CellProfiler
============

CellProfiler is a free open-source software for quantitative analysis of biological images. We demonstrate how to integrate CellProfiler and OMERO using the CellProfiler Python API and the OMERO Python API.

For more details, visit the `CellProfiler website <https://cellprofiler.org/>`_.

Follow the instructions in the
:download:`README.md <https://github.com/ome/omero-guide-cellprofiler/blob/master/README.md>` file to run the notebooks either locally or on `mybinder.org <https://mybinder.org/v2/gh/ome/omero-guide-cellprofiler/master?filepath=notebooks>`_.

.. image:: https://mybinder.org/badge_logo.svg
   :target: https://mybinder.org/v2/gh/ome/omero-guide-cellprofiler/master?filepath=notebooks
 
Contents
--------

.. toctree::
   setup
   gettingstarted
   cellprofiler
   :maxdepth: 1


Contribute
----------

Changes to the documentation or the materials should be made directly in the `omero-guide-cellprofiler repository <https://github.com/ome/omero-guide-cellprofiler>`_.