Anne E. Carpenter, Thouis R. Jones, and the Cimini Lab at the Broad Institute / Whitehead Institute / MIT (released December 2005)
Core Principles & Analysis
Released in December 2005 by Anne Carpenter and Thouis Jones at the Whitehead Institute and MIT (and rewritten from MATLAB into Python in 2010), CellProfiler enables biologists to build reproducible image-analysis pipelines without programming.
Pipelines chain illumination correction, primary nuclear segmentation, secondary cell-body identification, and measurement modules to extract thousands of morphological features (size, shape, texture, intensity, and organelle granularity) per cell.
In morphological profiling assays such as Cell Painting, CellProfiler converts multi-channel fluorescence images from 384- and 1536-well plates into high-dimensional phenotypic fingerprints that cluster drugs by mechanism of action.