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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.
CellProfiler is open-source software helping biologists turn images into cell measurements.
CellProfiler is designed to serve biologists as well as bioimage analysts who want a flexible system that is easy to deploy to collaborators who lack computational skills. It is commonly used for small-scale experiments involving a few images but is also routinely run on millions of images using cluster or cloud computing resources at some of the largest pharmaceutical companies and academic screening centers in the world.
We curate the overwhelming number of computer-vision algorithms to a small number that are robust, powerful, and well-suited to biological problems. We translate computer vision techniques into language familiar to biologists. The software uses a pipeline workflow, with modules that map to biologists’ goals. Once a pipeline is configured, most analyses are fully automated. We focus on components applicable to many biologists’ use cases rather than heavily customized to unique experimental setups. We provide sensible defaults, example pipelines, extensive documentation, and an active Q&A forum to get new users up and running quickly. We enable convenient workflows by making connections with other bioimaging software.
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.