Problem with Cellprofiler on windows2003 server x64




our IT manager has set up a new terminal server (windows2003 server x64) which we want to use for cellprofiler and cellvisualizer applications.

we have the latest Cellprofiler developers version installed

the server has the latest Matlab version (2007a) 64-bit

now I tried to run an existing cellprofiler pipeline (extracted from a previous output file), but always get the following error with the
IdentifySecondary module:

“undefined function or method ‘IdentifySecPropagateSubfunction’ for input arguments of type ‘double’”

The same pipeline is running smoothely on a 32-bit system (with the same Cellprofiler version, but a 32-bit matlab).

Can you help my with any ideas what the problem could be?

Thanks a lot in advance!



Hi Markus,
Sorry to hear that you are receiving that error in the IdentifySecodary module. Luckily, I happened to be working on preparing our software for a new release. Please check the website soon for the next posting.



Hi Martha,

Thanks for the quick reply. Do I understand you correctly that you know about this issue and are about to fix it for the new release of Cellprofiler?
Would be great!

Can you give me a rough idea about when I can expect the new release?

Best regards,



Hi Markus,
Yes, I am aware of this issue and the new release will be posted in less than 1 week.



A new version of CellProfiler is available and should fix this problem.


Thanks for the notification!

Just noticed that the new developers version-download lacks the Cellprofiler.m file. Should we take the one from the previous version?

Thanks again,


I fixed the problem. Please download a new copy.



I receive the following error running CP devel version on MacOSX:
“undefined function or method ‘IdentifySecPropagateSubfunction’ for input arguments of type ‘double’”

I then tried running the same pipeline using the Mac intel binary install, but IdentifySecondary crashes due to memory errors.
Any suggestions?


If you are using the Matlab version, you may need to compile the mex file. Here is a good reference page: … ial&hs=oow

First, check that the mex setup is correct (mex -setup). Then run :
mex IdentifySecPropagateSubfunction.cpp

This should create the necessary MEX file for your OS. We compile the MEX prior to compiling CellProfiler, so each release version will work with that corresponding OS.

Hope this helps!


Hi Martha,

Thanks for your response. I was wondering if perhaps I have an old version- since many of the files were last modified in Dec 2005?
Anyhow, this did fix the double error, but now I obtain another error in this module (IdentifySecondary)- “Error usig CP threshold. Too many input arguments”.

Further, I still have memory problems.
What is your experience with segmenting dense images with many objects?



We usually experience memory problems if All windows are being displayed. To get around this, you can change your preferences to only display those windows that you choose. However, we do not have memory problems with dense images. How much memory does your computer have?

Which files are you referring to that were modified in Dec 2005? (Depending on what files they are, it might explain the ‘too many input arguements’ error you are referring to.)


I don’t know how, but I must have obtained an old dev version.
I have now installed the latest version (Dec 2007) and am attempting to run the analysis again.
I have set preferences to only display a few windows, but I still get memory errors: “There was a problem running the analysis module IdentifySecondary… Error using sort. Out of memory”.
I am running a tiny subset of the data too- eg I can not get through image 2 of 9.
My machine has 16GB of RAM. I assume that this memory can not be completely utilized by the 32bit versions I am running. I guess that using the Linux 64-bit version will improve this, but I still thought I could manage to process a handful without using a cluster or 64bit version.


Please send me a copy of your pipeline and a sample set of your images to .