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CellProfiler

CellProfiler—developed by the Broad Institute‘s 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 loci_tools.jar with a newer version.

  • For example, on Mac OS X, Ctrl+click the CellProfiler icon, choose Show Package Contents, and replace the following files:
    • Contents/Resources/bioformats/loci_tools.jar
    • Contents/Resources/lib/python2.5/bioformats/loci_tools.jar