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 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: