CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. More information can be found in the CellProfiler Wiki.

We recommend the stable release of CellProfiler.

You can download a stable release for macOS and Windows from the CellProfiler website.

If you’re contributing or planning to contribute to CellProfiler, you should compile CellProfiler from source. Instructions for compiling CellProfiler on Linux, macOS and Windows are available from CellProfiler’s GitHub wiki.

If you’re the maintainer of a third-party CellProfiler module, you should use the nightly release of CellProfiler. You can download a nightly release for macOS and Windows from the CellProfiler website. Let us know if we’ve inadvertently broken your module by submitting a GitHub issue.

If you’re an enthusiastic CellProfiler user, you should try the beta release of CellProfiler. You can download a beta release for macOS and Windows from the CellProfiler website. Let us know if you encounter a bug by submitting a GitHub issue.