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Software for exploring and analyzing large, high-dimensional image-derived data.
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CellProfiler Analyst 2.2.0 (Development)

Note: This version is heavily under development and not production-ready yet

Authors: Adam Fraser, Thouis R. Jones, David Dao, Jane Hung

Current Developers: David Dao, Jane Hung


Copyright 2016, The Broad Institute of MIT and Harvard.

Distributed under the BSD license.

Beta Apps

Download current beta of Version 2.2.0 for Mac here: App for Mac OS

Download untested beta of Version 2.2.0 for Windows here: App for Windows

The app requires JDK 1.8 to be installed (not just JRE). Check the Java path.

Please note that CPA 2.2.0 is WIP and we will update the link on regular basis.

For a head start, download example dataset here: Example Dataset for CPA (zipped)


Builds upon CellProfiler dependencies, we need

  • Pandas
  • Seaborn
  • Scikit-learn
  • Javabridge
  • Verlib
  • Python-bioformats

About CellProfiler Analyst


CellProfiler Analyst allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells.

Current Development

  • Restoring visualization functionalities
  • Cleaning up files
  • Improving Evaluation for Classifier
  • Including testing
  • Include documentation
  • Pixel-based Classifier (Deep Learning)
  • Image Gallery
  • Image Classification



CellProfiler Analyst development is discussed on the CellProfiler Forum list.

How to file new issues

Please attach sufficient information to reproduce the bug. For many bugs, it is appropriate to attach a properties file, a training set, or a screenshot.

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