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README.md

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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

Website: cellprofiler.org

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). http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html 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)

Requirements

Builds upon CellProfiler dependencies, we need

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

About CellProfiler Analyst

Workflow

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

Wiki

http://cellprofiler.org/wiki/index.php

Forum

CellProfiler Analyst development is discussed on the CellProfiler Forum list.

http://forum.cellprofiler.org/

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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