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.
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.