‘org.openmicroscopy:ome-codecs’
Updated build system:
ant now removes the build files of the bundles during ‘clean’ to prevent a mix of dependencies
5.5.3 (2017 July 5)
File format fixes and improvements:
- Zeiss CZI
fix to store Bézier ROIs as polygons, using the control points for the set of Bézier curves to form an approximation of the ROI
improved parsing of stage positions in metadata
improved parsing of detector gain values
removed OME-XML validation errors by fixing potential for duplicate detector IDs
removed invalid XML failures for Modulo label elements
time increment metadata now populated on
Pixelselementfix to deal with consecutive empty planes in a series (thanks to Nicholas Trahearn)
- DICOM
no longer allow core metadata to be modified when determining if files belong to a DICOM dataset
- Nikon NIS-Elements ND2
fixed calculation for scanline padding
- Kodak BIP
stricter file type checking enforced by no longer relying only on the file suffix
- MINC MRI
improved parsing of metadata by correcting units for physical sizes, pixel type and capturing XYZ plane positions in OME-XML
- Bio-Rad Gel
fixed the width of pixel data offset field
- DeltaVision
improved accuracy of format detection checking for input streams
- Andor SIF
fixed support for cropped images by parsing bounding box of the stored image
Documentation improvements:
Olympus cellSens VSI updated to include list of available specifications
5.5.2 (2017 June 15)
File format fixes and improvements:
- Olympus FluoView FV1000
fix for
java.lang.ArrayIndexOutOfBoundsExceptioncaused by filter names of “—” (thanks to Stefan Helfrich)refactored channel metadata population and increased usage of
DataToolsutility functions
- Zeiss CZI
fixed detection of Z line scans that caused incorrect dimensions in certain filesets
improved exception handling of truncated/invalid files
- Veeco AFM
fixed reading of tiled images
- Hamamatsu ndpi
prevented potential memory leak by ensuring all
TiffParserstreams are closed
Bug fixes:
- OMEXMLServiceImpl
improved exception handling to deal with potential
java.lang.NullPointerExceptionwhen unable to locate OME-XML version while attempting to transform to the latest version
Documentation improvements:
updated documentation to be compatible with the latest version of Sphinx 1.6
fixed the usage/references of the option markup in documentation
fixed the table in the Micro-Manager user page
updated metadata ratings for supported formats
Updated build system:
- OME-Model version bump
the ome-model component has been updated to 5.5.4 which includes improvements to performance, documentation and the C++ model implementation
5.5.1 (2017 May 25)
File format improvements:
- CellH5
fix for
HDF5SymbolTableExceptionwhen recycling an IFormatReader to reopen another CellH5 filebug fix related to opening of subsets of CellH5 files, namely
openBytes(r, no, x, y, w, h)for y>0
- Zeiss CZI
fix pyramid resolution indexing for pyramids of different depths
fix for incorrect channel names and colors
- Zeiss AxioVision ZVI
correct parsing of epoch for Zeiss TIFF and Zeiss ZVI
Bug fixes:
- Command line tools
fix for
java.lang. NegativeArraySizeExceptioncaused by incorrect dimensions when using showinf via command line with options set to autoscale and crop
- Format tools
fix for
java.lang. IndexOutOfBoundsExceptionwhen usinggetFilenamewith an image containing multiple samples per pixel channels and a single effective channel
Updated build system:
- Autogen jobs
fix for
gen-meta-supportto locate availableorg.openmicroscopy:ome-xmlsources from the Maven repository following the decoupling of the model components
- FileHandleTest
exclude JHDF5 native libraries from
FileHandleTestto enable CellH5 files to be included in daily tests
Documentation improvements:
added a new example file for reading and writing of XZ and YZ orthogonal planes
5.5.0 (2017 May 8)
New file formats:
- Olympus OIR
added support for Olympus .oir data (funded by a partnership between Glencoe Software and OLYMPUS EUROPA SE & Co. KG)
- PerkinElmer Columbus
added support for PerkinElmer Columbus data
File format improvements:
- Andor Bio-Imaging Division (ABD) TIFF
fixed acquisition date format from
MM/dd/yyyytodd/MM/yyyy
- Nikon NIS-Elements ND2
corrected logic used to determined
PixelTypeby parsing uiBpc tags
- Hamamatsu ndpi
improved handling of channels in NDPIS datasets (thanks to Manuel Stritt)
- Imspector OBF
fix for
SAXParseExceptionwhen description field in metadata is empty
Documentation improvements:
added links to public sample files for Cellomics
added links to public sample files for InCell 3000
5.4.1 (2017 April 13)
File format improvements:
- MIAS (Maia Scientific)
added a fix for a possible exception when image files are not found under channel-specific subdirectories
- BD Pathway
added fix to check if
Experiment.expis a directory or an experiment file
- Imspector OBF
enabled forward compatibility for future versions, as the OBF format is backwards compatible (thanks to Bjoern Thiel)
Documentation improvements:
updated external homepage link for FocalPoint
removed Imago from list of visualization and analysis applications as it is no longer available from the Mayachitra website
added links to public sample files for Hamamatsu NDPI and Hamamatsu VMS
listed OpenSlide as available software for supported formats
added a new developer page detailing in-memory reading and writing
updated the Bio-Formats API versioning policy, which now follows strict semantic versioning
a new options page has been added, detailing the usage of configurable format-specific options for readers and writers. Links to the available options are also included under the relevant supported formats
5.4.0 (2017 March 21)
File format improvements:
- DICOM
added support for DICOMDIR files, which allow multiple DICOM files in a single directory to be opened as a single dataset
plane position values for values X, Y and Z are now being set in OME-XML
correctly read the physical size X and Y values based on the available specification
- Nikon NIS-Elements ND2
performance improvements based on reading chunkmap. Processing of the chunkmap can be disabled via the MetadataOptions API using the boolean option
nativend2.chunkmap. For ImageJ users this option can be accessed via a checkbox in the Nikon ND2 section of the Bio-Formats configuration dialog (thanks to Christian Sachs)
- OME-TIFF
added an option to save an OME-TIFF dataset as a binary TIFF and companion XML. This can be used via the bfconvert command line tool by setting the value of option
ometiff.companionto the name of the companion file to use. For examplebfconvert -option ometiff.companion outputFile.companion.ome inputFile.tiff outputFile.ome.tiff
- CellVoyager
metadata fixes specifically the naming of plates. Additional refactoring of the reader for general maintainability
- Gatan Digital Micrograph
previously missing Image-Instrument reference has been added to OME-XML
- TiffSaver
ensure open resources are closed under all possible scenarios
- Zeiss CZI
improved performance of large uncompressed images. When tiles from a large uncompressed image with no internal tiling are requested, only the specific tile specified in the call to
openBytesis read from disk, instead of the entire image being read and then copied
- Zeiss AxioVision ZVI (Zeiss Vision Image)
ensure that the
bitsPerPixelfield is always set to match the final pixel type, and populate any channel colors that were parsed in the metadata. The bits per pixel update should only affectuint16orint16files where the acquisition bit depth is not a multiple of 8, and the RGB channel count is greater than 1
Updated build system:
updated dependency for NetCDF to 4.3.22
updated copyright headers from 2016 to 2017 and reviewed and fixed any incorrect header descriptions
documentation has been migrated to use
.rstfile format for Sphinx filesreviewed and cleaned up warnings such as unused variables and imports
added CellVoyager datasets to automated testing via continuous integration
unified the semantics for creating temporary directories within unit tests
Documentation improvements:
fixed link for PerkinElmer UltraVIEW system
fixed links for NIfTI public specification and data sets
available software for Hamamatsu ndpi has been updated from NDP.view to NDP.view2
5.3.4 (2017 February 21)
Bug fixes:
- ImageJ
fix for a NullPointerException when exporting images that were not opened via the Bio-Formats importer, and thus do not have a complete OMEXMLMetadata store
- Java 1.9
fix compile and runtime errors to enable building with Java 1.9
- ECAT7
update to add support for different versions of ECAT7 files (thanks to Torsten Stöter)
Updated build system:
updated dependency for ome-model in the POM to version 5.4.0. This allows for improved ROI handling by enabling support for Shape objects with Transform attributes. OME-XML schema version remains unchanged as OME schema 2016-06
Documentation improvements:
new public sample files added for ECAT7 (thanks to Torsten Stöter)
new public sample files added for Leica LIF (thanks to Michael Goelzer)
new specification document (Version 3.2) for Leica LIF
updated links to OMERO documentation as a result of decoupling
5.3.3 (2017 February 2)
Bug fixes:
- ImageJ
fix for issue when exporting from an ImagePlus that represents signed data. The pixel type will now remain unchanged as will the pixel values which had previously been scaled incorrectly
- Command line tools
fix for
java.lang.IllegalArgumentExceptionwhen using bfconvert via command line with option set to only convert a single time-point, channel or Z section
- Tiff writing
using TiffWriter to write tiled images now supports the writing of BigTIFF datasets
File format fixes:
- Applied Precision CellWorX
fix to now display the correct plate name and dimensions
- NIFTI
a few fixes for problems with byte alignment when reading non-core metadata from NIFTI headers
- Leica LIF
added support for timestamps of LIF files created with LAS AF 3.1 or newer. In the case of a halted acquisition only non-null timestamps are stored in the OME metadata (thanks to Michael Goelzer)
the physical pixel height and width were incorrectly calculated by dividing by the number of pixels. This has now been corrected to match the official Leica LIF specification documents by dividing by the number of pixels minus one (thanks to Michael Goelzer)
for backwards compatibility an option to preserve pre-5.3.3 physical sizes has been added. This can be set either via command line tools, through the API with the
loci.formats.in.DynamicMetadataOptionsclass, or in the Bio-Formats plugin configuration in ImageJ
- Improvision TIFF
channel colors are now being read and if present set correctly in image metadata
- MetaMorph
fix for
java.lang.OutOfMemoryErrorexceptions when reading large Metamorph TIFF plates
Updated build system:
version history file added to MATLAB bundle as NEWS.rst
increased TiffWriter test coverage
added test coverage framework for command line tools including new ImageConverterTest
Documentation improvements:
improved documentation and new examples for using tiled writing
updated developer documentation for use of Bio-Formats as a Maven, Gradle or Ivy dependency
documentation for Leica LIF bug fixes and use of backward compatibility options
fixes for a number of broken links
5.3.2 (2017 January 9)
Bug fixes:
- ImageJ
fixed race condition when opening multiple series from a dataset, as introduced by thumbnail loading changes in 5.3.0
updated thumbnail generation to be faster for datasets containing an image pyramid
- Metamorph
updated to read the refractive index and set
RefractiveIndexonObjectiveSettingsin the generated OME-XML (thanks to Marc Bruce)
- Metamorph TIFF
fixed Z and channel dimension counts when each channel has a unique Z position
updated to read the emission wavelength and set
EmissionWavelengthonLightSourceSettingsin the generated OME-XML
- QuickTime
fixed incorrect image data when reading of tiles from single channel files
- file grouping
fixed handling of
loci.formats.in.MetadataOptionsobjects by theloci.formats.FileStitcherreader
Documentation improvements:
fixed extensions listed for Zeiss TIFF
simplified markdown for creating tables
5.3.1 (2016 December 19)
File format fixes:
- TIFF
fixed invalid IFD values when writing TIFF or OME-TIFF files with Bio-Formats 5.3.0. This bug affected the writing of TIFF and OME-TIFF via client code using
loci.formats.TiffWriter, converting to a TIFF or OME-TIFF using ‘bfconvert’ command line tool or exporting to TIFF or OME-TIFF using ImageJ/FIJI Bio-Formats exporter.
5.3.0 (2016 December 12)
New features/API:
added support for JPEG-XR compressed CZI data (funded by a partnership between Glencoe Software and ZEISS), adding ‘ome:jxrlib’ as a new dependency of Bio-Formats
- improved tile-based image writing
added new methods to the
loci.formats.IFormatWriterinterface allowing to set and retrieve the tile along the X and Y dimensionsadded default implementations to the
loci.formats.FormatWriterabstract class defaulting to the entire image width/heightadded functionality to
loci.formats.TiffWriteradding support for tiled images writing for TIFF and derived formats like OME-TIFFadded developer documentation and samples for tiled reading/writing
added a new
MetadataOptionsimplementation supporting arbitrary key/value pairsupdated the display command line utility to support passing key/value options using
showinf -optionadded two options to the CZI reader to disable autostitching and exclude pyramid file attachments. Added new checkboxes to the CZI configuration interface of the ImageJ plugin to activate these options
Bug fixes/deprecations:
deprecated
loci.formats.meta.MetadataConverterin favor ofome.xml.meta.MetadataConverterupdated method deprecated in Octave 4.2.0 (thanks to Carnë Draug)
- OME-XML
fixed handling of Mask BinData elements
Component architecture changes/decoupling:
removed formats-common component - now decoupled to the new ome/ome-common-java GitHub repository and consumed as ‘org.openmicroscopy:ome-common’ artifact from Maven Central
removed ome-poi component - now decoupled to the new ome/ome-poi GitHub repository and consumed as ‘org.openmicroscopy:ome-poi’ artifact from Maven Central
removed specification, xsd-fu and ome-xml components - now decoupled to the new ome/ome-model GitHub repository and consumed as ‘org.openmicroscopy:{specification,ome-xml}’ artifacts from Maven Central
removed mdbtools component - now decoupled to the new ome/ome-mdbtools GitHub repository and consumed as ‘org.openmicroscopy:ome-mdbtools’ artifact from Maven Central
removed stubs components - now decoupled to the new ome/ome-stubs GitHub repository and consumed as ‘org.openmicroscopy:{lwf-stubs,mipav-stubs}’ artifacts from Maven Central
removed metakit component - now decoupled to the new ome/ome-metakit GitHub repository and consumed as ‘org.openmicroscopy:metakit’ artifacts from Maven Central
updated developer documentation for the decoupled components
Updated build system:
dropped embedded JARs and now use the Maven Ant Tasks plugin to unify the dependencies using the POM
improved Ant JAR and bundle target
dropped deprecated osgi targets, OME Tools bundle and ome-jxr component
removed PDF generation from the docs-sphinx target
added version number to Javadoc zip bundle name
migrated unit tests out of test-suite into formats-bsd
fixed test-suite targets, paths and symlink handling
fixed test-metadata and migrated it into test-suite
fixed mismatch between
ND2HandlerTestpackage and locationcleaned up test-build to remove obsolete and decoupled components and folders
simplified Travis build
POM repositories clean-up to reduce complexity and use Maven Central as the first location to look for dependencies
now storing all versions in the top-level POM
updated build versioning from Maven by unified versioning strategy, reviewing meta information stored in the manifests of each JAR and introspecting this information in the
FormatToolsAPI to retrieve version and revision numbersupdated developer documentation on updated build system
5.2.4 (2016 October 18)
Java bug fixes:
- OME-TIFF
fixed regression when populating plane metadata
- CZI
populated series metadata with the scene/position information
5.2.3 (2016 October 5)
Java bug fixes:
- CZI
fixed imageCount for RGB images
- ICS writing
fixed ordering of image dimensions
- DeltaVision
fixed reading of large time dimensions
Command-line tools improvements:
bftools.zipnow includes the version history asNEWS.rst(thanks to Gerhard Burger)
Code clean-up/improvements:
switched to String.indexOf(int) in GPL-licensed reader code so that a simpler library method can be used
strings now extended with characters where possible
completed deprecation of DataTools.sanitizeDouble()
deprecated unused OSGi and ome-tools bundle build targets
OME-XML changes/improvements:
bumped schema version number to 2 (schema namespace left unchanged)
added acquisition modes BrightField, SweptFieldConfocal and SPIM
added parsing for Laser Scan Confocal and Swept Field Confocal
Documentation improvements:
documented versioning policy
clarified supported versions for Micro-Manager and Olympus ScanR files
5.2.2 (2016 September 13)
Java bug fixes and improvements:
fixed a regression in which the DataTools number parsing API would not be thread-safe anymore
- InCell
improved handling of Analyzer 2000 datasets to find TIFF files
- FV1000
fixed preview names ordering
- OME-TIFF
enabled all BigTIFF extensions
various code cleanup across the Java code
added test coverage for all example codes in the developer documentations
added tests covering the semantics of the INI parser
ImageJ bug fixes and improvements:
fixed a bug in ImageJ when swapping dimensions of an image with multiple series of different dimensions
added an option to the exporter to pad filename indexes with zeros
Command-line tools improvements:
allowed the binaries to be symlinked (thanks to Gerhard Burger)
added an option to bfconvert to pad filename indexes with zeros
5.2.1 (2016 August 25)
Java bug fixes:
- Zeiss CZI
fixed NumberFormatException when the position object is not null but the values of child are null
- SimplePCI
made IniParser less stringent to allow reading of imperfectly formatted TIFF description headers
fixed stitching of file patterns in ImageJ to remove duplication of directory names in the file path
added an option to bfconvert to allow creation of OME-TIFF without lookup tables
addition of MetadataOnly elements containing no BinData or TiffData now handled via MetadataTools API in ImageInfo
example code in developer docs is now tested via a new Maven module
5.2.0 (2016 August 18)
Java format support improvements are listed below.
†Denotes a major breaking change to the reader (typically modification of core metadata). Code changes or re-import may be necessary in ImageJ/FIJI and OMERO.
added support (and public sample files) for Becker & Hickl .spc FIFO data
added support for Princeton Instruments .spe data
- bug fixes for many formats including:
- CellSens VSI†
fixes for correctly reading dimensions
- FlowSight
fixes to infer channel count from channel names (thanks to Lee Kamentsky)
- Hamamatsu VMS†
fixed dimensions of full-resolution images
- ICS writing
fixed dimension population for split files
- Kodak BIP
fixed handling of CCD temperature stored in hexadecimal
- Leica LIF
fixed incorrect plane offsets for large multi-tile files
- LiFlim
fixed
ExposureTimecheck and units usage
- Micro-Manager
fixed handling of large datasets saved as image stacks and split over multiple files
added user documentation for file saving options
- MRC and Spider
fixed format type checking
- Nifti
fixed
planeSizeto prevent crashes when loading large files (thanks to Christian Niedworok)added support for gzipped compressed .nii.gz files (thanks to Eric Barnhill)
added public samples and updated documented supported file extensions
- OME-TIFF
fixed
Planepopulation errorsfixed
NullPointerExceptionwhen closing reader for partial multi-file filesetsreduced buffer size for
RandomAccessInputStreamsto improve performancedeprecated
getMetadataStoreForConversionandgetMetadataStoreForDisplaymethods
- OME-XML
fixed metadata store
- PicoQuant
updated reader to always buffer data
PNG writing
- SDT
performance improvements for loading of large files
- Slidebook
Slidebook6Reader is now completely external and fully maintained by 3i (see http://www.openmicroscopy.org/info/slidebook) and is specified as such in the
readers.txtconfiguration file
- SVS
fixed
NumberFormatException
- Tiff
fixed integer overflow to read resolutions correctly
fixed handling of tiled images with tile width less than 64
- Zeiss CZI
fixed timestamp indexing when multiple separate channels are present
improved slide support - slides are now detected as a complete full-resolution image (instead of each tile being a separate series) and pyramid sub-resolutions and label/overview images are also detected
- Zeiss LSM
fixed
Planepopulation errors
- Zeiss ZVI†
reworked image ordering calculation to allow for tiles
Top-level Bio-Formats API changes:
Java 1.7 is now the minimum supported version
the native-lib-loader dependency has been bumped to version 2.1.4
the xalan dependency has been bumped to version 2.7.2
all the ome.jxr classes have been deprecated to make clear that there is no JPEG-XR support implemented in Bio-Formats as yet
- the DataTools API has been extended to add a number of utility functions to:
account for decimal separators in different locales
parse a
StringintoDouble,Float,Integeretchandle
NumberFormatExceptionthrown when parsing Unit tests
the Logging API has been updated to respect logging frameworks (log4j/logback) initialized via a binding-specific configuration file and to prevent
DebugTools.enableLogging(String)from overriding initialized logger levels (see Logging for more information)helper methods have been added to FormatTools allowing a stage position to be formatted from an input
Doubleand an input unitthe Formats API has also been updated to add a new validate property to
MetadataOptionsand support forMetadataOptionshas been moved to FormatHandler level to allow it to be used by both Readers and Writersinitial work on Reader discoverability extended the ClassList API to allow the
readers.txtconfiguration file to be annotated using key/value pairs to mark optional Readers and specify additional per-Reader options
Other general improvements include:
improved performance of
getUsedFilesfixes for
FilePatternBlock,AxisGuesser,FilePatternfixes for the detection of CSV pattern blocks by
FilePatternBlockbioformats_package.jarnow includes bio-formats-tools as a dependency soImageConverter,ImageFakerandImageInfoclasses are included in the bundlethe JACE C++ implementation has been decoupled as it does not function with Java 1.8 (see legacy repo)
- ImageJ fixes
to allow reader delegation when a legacy reader is enabled but not working
to allow ROIs to be imported to the ImageJ ROI manager or added to a new overlay
- MATLAB fixes
improved integration with Octave (thanks to Carnë Draug)
added logging initialization
- Command-line tools fixes
upgrade check no longer run when passing -version
common methods refactoring
showinf improvements to preload format
tiffcomment now warns that it requires an ImageDescription tag to be present in the TIFF file
added many automated tests and improved FakeReader testing framework
- documentation improvements include:
clarifying status of legacy Quicktime and ND2 readers
noting that the Gatan reader does not currently support stacks
more Java examples added to the developer documentation
new units page for developers
The Data Model version 2016-06 has been released to introduce Folders, and to simplify both the graphical aspects of the model and code generation. Full details are available in the OME Model and Formats Documentation. OME-XML changes include:
Map is now a complexType rather than an element and MapPairs has been dropped
extended enum metadata has been introduced to better support units
Shape and LightSource are now complexTypes rather than elements
BinData has been added to code generation to handle raw binary data
- various code generation improvements to:
simplify and standardize the generation process
remove a number of hard-coded exceptional cases allowing for easier maintenance and growth
allow for genuine abstract model types and enable C++ model implementation
updated OME-XML and OME-TIFF public sample files
The Bio-Formats C++ native implementation has been decoupled from the Java codebase and will be released as OME-Files C++ from now on, with the exception of OME-XML which is still within Bio-Formats at present (there is a plan to decouple both the Java and the C++ versions of OME-XML in future).
The following components have had their licensing updated to Simplified (2-clause) BSD:
XSL transforms
specification code
xsd-fu Python code
5.1.10 (2016 May 9)
Java bug fixes:
fixed warnings being thrown for ImageJ and other non-FIJI users on Windows (these warnings were triggered by the removal of the 3i Slidebook DLLs from the source code repository in Bio-Formats 5.1.9 and should now only be triggered when opening Slidebook files without the update site enabled - http://www.openmicroscopy.org/info/slidebook)
a fix in the ImageJ plugin for files grouped using the “Dimensions” option
a fix for writing TIFF files in tiles
5.1.9 (2016 April 14)
- Java bug fixes, including:
- SDT
fixed width padding calculation for single-pixel image
- Deltavision
fixed the parsing of the new date format
added support for parsing and storing the working distance in native units
- Micromanager
cleaned up JSON metadata parsing
- Olympus Fluoview
fixed null pointer exceptions while parsing metadata
- Leica LIF
fixed large multi-tiled files from having incorrect plane offsets after the 2GB mark
- EM formats (MRC and Spider)
added native length support for EM readers
- Gatan
fixed erroneous metadata parsing
added support for parsing and storing the physical sizes in native units
- OME-TIFF
improved handling of OME-TIFF multi-file fileset’s with partial metadata blocks
- Nikon ND2
fixed the parsing of emission wavelength
- Olympus CellR (APL)
fixed multiple parsing issues with the mtb file
- SlideBook
removed slidebook dlls from Bio-Formats repository
- Zeiss CZI
fixed parsing of files with multiple mosaics and positions
- Documentation updates, including:
improved documentation for the export of BigTIFFs in ImageJ
- C++:
no changes.
5.1.8 (2016 February 15)
- Java bug fixes, including:
- FEI TIFF
fixed stage position parsing and whitespace handling (thanks to Antoine Vandecreme)
- Pyramid TIFF
fixed tile reading when a cache (.bfmemo) file is present
- MicroManager
updated to parse JSON data from tags 50839 and 51123
fixed to detect
*_metadata.txtfiles in addition tometadata.txtfilesfixed to handle datasets with each stack in a single file
- OME-XML
updated to make .ome.xml an official extension
- OME-TIFF
fixed to ignore invalid BinaryOnly elements
- TIFF
fixed caching of BigTIFF files
- Slidebook
fixed handling of montages in Slidebook6Reader (thanks to Richard Myers)
Performance improvement for writing files to disk (thanks to Stephane Dallongeville)
- Build system
fixed Maven POMs to reduce calls to artifacts.openmicroscopy.org
fixed bioformats_package.jar to include the loci.formats.tools package
- Documentation updates, including:
updated format pages to include links to example data
clarified description of Qu for MATLAB (thanks to Carnë Draug)
added installation instructions for Octave (thanks to Carnë Draug)
- C++:
Bugfixes to the OME-TIFF writer to correct use of the metadata store with multiple series
Ensure file and writer state consistency upon close failure
5.1.7 (2015 December 7)
- Java bug fixes, including:
Prevent physical pixel sizes from being rounded to 0, for all formats
- Metamorph
fixed calculation of Z step size
fixed detection of post-processed dual camera acquisitions (thanks to Mark Kittisopikul)
- OME-XML
fixed XML validation when an ‘xmlns’ value is not present (thanks to Bjoern Thiel)
- MINC
fixed endianness of image data
- Andor/Fluoview TIFF
fixed calculation of Z step size
- MATLAB
improved performance by reducing static classpath checks (thanks to Mark Kittisopikul)
- Gatan
fixed physical size parsing in non-English locales
- Automated testing
fixed handling of non-default physical size and plane position units
- Documentation updates, including:
updated MapAnnotation example to show linkage of annotations to images
- C++:
no changes, released to keep version numbers in sync with Bio-Formats Java
5.1.6 (2015 November 16)
- Java bug fixes, including:
- Updated to use native units for following formats:
IMOD
Analyze
Unisoku
Olympus CellR (APL)
- Metamorph TIFF
fixed handling of multi-line descriptions
added support for dual camera acquisitions
- Zeiss LMS
fixed exception in type detection
- Zeiss CZI
fixed detection of line scan Airyscan data
- Slidebook
fixed calculation of physical Z size
- ImageJ plugins
fixed handling of non-default units
fixed setting of preferences via macros
- Automated testing
fixed handling of non-default units for physical sizes and timings
- C++ changes, including:
allow relocatable installation on Windows
reduce time required for debug builds
- Documentation updates, including:
addition of “Multiple Images” column to the supported formats table
addition of a MapAnnotation example
5.1.5 (2015 October 12)
- Java bug fixes, including:
- ImageJ plugins
fixed use of “Group files…” and “Open files individually” options
fixed placement of ROIs
fixed size of the “About Plugins > Bio-Formats Plugins” window
- xsd-fu (code generation)
removed OMERO-specific logic
- Metamorph
fixed physical Z size calculation
- Gatan DM3/DM4
fixed physical pixel size parsing
- BMP
added support for RLE compression
- DICOM
updated to respect the WINDOW_CENTER tag
fixed image dimensions when multiple sets of width and height values are present
- Fluoview and Andor TIFF
fixed physical Z size calculation
- Imspector OBF
updated to parse OME-XML metadata (thanks to Bjoern Thiel)
- C++ changes:
TIFF strip/tile row and column calulations corrected to compute the correct row and column count
Several compiler warnings removed (false positive warnings in third-party headers disabled, and additional warnings fixed)
It is now possible to build with Boost 1.59 and compile with a C++14 compiler
The source release is now provided in both tar.xz and zip formats
- Documentation updates, including:
- substantial updates to the format pages
improved linking of reader/writer classes to each format page
improved supported metadata pages for each format
updated format page formatting for clarity
added developer documentation for adding and modifying format pages
5.1.4 (2015 September 7)
- Bug fixes, including:
- Command line tools
fixed display of usage information
- Automated testing
fixed problems with symlinked data on Windows
added unit tests for checking physical pixel size creation
- Cellomics
fixed reading of sparse plates
- SlideBook
fixed a few lingering issues with native library packaging
- SimplePCI/HCImage TIFF
fixed bit depth parsing for files from newer versions of HCImage
- SimplePCI/HCImage .cxd
fixed image dimensions to allow for extra padding bytes
- Leica LIF
improved reading of image descriptions
- ICS
fixed to use correct units for timestamps and physical pixel sizes
- MicroManager
fixed to use correct units for timestamps
- Gatan .dm3/.dm4
fixed problems with reading double-precision metadata values
- Hamamatsu NDPI
fixed reading of mask images
- Leica .lei
fixed reading of bit depth and endianness for datasets that were modified after acquisition
- FEI TIFF
updated to read metadata from files produced by FEI Titan systems
- QuickTime
fixed to handle planes with no stored pixels
- Leica .scn
fixed reading of files that contain fewer images than expected
- Zeiss .czi
fixed channel colors when an alpha value is not recorded
fixed handling of pre-stitched image tiles
- SDT
added support for Zip-compressed images
- Nikon .nd2
fixed to read image dimensions from new non-XML metadata
- OME-XML
fixed writing of integer metadata values
- Native C++ updates:
completed support for building on Windows
- Documentation updates, including:
updated instructions for running automated data tests
clarified JVM versions currently supported
5.1.3 (2015 July 21)
- Native C++ updates:
Added cmake superbuild to build core dependencies (zlib, bzip2, png, icu, xerces, boost)
Progress on support for Windows
- Bug fixes, including:
Fixed segfault in the showinf tool used with the C++ bindings
Allow reading from https URLs
- ImageJ
improved performance of displaying ROIs
- Command line tools
fixed bfconvert to correctly create datasets with multiple files
- Metamorph
improved detection of time series
fixed .nd datasets with variable Z and T counts in each channel
fixed .nd datasets that contain invalid TIFF/STK files
fixed dimensions when the number of planes does not match the recorded Z, C, and T sizes
- SlideBook
improved native library detection (thanks to Richard Myers)
- JPEG
fixed decompression of lossless files with multiple channels (thanks to Aaron Avery)
- Imspector OBF
updated to support version 2 files (thanks to Bjoern Thiel)
- Imspector MSR
improved detection of Z stacks
- PerkinElmer Opera Flex
improved handling of multiple acquisitions of the same plate
- Zeiss CZI
fixed error when opening single-file datasets whose names contained “(” and “)”
- TIFF
improved speed of reading files with many tiles
- AVI
updated to read frame index (idx1) tables
- Nikon ND2
fixed channel counts for files with more than 3 channels
- PNG
fixed decoding of interlaced images with a width or height that is not a multiple of 8
- PSD
improved reading of compressed images
- Documentation improvements, including:
updated instructions for writing a new file format reader
updated usage information for command line tools
new Javadocs for the MetadataStore and MetadataRetrieve interfaces
5.1.2 (2015 May 28)
Added OME-TIFF writing support to the native C++ implementation
OME-TIFF export: switch to BigTIFF if .ome.tf2, .ome.tf8, or .ome.btf extensions are used
Improved MATLAB developer documentation
Added SlideBook reader that uses the SDK from 3I (thanks to Richard Myers and 3I - Intelligent Imaging Innovations)
Preliminary work to make MATLAB toolbox work with Octave
- Many bug fixes, including:
- ImageJ
fixed regression in getPlanePosition* macro extension methods
fixed display of composite color virtual stacks
- Nikon ND2
improved parsing of plane position and timestamp data
- TIFF
reduced memory required to read color lookup tables
- Zeiss LSM
improved parsing of 16-bit color lookup tables
- Zeiss CZI
fixed ordering of original metadata table
fixed reading of large pre-stitched tiled images
- AIM
fixed handling of truncated files
- Metamorph/MetaXpress TIFF
improved UIC1 metadata tag parsing
5.1.1 (2015 April 28)
Add TIFF writing support to the native C++ implementation
Fixed remaining functional differences between Windows and Mac/Linux
Improved performance of ImageJ plugin when working with ROIs
TIFF export: switch to BigTIFF if .tf2, .tf8, or .btf extensions are used
- Many bug fixes, including:
fixed upgrade checking to more accurately report when a new version is available
- Zeiss CZI
fixed ordering of multiposition data
improved support for RGB and fused images
- Nikon ND2
improved ordering of multiposition data
- Leica LIF
improved metadata validity checks
improved excitation wavelength detection
- Metamorph STK/TIFF
record lens numerical aperture
fixed millisecond values in timestamps
- Gatan DM3
correctly detect signed pixel data
- Imaris HDF
fix channel count detection
- ICS export
fix writing of files larger than 2GB
5.1.0 (2015 April 2)
Improvements to performance with network file systems
Improvements to developer documentation
Initial version of native C++ implementation
Improved support for opening and saving ROI data with ImageJ
Added support for CellH5 data (thanks to Christoph Sommer)
Added support for Perkin Elmer Nuance data (thanks to Lee Kamentsky)
Added support for Amnis FlowSight data (thanks to Lee Kamentsky and Sebastien Simard)
Added support for Veeco AFM data
Added support for Zeiss .lms data (not to be confused with .lsm)
Added support for I2I data
Added support for writing Vaa3D data (thanks to Brian Long)
Updated to OME schema 2015-01
Update RandomAccessInputStream and RandomAccessOutputStream to read and write bits
- Many bug fixes, including:
- Leica SCN
fix pixel data decompression
fix handling of files with multiple channels
parse magnification and physical pixel size data
- Olympus/CellSens .vsi
more thorough parsing of metadata
improved reading of thumbnails and multi-resolution images
- NDPI
fix reading of files larger than 4GB
parse magnification data
- Zeiss CZI
improve parsing of plane position coordinates
- Inveon
fix reading of files larger than 2 GB
- Nikon ND2
many improvements to dimension detection
many improvements to metadata parsing accuracy
update original metadata table to include PFS data
- Gatan DM3
fix encoding when parsing metadata
fix physical pixel size parsing
- Metamorph
fix off-by-one in metadata parsing
fix number parsing to be independent of the system locale
- JPEG
parse EXIF data, if present (thanks to Paul Van Schayck)
- OME-XML/OME-TIFF
fix handling of missing image data
- PrairieView
improved support for version 5.2 data (thanks to Curtis Rueden)
- DICOM
fix dimensions for multi-file datasets
fix pixel data decoding for files with multiple images
- PNG
reduce memory required to read large images
- Imspector OBF
fix support for version 5 data (thanks to Bjoern Thiel)
- PCORAW
fix reading of files larger than 4 GB
- AIM
fix reading of files larger than 4 GB
- MRC
add support for signed 8-bit data
Fix build errors in MIPAV plugin
- ImageJ
fix export from a script/macro
fix windowless export
allow exporting from any open image window
allow the “Group files with similar names” and “Swap dimensions” options to be used from a script/macro
- bfconvert
fix writing each channel, Z section, and/or timepoint to a separate file
add options for configuring the tile size to be used when saving images
5.0.8 (2015 February 10)
No changes - release to keep version numbers in sync with OMERO
5.0.7 (2015 February 5)
- Several bug fixes, including:
ND filter parsing for DeltaVision
Timepoint count and original metadata parsing for Metamorph
Build issues when Genshi or Git are missing
LZW image decoding
5.0.6 (2014 November 11)
- Several bug fixes, including:
Pixel sign for DICOM images
Image dimensions for Zeiss CZI and Nikon ND2
Support for Leica LIF files produced by LAS AF 4.0 and later
5.0.5 (2014 September 23)
Documentation improvements
Support for non-spectral Prairie 5.2 datasets
5.0.4 (2014 September 3)
Fix compile and runtime errors under Java 1.8
Improvements to Nikon .nd2 metadata parsing
Added support for PicoQuant .bin files (thanks to Ian Munro)
5.0.3 (2014 August 7)
Many bug fixes for Nikon .nd2 files
- Several other bug fixes, including:
LZW image decoding
Stage position parsing for Zeiss CZI
Exposure time units for ScanR
Physical pixel size units for DICOM
NDPI and Zeiss LSM files larger than 4GB
Z and T dimensions for InCell 6000 plates
Export of RGB images in ImageJ
Improved metadata saving in MATLAB functions
5.0.2 (2014 May 28)
Many bug fixes for Zeiss .czi files
- Several other bug fixes, including:
Gatan .dm3 units and step count parsing
Imspector .msr 5D image support
DICOM reading of nested tags
Update native-lib-loader version (to 2.0.1)
Updates and improvements to user documentation
5.0.1 (2014 Apr 7)
Added image pyramid support for CellSens .vsi data
- Several bug fixes, including:
Woolz import into OMERO
Cellomics file name parsing (thanks to Lee Kamentsky)
Olympus FV1000 timestamp support (thanks to Lewis Kraft and Patrick Riley)
(A)PNG large image support
Zeiss .czi dimension detection for SPIM datasets
Performance improvements for Becker & Hickl .sdt file reading (thanks to Ian Munro)
Performance improvements to directory listing over NFS
Update slf4j and logback versions (to 1.7.6 and 1.1.1 respectively)
Update jgoodies-forms version (to 1.7.2)
5.0.0 (2014 Feb 25)
New bundled ‘bioformats_package.jar’ for ImageJ
Now uses logback as the slf4j binding by default
Updated component names, .jar file names, and Maven artifact names
Fixed support for Becker & Hickl .sdt files with multiple blocks
Fixed tiling support for TIFF, Hamamatsu .ndpi, JPEG, and Zeiss .czi files
Improved continuous integration testing
Updated command line documentation
5.0.0-RC1 (2013 Dec 19)
Updated Maven build system and launched new Artifactory repository (http://artifacts.openmicroscopy.org)
- Added support for:
Yokogawa CellVoyager (thanks to Jean-Yves Tinevez)
Woolz (thanks to Bill Hill)
Added support for populating and parsing ModuloAlong{Z, C, T} annotations for FLIM/SPIM data
Updated netCDF and slf4j version requirements - netCDF 4.3.19 and slf4j 1.7.2 are now required
Updated and improved MATLAB users and developers documentation
Many bug fixes including for Nikon ND2, Zeiss CZI, and CellWorX formats
5.0.0-beta1 (2013 June 20)
Updated to 2013-06 OME-XML schema
Improved the performance in tiled formats
Added caching of Reader metadata using https://github.com/EsotericSoftware/kryo
- Added support for:
- Many bug fixes, including:
Add ZEN 2012/Lightsheet support to Zeiss CZI
Improved testing of autogenerated code
Moved OME-XML specification into Bio-Formats repository
4.4.10 (2014 Jan 15)
Bug fixes including CellWorx, Metamorph and Zeiss CZI
Updates to MATLAB documentation
4.4.9 (2013 Oct 16)
Many bug fixes including improvements to support for ND2 format
Java 1.6 is now the minimum supported version; Java 1.5 is no longer supported
4.4.8 (2013 May 2)
No changes - release to keep version numbers in sync with OMERO
4.4.7 (2013 April 25)
Many bug fixes to improve support for more than 20 formats
Improved export to multi-file datasets
Now uses slf4j for logging rather than using log4j directly, enabling other logging implementations to be used, for example when Bio-Formats is used as a component in other software using a different logging system.
4.4.6 (2013 February 11)
Many bug fixes
Further documentation improvements
4.4.5 (2012 November 13)
Restructured and improved documentation
- Many bug fixes, including:
File grouping in many multi-file formats
Maven build fixes
ITK plugin fixes
4.4.4 (2012 September 24)
Many bug fixes
4.4.2 (2012 August 22)
Security fix for OMERO plugins for ImageJ
4.4.1 (2012 July 20)
Fix a bug that prevented BigTIFF files from being read
Fix a bug that prevented PerkinElmer .flex files from importing into OMERO
4.4.0 (2012 July 13)
Many, many bug fixes
- Added support for:
.nd2 files from Nikon Elements version 4
PerkinElmer Operetta data
MJPEG-compressed AVIs
MicroManager datasets with multiple positions
Zeiss CZI data
IMOD data
4.3.3 (2011 October 18)
- Many bug fixes, including:
Speed improvements to HCImage/SimplePCI and Zeiss ZVI files
Reduce memory required by Leica LIF reader
More accurately populate metadata for Prairie TIFF datasets
Various fixes to improve the security of the OMERO plugin for ImageJ
Better dimension detection for Bruker MRI datasets
Better thumbnail generation for histology (SVS, NDPI) datasets
Fix stage position parsing for Metamorph TIFF datasets
Correctly populate the channel name for PerkinElmer Flex files
4.3.2 (2011 September 15)
- Many bug fixes, including:
Better support for Volocity datasets that contain compressed data
More accurate parsing of ICS metadata
More accurate parsing of cellSens .vsi files
- Added support for a few new formats
.inr
Canon DNG
Hitachi S-4800
Kodak .bip
JPX
Volocity Library Clipping (.acff)
Bruker MRI
Updated Zeiss LSM reader to parse application tags
Various performance improvements, particularly for reading/writing TIFFs
Updated OMERO ImageJ plugin to work with OMERO 4.3.x
4.3.1 (2011 July 8)
- Several bug fixes, including:
Fixes for multi-position DeltaVision files
Fixes for MicroManager 1.4 data
Fixes for 12 and 14-bit JPEG-2000 data
Various fixes for reading Volocity .mvd2 datasets
Added various options to the ‘showinf’ and ‘bfconvert’ command line tools
Added better tests for OME-XML backwards compatibility
Added the ability to roughly stitch tiles in a multi-position dataset
4.3.0 (2011 June 14)
- Many bug fixes, including:
Many fixes for reading and writing sub-images
Fixes for stage position parsing in the Zeiss formats
File type detection fixes
Updated JPEG-2000 reading and writing support to be more flexible
- Added support for 9 new formats:
InCell 3000
Trestle
Hamamatsu .ndpi
Hamamatsu VMS
SPIDER
Volocity .mvd2
Olympus SIS TIFF
IMAGIC
cellSens VSI
Updated to 2011-06 OME-XML schema
Minor speed improvements in many formats
Switched version control system from SVN to Git
Moved all Trac tickets into the OME Trac: https://trac.openmicroscopy.org
Improvements to testing frameworks
Added Maven build system as an alternative to the existing Ant build system
Added pre-compiled C++ bindings to the download page
4.2.2 (2010 December 6)
- Several bug fixes, notably:
Metadata parsing fixes for Zeiss LSM, Metamorph STK, and FV1000
Prevented leaked file handles when exporting to TIFF/OME-TIFF
Fixed how BufferedImages are converted to byte arrays
Proper support for OME-XML XML annotations
Added support for SCANCO Medical .aim files
Minor improvements to ImageJ plugins
Added support for reading JPEG-compressed AVI files
4.2.1 (2010 November 12)
Many, many bug fixes
- Added support for 7 new formats:
CellWorX .pnl
ECAT7
Varian FDF
Perkin Elmer Densitometer
FEI TIFF
Compix/SimplePCI TIFF
Nikon Elements TIFF
Updated Zeiss LSM metadata parsing, with generous assistance from Zeiss, FMI, and MPI-CBG
Lots of work to ensure that converted OME-XML validates
Improved file stitching functionality; non-numerical file patterns and limited regular expression-style patterns are now supported
4.2.0 (2010 July 9)
Fixed many, many bugs in all aspects of Bio-Formats
Reworked ImageJ plugins to be more user- and developer-friendly
Added many new unit tests
Added support for approximately 25 new file formats, primarily in the SPM domain
Rewrote underlying I/O infrastructure to be thread-safe and based on Java NIO
Rewrote OME-XML parsing/generation layer; OME-XML 2010-06 is now supported
Improved support for exporting large images
Improved support for exporting to multiple files
Updated logging infrastructure to use slf4j and log4j
4.1.1 (2009 December 3)
Fixed many bugs in popular file format readers
4.1 (2009 October 21):
Fixed many bugs in most file format readers
Significantly improved confocal and HCS metadata parsing
Improved C++ bindings
Eliminated references to Java AWT classes in core Bio-Formats packages
Added support for reading Flex datasets from multiple servers
Improved OME-XML generation; generated OME-XML is now valid
Added support for Olympus ScanR data
Added OSGi information to JARs
Added support for Amira Mesh files
Added support for LI-FLIM files
Added more informative exceptions
Added support for various types of ICS lifetime data
Added support for Nikon EZ-C1 TIFFs
Added support for Maia Scientific MIAS data
4.0.1 (2009 June 1)
Lots of bug fixes in most format readers and writers
Added support for Analyze 7.1 files
Added support for Nifti files
Added support for Cellomics .c01 files
Refactored ImageJ plugins
Bio-Formats, the common package, and the ImageJ plugins now require Java 1.5
Eliminated native library dependency for reading lossless JPEGs
Changed license from GPL v3 or later to GPL v2 or later
Updated Olympus FV1000, Zeiss LSM, Zeiss ZVI and Nikon ND2 readers to parse ROI data
Added option to ImageJ plugin for displaying ROIs parsed from the chosen dataset
Fixed BufferedImage construction for signed data and unsigned int data
4.0.0 (2009 March 3)
Improved OME data model population for Olympus FV1000, Nikon ND2, Metamorph STK, Leica LEI, Leica LIF, InCell 1000 and MicroManager
Added TestNG tests for format writers
Added option to ImageJ plugin to specify custom colors when customizing channels
Added ability to upgrade the ImageJ plugin from within ImageJ
Fixed bugs in Nikon ND2, Leica LIF, BioRad PIC, TIFF, PSD, and OME-TIFF
Fixed bugs in Data Browser and Exporter plugins
Added support for Axon Raw Format (ARF), courtesy of Johannes Schindelin
Added preliminary support for IPLab-Mac file format
2008 December 29
Improved metadata support for DeltaVision, Zeiss LSM, MicroManager, and Leica LEI
Restructured code base/build system to be component-driven
Added support for JPEG and JPEG-2000 codecs within TIFF, OME-TIFF and OME-XML
Added support for 16-bit compressed Flex files
Added support for writing JPEG-2000 files
Added support for Minolta MRW format
Added support for the 2008-09 release of OME-XML
Removed dependency on JMagick
Re-added caching support to data browser plugin
Updated loci.formats.Codec API to be more user-friendly
Expanded loci.formats.MetadataStore API to better represent the OME-XML model
Improved support for Nikon NEF
Improved support for TillVision files
Improved ImageJ import options dialog
Fixed bugs with Zeiss LSM files larger than 4 GB
Fixed minor bugs in most readers
Fixed bugs with exporting from an Image5D window
Fixed several problems with virtual stacks in ImageJ
2008 August 30
Fixed bugs in many file format readers
Fixed several bugs with swapping dimensions
Added support for Olympus CellR/APL files
Added support for MINC MRI files
Added support for Aperio SVS files compressed with JPEG 2000
Added support for writing OME-XML files
Added support for writing APNG files
Added faster LZW codec
Added drag and drop support to ImageJ shortcut window
Re-integrated caching into the data browser plugin
2008 July 1
Fixed bugs in most file format readers
Fixed bugs in OME and OMERO download functionality
Fixed bugs in OME server-side import
Improved metadata storage/retrieval when uploading to and downloading from the OME Perl server
Improved Bio-Formats ImageJ macro extensions
Major updates to MetadataStore API
Updated OME-XML generation to use 2008-02 schema by default
Addressed time and memory performance issues in many readers
Changed license from LGPL to GPL
Added support for the FEI file format
Added support for uncompressed Hamamatsu Aquacosmos NAF files
Added support for Animated PNG files
Added several new options to Bio-Formats ImageJ plugin
Added support for writing ICS files
2008 April 17
Fixed bugs in Slidebook, ND2, FV1000 OIB/OIF, Perkin Elmer, TIFF, Prairie, Openlab, Zeiss LSM, MNG, Molecular Dynamics GEL, and OME-TIFF
Fixed bugs in OME and OMERO download functionality
Fixed bugs in OME server-side import
Fixed bugs in Data Browser
Added support for downloading from OMERO 2.3 servers
Added configuration plugin
Updates to MetadataStore API
Updates to OME-XML generation - 2007-06 schema used by default
Added support for Li-Cor L2D format
Major updates to TestNG testing framework
Added support for writing multi-series OME-TIFF files
Added support for writing BigTIFF files
2008 Feb 12
Fixed bugs in QuickTime, SimplePCI and DICOM
Fixed a bug in channel splitting logic
2008 Feb 8
Many critical bugfixes in format readers and ImageJ plugins
- Newly reborn Data Browser for 5D image visualization
some combinations of import options do not work yet
2008 Feb 1
Fixed bugs in Zeiss LSM, Metamorph STK, FV1000 OIB/OIF, Leica LEI, TIFF, Zeiss ZVI, ICS, Prairie, Openlab LIFF, Gatan, DICOM, QuickTime
Fixed bug in OME-TIFF writer
Major changes to MetadataStore API
Added support for JPEG-compressed TIFF files
- Added basic support for Aperio SVS files
JPEG2000 compression is still not supported
Improved “crop on import” functionality
Improvements to bfconvert and bfview
Improved OME-XML population for several formats
Added support for JPEG2000-compressed DICOM files
EXIF data is now parsed from TIFF files
2007 Dec 28
Fixed bugs in Leica LEI, Leica TCS, SDT, Leica LIF, Visitech, DICOM, Imaris 5.5 (HDF), and Slidebook readers
Better parsing of comments in TIFF files exported from ImageJ
Fixed problem with exporting 48-bit RGB data
Added logic to read multi-series datasets spread across multiple files
Improved channel merging in ImageJ - requires ImageJ 1.39l
Support for hyperstacks and virtual stacks in ImageJ - requires ImageJ 1.39l
Added API for reading directly from a byte array or InputStream
Metadata key/value pairs are now stored in ImageJ’s “Info” property
Improved OMERO download plugin - it is now much faster
Added “open all series” option to ImageJ importer
ND2 reader based on Nikon’s SDK now uses our own native bindings
Fixed metadata saving bug in ImageJ
Added sub-channel labels to ImageJ windows
Major updates to 4D Data Browser
Minor updates to automated testing suite
2007 Dec 1
Updated OME plugin for ImageJ to support downloading from OMERO
Fixed bug with floating point TIFFs
Fixed bugs in Visitech, Zeiss LSM, Imaris 5.5 (HDF)
Added alternate ND2 reader that uses Nikon’s native libraries
Fixed calibration and series name settings in importer
Added basic support for InCell 1000 datasets
2007 Nov 21
Fixed bugs in ND2, Leica LIF, DICOM, Zeiss ZVI, Zeiss LSM, FV1000 OIB, FV1000 OIF, BMP, Evotec Flex, BioRad PIC, Slidebook, TIFF
Added new ImageJ plugins to slice stacks and do “smart” RGB merging
- Added “windowless” importer plugin
uses import parameters from IJ_Prefs.txt, without prompting the user
Improved stack slicing and colorizing logic in importer plugin
- Added support for DICOM files compressed with lossless JPEG
requires native libraries
Fixed bugs with signed pixel data
Added support for Imaris 5.5 (HDF) files
Added 4 channel merging to importer plugin
Added API methods for reading subimages
Major updates to the 4D Data Browser
2007 Oct 17
Critical OME-TIFF bugfixes
Fixed bugs in Leica LIF, Zeiss ZVI, TIFF, DICOM, and AVI readers
Added support for JPEG-compressed ZVI images
Added support for BigTIFF
Added importer plugin option to open each plane in a new window
Added MS Video 1 codec for AVI
2007 Oct 1
Added support for compressed DICOM images
Added support for uncompressed LIM files
Added support for Adobe Photoshop PSD files
Fixed bugs in DICOM, OME-TIFF, Leica LIF, Zeiss ZVI, Visitech, PerkinElmer and Metamorph
Improved indexed color support
Addressed several efficiency issues
Fixed how multiple series are handled in 4D data browser
Added option to reorder stacks in importer plugin
Added option to turn off autoscaling in importer plugin
Additional metadata convenience methods
2007 Sept 11
Major improvements to ND2 support; lossless compression now supported
Support for indexed color images
Added support for Simple-PCI .cxd files
Command-line OME-XML validation
Bugfixes in most readers, especially Zeiss ZVI, Metamorph, PerkinElmer and Leica LEI
Initial version of Bio-Formats macro extensions for ImageJ
2007 Aug 1
Added support for latest version of Leica LIF
Fixed several issues with Leica LIF, Zeiss ZVI
Better metadata mapping for Zeiss ZVI
Added OME-TIFF writer
Added MetadataRetrieve API for retrieving data from a MetadataStore
Miscellaneous bugfixes
2007 July 16
Fixed several issues with ImageJ plugins
Better support for Improvision and Leica TCS TIFF files
Minor improvements to Leica LIF, ICS, QuickTime and Zeiss ZVI readers
Added searchable metadata window to ImageJ importer
2007 July 2
Fixed issues with ND2, Openlab LIFF and Slidebook
Added support for Visitech XYS
Added composite stack support to ImageJ importer
2007 June 18
Fixed issues with ICS, ND2, MicroManager, Leica LEI, and FV1000 OIF
Added support for large (> 2 GB) ND2 files
Added support for new version of ND2
Minor enhancements to ImageJ importer
Implemented more flexible logging
Updated automated testing framework to use TestNG
Added package for caching images produced by Bio-Formats
2007 June 6
Fixed OME upload/download bugs
Fixed issues with ND2, EPS, Leica LIF, and OIF
Added support for Khoros XV
Minor improvements to the importer
2007 May 24
Better Slidebook support
Added support for Quicktime RPZA
Better Leica LIF metadata parsing
Added support for BioRad PIC companion files
Added support for bzip2-compressed files
Improved ImageJ plugins
Native support for FITS and PGM
2007 May 2
Added support for NRRD
Added support for Evotec Flex (requires LuraWave Java SDK with license code)
Added support for gzip-compressed files
Added support for compressed QuickTime headers
Fixed QuickTime Motion JPEG-B support
Fixed some memory issues (repeated small array allocations)
Fixed issues reading large (> 2 GB) files
Removed “ignore color table” logic, and replaced with Leica-specific solution
Added status event reporting to readers
Added API to toggle metadata collection
Support for multiple dimensions rasterized into channels
Deprecated reader and writer methods that accept the ‘id’ parameter
Deprecated IFormatWriter.save in favor of saveImage and saveBytes
Moved dimension swapping and min/max calculation logic to delegates
Separate GUI logic into isolated loci.formats.gui package
Miscellaneous bugfixes and tweaks in most readers and writers
Many other bugfixes and improvements
2007 Mar 16
Fixed calibration bugs in importer plugin
Enhanced metadata support for additional formats
Fixed LSM bug
2007 Mar 7
Added support for Micro-Manager file format
Fixed several bugs – Leica LIF, Leica LEI, ICS, ND2, and others
Enhanced metadata support for several formats
Load series preview thumbnails in the background
Better implementation of openBytes(String, int, byte[]) for most readers
Expanded unit testing framework
2007 Feb 28
Better series preview thumbnails
Fixed bugs with multi-channel Leica LEI
Fixed bugs with “ignore color tables” option in ImageJ plugin
2007 Feb 26
Many bugfixes: Leica LEI, ICS, FV1000 OIB, OME-XML and others
Better metadata parsing for BioRad PIC files
Enhanced API for calculating channel minimum and maximum values
Expanded MetadataStore API to include more semantic types
Added thumbnails to series chooser in ImageJ plugin
Fixed plugins that upload and download from an OME server
2007 Feb 7
Added plugin for downloading images from OME server
Improved HTTP import functionality
Added metadata filtering – unreadable metadata is no longer shown
Better metadata table for multi-series datasets
Added support for calibration information in Gatan DM3
Eliminated need to install JAI Image I/O Tools to read ND2 files
Fixed ZVI bugs: metadata truncation, and other problems
Fixed bugs in Leica LIF: incorrect calibration, first series labeling
Fixed memory bug in Zeiss LSM
Many bugfixes: PerkinElmer, DeltaVision, Leica LEI, LSM, ND2, and others
IFormatReader.close(boolean) method to close files temporarily
Replaced Compression utility class with extensible Compressor interface
Improved testing framework to use .bioformats configuration files
2007 Jan 5
Added support for Prairie TIFF
Fixed bugs in Zeiss LSM, OIB, OIF, and ND2
Improved API for writing files
Added feature to read files over HTTP
Fixed bugs in automated testing framework
Miscellaneous bugfixes
2006 Dec 22
Expanded ImageJ plugin to optionally use Image5D or View5D
Improved support for ND2 and JPEG-2000 files
Added automated testing framework
Fixed bugs in Zeiss ZVI reader
Miscellaneous bugfixes
2006 Nov 30
Added support for ND2/JPEG-2000
Added support for MRC
Added support for MNG
Improved support for floating-point images
Fixed problem with 2-channel Leica LIF data
Minor tweaks and bugfixes in many readers
Improved file stitching logic
Allow ImageJ plugin to be called from a macro
2006 Nov 2
Bugfixes and improvements for Leica LIF, Zeiss LSM, OIF and OIB
Colorize channels when they are split into separate windows
Fixed a bug with 4-channel datasets
2006 Oct 31
Added support for Imaris 5 files
Added support for RGB ICS images
2006 Oct 30
Added support for tiled TIFFs
Fixed bugs in ICS reader
Fixed importer plugin deadlock on some systems
2006 Oct 27
Multi-series support for Slidebook
Added support for Alicona AL3D
Fixed plane ordering issue with FV1000 OIB
Enhanced dimension detection in FV1000 OIF
Added preliminary support for reading NEF images
Added option to ignore color tables
Fixed ImageJ GUI problems
Fixed spatial calibration problem in ImageJ
Fixed some lingering bugs in Zeiss ZVI support
Fixed bugs in OME-XML reader
Tweaked ICS floating-point logic
Fixed memory leaks in all readers
Better file stitching logic
2006 Oct 6
Support for 3i SlideBook format (single series only for now)
Support for 16-bit RGB palette TIFF
Fixed bug preventing import of certain Metamorph STK files
Fixed some bugs in PerkinElmer UltraView support
Fixed some bugs in Leica LEI support
Fixed a bug in Zeiss ZVI support
Fixed bugs in Zeiss LSM support
Fixed a bug causing slow identification of Leica datasets
Fixed bugs in the channel merging logic
Fixed memory leak for OIB format
Better scaling of 48-bit RGB data to 24-bit RGB
Fixed duplicate channels bug in “open each channel in a separate window”
Fixed a bug preventing PICT import into ImageJ
Better integration with HandleExtraFileTypes
Better virtual stack support in Data Browser plugin
Fixed bug in native QuickTime random access
Keep aspect ratio for computed thumbnails
Much faster file stitching logic
2006 Sep 27
PerkinElmer: support for PE UltraView
Openlab LIFF: support for Openlab v5
Leica LEI: bugfixes, and support for multiple series
ZVI, OIB, IPW: more robust handling of these formats (eliminated custom OLE parsing logic in favor of Apache POI)
OIB: better metadata parsing (but maybe still not perfect?)
LSM: fixed a bug preventing import of certain LSMs
Metamorph STK: fixed a bug resulting in duplicate image planes
User interface: use of system look & feel for file chooser dialog when available
Better notification when JAR libraries are missing
2006 Sep 6
Leica LIF: multiple distinct image series within a single file
Zeiss ZVI: fixes and improvements contributed by Michel Boudinot
Zeiss LSM: fixed bugs preventing the import of certain LSM files
TIFF: fixed a bug preventing import of TIFFs created with Bio-Rad software
2006 Mar 31
First release
Reporting a bug
Before filing a bug report
If you think you have found a bug in Bio-Formats, the first thing to do is update your version of Bio-Formats to the latest version to check if the problem has already been addressed. The Fiji updater will automatically do this for you, while in ImageJ you can select .
You can also download the latest version of Bio-Formats from the OME website.
Common issues to check
If you get an error message similar to:
java.lang.UnsupportedClassVersionError: loci/plugins/LociImporter : Unsupported major.minor version 52.0 This plugin requires Java 1.8 or later.
you need to upgrade your system Java version to Java 8 or above, or download a new version of ImageJ/Fiji bundled with Java 8.
If your 12, 14 or 16-bit images look all black when you open them, typically the problem is that the pixel values are very, very small relative to the maximum possible pixel value (4095, 16383, and 65535, respectively), so when displayed the pixels are effectively black. In ImageJ/Fiji, this is fixable by checking the “Autoscale” option; with the command line tools, the “-autoscale -fast” options should work.
If the file is very, very small (4096 bytes) and any exception is generated when reading the file, then make sure it is not a Mac OS X resource fork. The ‘file’ command should tell you:
$ file /path/to/suspicious-file suspicious-file: AppleDouble encoded Macintosh file
If you get an
OutOfMemoryorNegativeArraySizeerror message when attempting to open an SVS or JPEG-2000 file then the amount of pixel data in a single image plane exceeds the amount of memory allocated to the JVM or 2 GB, respectively. For the former, you can increase the amount of memory allocated; in the latter case, you will need to open the image in sections. If you are using Bio-Formats as a library, this means using theopenBytes(int, int, int, int, int)method in loci.formats.IFormatReader. If you are using Bio-Formats within ImageJ, you can use the option.Note that JPEG-2000 is a very efficient compression algorithm - thus the size of the file on disk will be substantially smaller than the amount of memory required to store the uncompressed pixel data. It is not uncommon for a JPEG-2000 or SVS file to occupy less than 200 MB on disk, and yet have over 2 GB of uncompressed pixel data.
Sending a bug report
If you can still reproduce the bug after updating to the latest version of Bio-Formats, and your issue does not relate to anything listed above or noted on the relevant file format page, please send a bug report to the forums. You can upload sample files to Zenodo, or for files over 50 GB, we can provide you with an FTP server address.
To ensure that any inquiries you make are resolved promptly, please include the following information:
Exact error message. Copy and paste any error messages into the text of your email. Alternatively, attach a screenshot of the relevant windows.
Version information. Indicate which release of Bio-Formats, which operating system, and which version of Java you are using.
Non-working data. If possible, please send a non-working file. This helps us ensure that the problem is fixed for next release and will not reappear in later releases. Note that any data provided is used for internal testing only; we do not make images publicly available unless given explicit permission to do so.
Metadata and screenshots. If possible, include any additional information about your data. We are especially interested in the expected dimensions (width, height, number of channels, Z slices, and timepoints). Screenshots of the image being successfully opened in other software are also useful.
Format details. If you are requesting support for a new format, we ask that you send as much data as you have regarding this format (sample files, specifications, vendor/manufacturer information, etc.). This helps us to better support the format and ensures future versions of the format are also supported.
Please be patient - it may be a few days until you receive a response, but we reply to every email inquiry we receive.