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.


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


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 Show Package Contents, and replace the following file:

    • Contents/Resources/bioformats/jars/bioformats_package.jar

See also


Website of the CellProfiler software

Using Bio-Formats in Python

Section of the developer documentation describing the Python wrapper for Bio-Formats used by CellProfiler