Published on Wed Jun 30 2021

CellProfiler 4: Improvements in Speed, Utility and Usability

Stirling, D. R., Swain-Bowden, M. J., Lucas, A. M., Carpenter, A. E., Cimini, B. A., Goodman, A.

CellProfiler is a free, open source image analysis program. It enables researchers to generate modular pipelines with which to process microscopy images. The software has been ported to the Python 3 language.

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Abstract

CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements. Here we describe CellProfiler 4, a new version of this software which has been ported to the Python 3 language. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimisations to reduce the time and cost associated with running common large-scale analysis pipelines. This release will ensure that researchers will have continued access to CellProfilers powerful computational tools in the coming years.