We are now distributing CellProfiler 2.0,
rewritten in Python and backwards-compatible
with CP 1.0 pipelines. See the new features and known issues.)
CellProfiler 1.0 (the MATLAB version) will no longer be actively developed, though we may fix bugs.
Download CellProfiler 2.0 DMG for Mac (r10211)
(then open the DMG, copy CellProfiler.app to the Applications folder)
Download CellProfiler 2.0 EXE for 32-bit Windows (r10211)
(then run the EXE and follow the prompts)
Download CellProfiler 2.0 EXE for 64-bit Windows (r10211)
(then run the EXE and follow the prompts)
You can contact us for advice on running
CellProfiler on Linux or on a cluster,
or consult the developers' wiki.
CellProfiler 2.0 Manual
Windows XP 32-bit (r9717) (MCRInstaller for XP32)
Windows XP 64-bit (r9717) (MCRInstaller for XP64)
Windows Vista 32-bit (r9717) (MCRInstaller for Vista32)
Windows Vista 64-bit (r9717) (MCRInstaller for Vista64)
Intel Macintosh OS X 10.4+ 32/64-bit (r9717) (MCRInstaller Intel32.dmg)
PowerPC Mac (Note: r5811) (MCR 7.6 is bundled with CP)
Linux 64-bit (r9717) (MCRInstaller for GNU Linux 64-bit)
Linux 32-bit (r9717) (MCRInstaller for GNU Linux 32-bit)
CPCluster: CellProfiler for cluster computing
Linux 64-bit (MCRInstaller for GNU Linux 64-bit)
Matlab Source (Requires MATLAB R2009+)
CellProfiler 1.0 Manual
CellProfiler 1.0 Installation Instructions
Source Code
The following are links to our SVN repositories where you can get the most current version of the source code and accompanying files.
- CellProfiler 2.0 (Python 2.5): https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/
- CellProfiler 1.0 (Matlab, no longer under development): https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler_old_matlab/
