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https://github.com/ome/bioformats

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.
https://github.com/ome/bioformats

bio-formats format-converter format-reader image java life-sciences-image lightsheet metadata whole-slide-imaging wsi

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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 

        
# Bio-Formats



[![Actions Status](https://github.com/ome/bioformats/workflows/Ant/badge.svg)](https://github.com/ome/bioformats/actions)

[![Actions Status](https://github.com/ome/bioformats/workflows/Maven/badge.svg)](https://github.com/ome/bioformats/actions)



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](./SUPPORT.md).



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](https://docs.openmicroscopy.org/latest/bio-formats/about/index.html)

for further information.



Supported formats

-----------------



Bio-Formats supports [more than a hundred file

formats](https://docs.openmicroscopy.org/latest/bio-formats/supported-formats.html).



For users

---------



[Many software packages](https://docs.openmicroscopy.org/latest/bio-formats/users/index.html)

use Bio-Formats to read and write microscopy formats.



For developers

--------------



You can use Bio-Formats to easily [support these formats in your software](https://docs.openmicroscopy.org/latest/bio-formats/developers/java-library.html).



More information

----------------



For more information, see the [Bio-Formats web

site](https://www.openmicroscopy.org/bio-formats).



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](https://github.com/ome/bio-formats-documentation/blob/master/sphinx/developers/commit-testing.rst)

   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