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  • Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research. Designed by and for biologists, CellProfiler equips researchers with powerful computational tools via a well-documented user interface, empowering biologists in all fields to create quantitative, reproducible image analysis workflows. The first version of CellProfiler was introduced in 2005 and published in 2006 [4]. A second major version of CellProfiler, rewritten in Python from its original MATLAB implementation, was published in 2011 [5] and included methods for tracking cells in movies and measuring neurons, worms, and tissue samples. In the CellProfiler 3.0 release, we introduced methods for analyzing 3D images, using deep learning architectures and cloud computing resources, and other improvements to CellProfiler’s usability and capabilities. (B) Evaluation of CellProfiler 3.0 performance in comparison to the MorphoLibJ plugin in Fiji software.
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