Cellprofiler for open source OS

cellprofiler

#1

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?


#2

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.

Regards,
Mike


#3

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.

Jos


#4

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.

Jos


#5

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.

Mike


#6

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.

Jos


#7

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

Thanks,
Mike