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CellProfiler Analyst: data exploration and analysis software for complex image-based screens

Thouis R Jones123, In Han Kang3, Douglas B Wheeler2, Robert A Lindquist2, Adam Papallo12, David M Sabatini24, Polina Golland3 and Anne E Carpenter12*

Author affiliations

1 Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

2 Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA

3 Computer Sciences and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA

4 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA

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Citation and License

BMC Bioinformatics 2008, 9:482  doi:10.1186/1471-2105-9-482

Published: 15 November 2008



Image-based screens can produce hundreds of measured features for each of hundreds of millions of individual cells in a single experiment.


Here, we describe CellProfiler Analyst, open-source software for the interactive exploration and analysis of multidimensional data, particularly data from high-throughput, image-based experiments.


The system enables interactive data exploration for image-based screens and automated scoring of complex phenotypes that require combinations of multiple measured features per cell.