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

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