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.

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:

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.

  1. 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.
  2. 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.
  3. 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.