Cellprofiler for open source OS



Although cellprofiler is “free and open source”, it seems not to be available for free and open source operating systems. Do you happen to have a linux version of cellprofiler?


Good point! Check the downloads page, we added a Linux version. Let me know if anything doesn’t work right, since it has only been tested on Fedora Core 4.



Wow, that’s quick, thanks! I’m working with Fedora 4, so I’m not going to test it on another linux version for you…

I’ll probably get back to this forum if I managed to install it.



Hm, what’s the “export mcr_path=dirname $0/MCR/v73” doing in the CellProfiler.command? I get this output:

[jos@gillenia CellProfiler]$ CellProfiler.command
libmwlapack: load error: libg2c.so.0: cannot open shared object file: No such fi le or directory
Warning: latest version of matlab app-defaults file not found.
Contact your system administrator to have this file installed.

However, I have libg2c.so.0 somewhere on my system, in the matlab installation. I’m not very familiar with scripting language, so I don’t know what
export mcr_path=dirname $0/MCR/v73
exactly should be doing. In any case, mcr_path doesn’t seem to get exported, because “echo $mcr_path” yields nothing.



Hi Jos,

The command ‘dirname $0’ returns the directory where the program was started from. Doing “echo $mcr_path” will not work in a different terminal window because it is local to the .command terminal. If you put the echo command inside of the CellProfiler.command after the export of mcr_path, it should then show up when you run the program.

Does the folder where CellProfiler is stored have spaces? For example, if it is in “/home/user/Desktop/CellProfiler Folder/” then the command will not work because of the space. If that does not work, put the echo statement after the export mcr_path line and let me know what the output is from the terminal.

You can ignore the app-defaults warning, I get that on our computers too and it runs just fine.



The echo $mgr_path indeeds returns ./MCR/v73 from the script. But CellProfiler can’t find libg2c.so.0 (libmwlapack: load error: libg2c.so.0: cannot open shared object file: No such file or directory). In the meanwhile, I installed matlab, and ran the developers’ version, which works fine. And I also noticed a libg2c.so.0 in the matlab install directory. So I made a symbolic link to the matlab libg2c.so.0 in one of the LD_LIBRARY_PATH dirs mentioned in the CellProfiler.command scripts, and now the binary version works as well. It seems that you forgot to include a libg2c.so.0 copy in the downloadable Linux version.



Interesting, the MCR files are exported by MATLAB. I’ll definitely include that file ASAP.