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Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
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dgault Merge pull request #3556 from sbesson/obf_version_metadata
Add OBF file format version and stack version to the global metadata
Latest commit 78ca5df May 15, 2020


Type Name Latest commit message Commit time
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ant Merge remote-tracking branch 'origin/develop' into ome-common_6.0.0-m2 Dec 9, 2018
components Fix version variable name May 8, 2020
config Require a minimum Java version of 1.8 Dec 6, 2018
jar Use file-leak-detector from Maven instead of committed jar Apr 2, 2019
lib Remove libJWlz*.so from the lib/ directory Nov 11, 2013
tools Have ijview suggest HTTPS URL for fetching ImageJ upgrades. Nov 4, 2019
.appveyor.yml ci: appveyor: Test with JDK11 Nov 20, 2018
.classpath-template Remove sphinx documentation Mar 28, 2018
.gitattributes prevent utests/test.mdb from confusing git Apr 14, 2015
.gitignore Speed up TiffSaver.writeImage with bulk array writes Oct 11, 2018
.mailmap Add .mailmap for better "git shortlog" reports Dec 15, 2012
.travis.settings.xml Add deployment mechanism for uploading artifacts to OME Artifactory Oct 4, 2019
.travis.yml Restrict the deployment Oct 4, 2019 Remove sphinx documentation Mar 28, 2018
Dockerfile Use GMT timezone Dec 14, 2017
LICENSE.txt Update project licenses May 15, 2012 Update Travis CI badge Oct 23, 2019 missing full stop Dec 1, 2017
build.xml Remove sphinx documentation Mar 28, 2018
checkstyle.xml Finish fixing header names and documentation links Feb 27, 2014
excludebugs.xml Update findbugs configuration to pick up SBSC_USE_STRINGBUFFER_CONCAT… Nov 14, 2017
pom.xml Bump jxrlib version to 0.2.4 May 11, 2020


Build Status

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.

If you are having an issue with Bio-Formats and need support, please see the support page.


Bio-Formats' primary purpose is to convert proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format. See About Bio-Formats for further information.

Supported formats

Bio-Formats supports more than a hundred file formats.

For users

Many software packages use Bio-Formats to read and write microscopy formats.

For developers

You can use Bio-Formats to easily support these formats in your software.

More information

For more information, see the Bio-Formats web site.

Pull request testing

We welcome pull requests from anyone, but ask that you please verify the following before submitting a pull request:

  • verify that the branch merges cleanly into develop
  • verify that the branch compiles with the clean jars tools Ant targets
  • verify that the branch compiles using Maven
  • verify that the branch does not use syntax or API specific to Java 1.8+
  • run the unit tests (ant test) and correct any failures
  • test at least one file in each affected format, using the showinf command
  • internal developers only: run the data tests against directories corresponding to the affected format(s)
  • make sure that your commits contain the correct authorship information and, if necessary, a signed-off-by line
  • make sure that the commit messages or pull request comment contains sufficient information for the reviewer(s) to understand what problem was fixed and how to test it
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