Abstract
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 (Classifier), as well as visualization tools to overview an experiment (Plate Viewer and Image Gallery). Availability and Implementation: CellProfiler Analyst 2.0 is free and open source, available at http://www.cellprofiler.org and from GitHub (https://github.com/CellProfiler/CellProfiler-Analyst) 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@broadinstitute.org Supplementary information: Supplementary data are available at Bioinformatics online.
Highlights
CellProfiler Analyst is open-source software for biological image-based classification, data exploration, and visualization with an interactive user interface designed for biologists and data scientists
Using data from feature extraction software such as CellProfiler (Kamentsky et al 2011), CellProfiler Analyst offers easy-to-use tools for exploration and mining of image data, which is being generated in ever increasing amounts, in high-content screens (HCS)
Some distinctive and critical features of CellProfiler Analyst are its userfriendly object-based machine learning interface, its ability to handle the tremendous scale of HCS experiments, its brushing and gating capabilities that allow observing relationships among different data displays, and its exploration tools which enable interactively viewing connections between cell-level data and well-level data, and among raw images, processed/segmented images, extracted features, and sample metadata
Summary
CellProfiler Analyst is open-source software for biological image-based classification, data exploration, and visualization with an interactive user interface designed for biologists and data scientists. Using data from feature extraction software such as CellProfiler (Kamentsky et al 2011), CellProfiler Analyst offers easy-to-use tools for exploration and mining of image data, which is being generated in ever increasing amounts, in high-content screens (HCS).
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