Julien, I think this may be the bug reported here: github.com/CellProfiler/CellProfiler/issues/879. If you could reproduce the bug, click the “details” button in the error report and copy the stack trace, that would be helpful. Also, if you could report your matplotlib version number, that would be helpful:
There’s a bug in the recently-released Matplotlib 1.3.0 that causes this problem. You can either hand-edit matplotlib as described in issue #879 or upgrade to 1.3.1 if it turns out you are running 1.3.0.
Another possibility is that it’s similar to a problematic interaction between Ubuntu and Eclipse: bugs.eclipse.org/bugs/show_bug.cgi?id=330563
The suggested work-around is to set the environment variable, “UBUNTU_MENUPROXY=0”. If this works for you, please tell me and I will have CellProfiler internally set this before it starts the GUI.
If neither of these work, I’d be glad to assist further. We’ve opened up an issue (github.com/CellProfiler/CellProfiler/issues/885) for you. If you can continue the thread there, I’ll notice it sooner and respond more quickly.