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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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README.md

Bio-Formats

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.

Purpose

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

About

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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