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

D. Dao, A. N. Fraser, J. Hung, V. Ljosa, S. Singh, A. E. Carpenter
doi: https://doi.org/10.1101/057976
D. Dao
1Imaging Platform, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 02142
2Department of Informatics, Technical University of Munich, Munich, Bavaria, Germany 80333
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A. N. Fraser
1Imaging Platform, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 02142
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J. Hung
1Imaging Platform, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 02142
4Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 02139
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V. Ljosa
1Imaging Platform, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 02142
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S. Singh
1Imaging Platform, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 02142
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A. E. Carpenter
1Imaging Platform, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 02142
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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 (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 http://www.cellprofiler.org/releases 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{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

Footnotes

  • ↵3 Presently at Boundless.com, Boston, MA

  • ↵5 Presently at Yieldbot, Maynard, MA

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 09, 2016.
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CellProfiler Analyst: interactive data exploration, analysis, and classification of large biological image sets
D. Dao, A. N. Fraser, J. Hung, V. Ljosa, S. Singh, A. E. Carpenter
bioRxiv 057976; doi: https://doi.org/10.1101/057976
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CellProfiler Analyst: interactive data exploration, analysis, and classification of large biological image sets
D. Dao, A. N. Fraser, J. Hung, V. Ljosa, S. Singh, A. E. Carpenter
bioRxiv 057976; doi: https://doi.org/10.1101/057976

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