CellProfiler[1][2] 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.

[6] Specialized modules for illumination correction may be applied as pre-processing step to remove distortions due to uneven lighting.

A wide variety of measurements can be generated for each identified cell or subcellular compartment, including morphology, intensity, and texture among others.

These measurements are accessible by using built-in viewing and plotting data tools, exporting in a comma-delimited spreadsheet format,[9] or importing into a MySQL or SQLite database.

[2] Version 3.0, supporting volumetric analysis of 3D image stacks and optional deep learning modules, was released in October 2017.