CellProfiler on Windows


I’m using the cellprofiler Devlopper version on Windows (unfortunately) with Matlab 7.0 R14 and noticed the following bug. There are no menus on the main CP window. They actually appear on the first “CP is loading…” window, which then replaced by the main CP window.
Also when I add my own Modules in the Module folder they do not appear in the module list. I tried to duplicate an existing module and rename to make sure that all the proper code was there, but it didn’t help. Is there a list of the available modules that can be editted?
Thanks in advance for your help,


Hi Serge,

This bug is fixed in MatLab 7.1 and is not a problem with CellProfiler.

The code looks for any .m files in the Modules folder, is this where you are keeping your new modules? All of the modules can be edited. Try copying a module with a different name in the Modules folder and see if it appears. Also, notice that there is a line which specifies the category that the module will appear under (File Processing, Measurements etc.), and if it does not fall under any of the specified categories it will appear under “Other” when you go to add the module.

Did this answer your questions?



Hi Mike,

I just started using Cell Profiler Windows developer’s edition. I am experiencing the same problem as reported by Serge (no menu), and I am using Matlab 7.3.

Any idea on that?




Hi Tiao,

We have experienced no problems with missing menu’s using MATLAB 7.3 on windows. I can only suggest removing your copy of CellProfiler, then downloading it fresh and adding the new path to MATLAB.

If you still continue to have this problem with the developer’s version, please post more exact information on the system you are using and I will attempt to re-create the problem.




I downloaded the developer version to a window computer and am experiencing the problem with missing file menus.

My Matlab version is (R2006b)
with the Image toolbox Version 5.3

I’m using window XP professional with the latest updates.

The CellProfiler version is MATLAB_CellProfilerv1.0.4303

I downloaded CP, extracted it then placed the whole folder in
C:\Program Files\MATLAB\R2006b\work\MATLAB_CellProfilerv1.0.4303

I started Matlab and did >>run ‘C:\Program Files\MATLAB\R2006b\work\MATLAB_CellProfilerv1.0.4303\CellProfiler.m’

CP started, but there are no menu options.

Help! Thanks, John


John here again with more information. I removed CP, restarted my computer, downloaded a fresh copy of CP (using firefox), went through the install procedure and still have the missing menus problem. As noted in an earlier post I too see the menus during the CP loading window, but they disappear when the main window loads. You are welcome to call during the work day (pacific time) if you want more information. You have my email address.

thanks, John


Hi John,

This appears to be a problem with R2006b. We are currently using R2006a and having no problems. I will attempt to get MATLAB R2006b and fix this issue. It is possible that this is an error on the MATLAB end, and if that is the case, you may want to try downloading the compiled version to use CellProfiler until MATLAB can fix this bug. I will update you as soon as I know more about what is going on.



I finally recieved MATLAB 2006b, and corrected the issue. I will hopefully release a new version of the software next week with this fix.

Thank you for your patience.