index.rst

CellProfiler

CellProfiler—developed by the Broad Institute Imaging Platform—is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. CellProfiler uses Bio-Formats to read images from disk, as well as write movies.

Installation

The CellProfiler distribution comes with Bio-Formats included, so no further installation is necessary.

Upgrading

It should be possible to use a newer version of Bio-Formats by replacing the bundled bioformats_package.jar with a newer version.

• For example, on Mac OS X, Ctrl+click the CellProfiler icon, choose :guilabel:`Show Package Contents`, and replace the following file:
  • :file:`Contents/Resources/bioformats/jars/bioformats_package.jar`

.. seealso::
    `CellProfiler`_
        Website of the CellProfiler software

    :doc:`/developers/python-dev`
        Section of the developer documentation describing the Python wrapper
        for Bio-Formats used by CellProfiler