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.
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 the statement of purpose for a thorough explanation and rationale.
Bio-Formats supports more than a hundred file formats.
Many software packages use Bio-Formats to read and write microscopy formats.
You can use Bio-Formats to easily support these formats in your software.
For more information, see the Bio-Formats web site.
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 toolsAnt targets - verify that the branch compiles using Maven
- verify that the branch does not use syntax or API specific to Java 1.7+
- if you are making any build system or packaging changes, verify that
OMERO builds when the
components/bioformatssubmodule is pointed to your branch - run the unit tests (
ant test) and correct any failures - test at least one file in each affected format, using the
showinfcommand - internal developers only: run the data tests. against directories corresponding to the affected format(s), as well as the test_per_commit directory
- 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