CellProfiler Analyst: interactive data exploration, analysis, and classification of large biological image sets

Summary CellProfiler Analyst allows the exploration and visualization of image-based data, together with the classification of complex biological phenotypes, via an interactive user interface designed for biologists and data scientists. CellProfiler Analyst 2.0, completely rewritten in Python, builds on these features and adds enhanced supervised machine learning capabilities (in Classifier), as well as visualization tools to overview an experiment (Plate Viewer and Image Gallery). Availability CellProfiler Analyst 2.0 is free and open source, available at and from GitHub () under the BSD license. It is available as a packaged application for Mac OS X and Microsoft Windows and can be compiled for Linux. We implemented an automatic build process that supports nightly updates and regular release cycles for the software. Contact anne{at}broadinstitute.org Supplementary information Supplementary Text 1: Manual to CellProfiler Analyst; updated versions are available at CellProfiler.org/CPA Supplementary Data 1: Benchmarking performance of classifiers in CPA 2.0 versus CPA 1.0