CellProfiler/python-bioformats

Read and write life sciences file formats

Python

144

124 commits

updated Oct 3, 2026

See the code

README

NOTE: We have not archived this repository to allow us to make rare, mandatory updates for our own internal use, however it is not actively maintained and should be considered archived. You may be interested in scyjava instead: https://github.com/scijava/scyjava.

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

Python-bioformats is a Python wrapper for Bio-Formats, a standalone
Java library for reading and writing life sciences image file
formats. Bio-Formats is capable of parsing both pixels and metadata
for a large number of formats, as well as writing to several
formats. Python-bioformats uses the python-javabridge to start a Java
virtual machine from Python and interact with it. Python-bioformats
was developed for and is used by the cell image analysis software
CellProfiler (cellprofiler.org).  While we are gratified that others
outside the CellProfiler team find it useful, we maintain python-bioformats
essentially for the CellProfiler project and **cannot guarantee support 
for other users.** Please consider visiting our forum at forum.image.sc 
for additional support help.

PyPI record: https://pypi.python.org/pypi/python-bioformats

Documentation: http://pythonhosted.org/python-bioformats/

GitHub repository: https://github.com/CellProfiler/python-bioformats

Report bugs here: https://github.com/CellProfiler/python-bioformats/issues

python-bioformats is licensed under the GNU General Public License
(GPL).  Many files are licensed under the more permissive BSD license.
See the accompanying files COPYING and LICENSE for details.

Copyright (c) 2009-2021 Broad Institute. All rights reserved.


.. |Travis CI Status| image:: https://travis-ci.org/CellProfiler/python-bioformats.svg?branch=master
   :target: https://travis-ci.org/CellProfiler/python-bioformats

Not written in Markdown, so it's shown here as plain text — view it formatted on GitHub.

CellProfiler/python-bioformats

Read and write life sciences file formats

Python

144

124 commits

updated Oct 3, 2026

See the code

README

NOTE: We have not archived this repository to allow us to make rare, mandatory updates for our own internal use, however it is not actively maintained and should be considered archived. You may be interested in scyjava instead: https://github.com/scijava/scyjava.

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

Python-bioformats is a Python wrapper for Bio-Formats, a standalone
Java library for reading and writing life sciences image file
formats. Bio-Formats is capable of parsing both pixels and metadata
for a large number of formats, as well as writing to several
formats. Python-bioformats uses the python-javabridge to start a Java
virtual machine from Python and interact with it. Python-bioformats
was developed for and is used by the cell image analysis software
CellProfiler (cellprofiler.org).  While we are gratified that others
outside the CellProfiler team find it useful, we maintain python-bioformats
essentially for the CellProfiler project and **cannot guarantee support 
for other users.** Please consider visiting our forum at forum.image.sc 
for additional support help.

PyPI record: https://pypi.python.org/pypi/python-bioformats

Documentation: http://pythonhosted.org/python-bioformats/

GitHub repository: https://github.com/CellProfiler/python-bioformats

Report bugs here: https://github.com/CellProfiler/python-bioformats/issues

python-bioformats is licensed under the GNU General Public License
(GPL).  Many files are licensed under the more permissive BSD license.
See the accompanying files COPYING and LICENSE for details.

Copyright (c) 2009-2021 Broad Institute. All rights reserved.


.. |Travis CI Status| image:: https://travis-ci.org/CellProfiler/python-bioformats.svg?branch=master
   :target: https://travis-ci.org/CellProfiler/python-bioformats

Not written in Markdown, so it's shown here as plain text — view it formatted on GitHub.

Project health

Overall

1.9/10

Maintained

1/10

Code review

0/10
OpenSSF Scorecard

Latest release

4.1.0 · Sep 13, 2024

Releases this year

0

Significant stargazers

Laura Luebbert, Ph.D.

146 followers · starred Nov 2020