Open-source software for exploring and analyzing large, high-dimensional image-derived data.
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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 complex and subtle phenotypes, for automatic scoring of millions of cells.


Download CellProfiler Analyst for Mac here: App for Mac OS

Download CellProfiler Analyst for Windows here: Exe for Windows

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

Please note that this is the development branch of CPA and it will be updated on regular basis.

Find all releases here.

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

Developer build

Building CPA on your machine requires CellProfiler dependencies. Check the wiki for more detailed installation instructions.

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




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.


David Dao, Adam Fraser, Vebjorn Ljosa, Thouis R. Jones, Jane Hung, Shantanu Singh, Mark Bray, Lee Kamentsky, Anne Carpenter


David Logan, Allen Goodman, Alison Kozol, Mohammad Hossein Rohban

Copyright 2016, The Broad Institute of MIT and Harvard. Distributed under the BSD license.