CellProfiler on Linux


I have tried to run Cell Profiler on both Ubuntu 9.04 and Fedora 11 (both 32-bit) without success. I’m using the 32-bit compiled version of CellProfiler. The error I’m seeing is shown below.

If anyone else has managed to get it running then your help would be much appreciated!



[mwoodbri@localhost CompiledCellProfiler_Linux32_7522]$ ./run_CellProfiler.sh …/MATLAB_Compiler_Runtime/v78

Setting up environment variables

LD_LIBRARY_PATH is .:…/MATLAB_Compiler_Runtime/v78/runtime/glnx86:…/MATLAB_Compiler_Runtime/v78/bin/glnx86:…/MATLAB_Compiler_Runtime/v78/sys/os/glnx86:…/MATLAB_Compiler_Runtime/v78/sys/java/jre/glnx86/jre/lib/i386/native_threads:…/MATLAB_Compiler_Runtime/v78/sys/java/jre/glnx86/jre/lib/i386/server:…/MATLAB_Compiler_Runtime/v78/sys/java/jre/glnx86/jre/lib/i386/client:…/MATLAB_Compiler_Runtime/v78/sys/java/jre/glnx86/jre/lib/i386
./CellProfiler: symbol lookup error: ./CellProfiler: undefined symbol: mclSetCmdLineUserData_proxy

Hi Mark,

Sorry for the late reply, but I’m not sure what the solution is. We don’t have ready access to a 32-bit Linux machine, and had to ask around even to get access to the one we compiled this on. I suspect it’s a distribution-specific problem, but I’m not sure even what distribution it was compiled on. We also had to compile with Matlab 2008b (vs 2008a for all other of the latest release), which was the only one available on that machine. Have you had any breakthroughs?


Actually, it looks like you’re using the wrong MCR. You need MCR version 7.9, which is the Matlab 2008b version (since that’s what we compiled with). In your path it says v78. Try downloading the MCR on cellprofiler.org next to 32-bit Linux.

Let us know how it goes.

Thanks David. I have just checked and the 32-bit Linux MCR on cellprofiler.org is v78, so that’s probably the problem. Do you know of anywhere I can get v79?

I’ve managed to get hold of v710 and it works fine. Thanks again for your help.


I too want to use CellProfiler on a 32-bit pentium system running Fedora Core 11. I had no luck when I was trying with the MCR that downloads from the link on your download page (MCRInstaller- GNU Linux 32-bit). Then I found this post.

Can you please make available the proper MCR installer for 32-bit systems running linux?


The download link was indeed incorrect. I have corrected it and the 32-bit Linux MCR on cellprofiler.org site is v79 now.
Apologies for the delay!