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CellProfiler is open-source cellular image analysis software.

Octocat-spinner-32 BatchProfiler issue #37 use HDF5Dict directly to speed things up February 28, 2014
Octocat-spinner-32 bioformats ImageReader has changed a bit, for the better, but it broke some test… March 19, 2014
Octocat-spinner-32 cellprofiler issue #1109 store Kalman features as floats April 17, 2014
Octocat-spinner-32 contrib Updated Bio-Formats web URLs March 07, 2014
Octocat-spinner-32 imagej issue #1082 standardize versioning using the scijava POM. Got rid of … March 19, 2014
Octocat-spinner-32 java issue #1082 standardize versioning using the scijava POM. Got rid of … March 19, 2014
Octocat-spinner-32 jenkins Build and continuous integration (jenkins) for Linux March 27, 2014
Octocat-spinner-32 killjavabridge Happy new year January 24, 2014
Octocat-spinner-32 plugins Happy new year January 24, 2014
Octocat-spinner-32 shortcuts Automatic Linux builds using Jenkins August 30, 2013
Octocat-spinner-32 tutorial Added slide on tools, hide more complex examples May 24, 2013
Octocat-spinner-32 .gitattributes Developer tutorial March 08, 2013
Octocat-spinner-32 .gitignore .DS_Store banished! January 08, 2014
Octocat-spinner-32 COPYING License clarifications August 29, 2011
Octocat-spinner-32 CPy.py Happy new year January 24, 2014
Octocat-spinner-32 CellProfiler.iss issue #1061 delete JAR files when installing over pre-existing Window… March 28, 2014
Octocat-spinner-32 CellProfiler.py issue #989: twas pyreadline spewing all over everything March 21, 2014
Octocat-spinner-32 CellProfiler64.iss issue #1061 delete JAR files when installing over pre-existing Window… March 28, 2014
Octocat-spinner-32 CellProfilerIcon.icns missing items March 16, 2010
Octocat-spinner-32 CellProfilerIcon.ico separate 1.0 and 2.0 March 01, 2010
Octocat-spinner-32 CellProfilerIcon.png Fixed crlf and file mode issues (hopefully) January 23, 2013
Octocat-spinner-32 CellProfilerIcon_old.png Fixed crlf and file mode issues (hopefully) January 23, 2013
Octocat-spinner-32 CellProfiler_python.bat separate 1.0 and 2.0 March 01, 2010
Octocat-spinner-32 CellProfiler_python.command Fixed crlf and file mode issues (hopefully) January 23, 2013
Octocat-spinner-32 Cloning_in_git.txt Test April 13, 2012
Octocat-spinner-32 LICENSE Happy new year January 24, 2014
Octocat-spinner-32 Makefile.CP2 more copyright January 24, 2014
Octocat-spinner-32 Makefile.CP2.32 more copyright January 24, 2014
Octocat-spinner-32 Makefile.CP2.64 more copyright January 24, 2014
Octocat-spinner-32 Makefile.CP2.centos5.64 more copyright January 24, 2014
Octocat-spinner-32 Makefile.CP2.standard.64 more copyright January 24, 2014
Octocat-spinner-32 Makefile.CP2.standard.64.repoqt more copyright January 24, 2014
Octocat-spinner-32 Makefile.CP2.suse.64 more copyright January 24, 2014
Octocat-spinner-32 Makefile.CP2.ubuntu.64 more copyright January 24, 2014
Octocat-spinner-32 README.md Pointing to the wiki more December 05, 2013
Octocat-spinner-32 TestNewBatch.py Happy new year January 24, 2014
Octocat-spinner-32 cp_logo_small.png separate 1.0 and 2.0 March 01, 2010
Octocat-spinner-32 cpnose.py Happy new year January 24, 2014
Octocat-spinner-32 decorator.py Fixed crlf and file mode issues (hopefully) January 23, 2013
Octocat-spinner-32 external_dependencies.py Upgraded to Bio-Formats 5.0.0.rc4 and ImageJ Beta7.7 in order to supp… March 18, 2014
Octocat-spinner-32 install.py Happy new year January 24, 2014
Octocat-spinner-32 python-2.6.sh issue #1063 clear the pythonpath in the python-2.6.sh script March 03, 2014
Octocat-spinner-32 python-centos.sh Fixed crlf and file mode issues (hopefully) January 23, 2013
Octocat-spinner-32 requirements.txt Linux build October 09, 2013
Octocat-spinner-32 setup.py Happy new year January 24, 2014
Octocat-spinner-32 usr-bin-cellprofiler Linux: Don't change directory before starting CellProfiler. December 06, 2013
Octocat-spinner-32 windows_setup.py Happy new year January 24, 2014
README.md

CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

Our website, cellprofiler.org, is aimed at non-developer users and has lots of information about CellProfiler and how to use it.

The developer wiki covers topic such as how to build CellProfiler from source, how to set up a development environment with all of CellProfiler's dependencies, and the various resources set up to support CellProfiler development.

How to file new issues

If you have a bug or other issue to report, please read the wiki page on how to file new issues to learn the best way to report it.

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