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 -crop is of the format x,y,width,height. The (x, y) coordinate (0, 0) is the upper-left corner of the image; x + width must be less than or equal to the image width and y + height must 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 -fast option 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 -format option is passed, the file will be opened with loci.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.

-

Batch process multiple files reading file names and any additional options line by line from stdin. For every line from stdin showinf is invoked as called from the command prompt, but substituting - with the stdin line.

ls *.tiff | showinf -

Added in version 8.0.0.