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This wiki orients developers to CellProfiler-related resources, the structure of CellProfiler’s code, the details of how modules function, the proper use of settings and their display in the user interface, and how image and object measurements are processed and stored.
Release versions of CellProfiler (including past versions) are available at www.cellprofiler.org.
The source code for the CellProfiler project is hosted in Git repositories administered by GitHub. The code can be checked out from these locations (specific instructions for each OS are found on separate wiki pages, listed to the right):
- CellProfiler: https://github.com/CellProfiler/CellProfiler/
- CellProfiler Analyst: https://github.com/CellProfiler/CellProfiler-Analyst/
- CellProfiler 1.0 (MATLAB, no longer under development): https://github.com/CellProfiler/CellProfiler1.0
- CellProfiler Analyst 1.0 (Java 1.6, no longer under development); formerly located at https://svn.broadinstitute.org/CellProfiler/trunk/oldCPA/
We perform regular builds of our source code for both CellProfiler and CellProfiler Analyst. They are not as heavily vetted as our releases, but are available here.
Most users should use the CellProfiler forum to ask for help and report issues. We monitor the forum and may be able to help you find a workaround for the problem. If you have discovered a new bug, we will take care of filing a bug report on your behalf and include all necessary technical information.
The issue tracker on Github is primarily for developer of CellProfiler and related software. For non-developers, please post questions with attachments on our Forum. Please attach sufficient information to reproduce the bug. For many bugs, it is appropriate to attach a CellProfiler pipeline and an image. Please see the Posting Tips on our Forum for more information.
This page has a detailed discussion of issues and strategies involving integrating CellProfiler into a LIMS or cluster environment. The page also has a list and explanation of the CellProfiler command-line switches that are designed to be used in an integration.