IdentifySecondary Error


So I’m getting an IdentifySecondary -> Propagate MatLab error using R2011a, and after reading this post: … 371&p=1238

I’m thinking it’s because IdentifySecondary Propagate is a subfunction that was specific to R2007a. The above post seems to give instructions as to how one could compile CP to run on a cluster and overcome this problem, but I’m having an issue applying this to my personal computer, which is a MacBook.

Is there a way to make this function work?

Thanks a heap!


Hi Erin,

Could you mind posting what the error message is? Also, you may want to consider upgrading to CellProfiler 2.0, since we fully support the newer software and also it is highly likely that you will not encounter this problem (unless you’ve done so and run into an issue of some kind?)


See if this discussion about compiling certain functions helps:


Thanks for the reply guys, the error message is:

There was a problem running the image analysis. Sorry, it is unclear what the problem is. It would be wise to close the entire CellProfiler program in case something strange has happened to the settings. The output file may be unreliable as well. Matlab says the error is: Undefined function or method ‘IdentifySecPropagateSubfunction’ for input arguments of type ‘double’. in the IdentifySecondary module, which is module #46 in the pipeline.

IdentifySecondary in /Applications/CellProfiler/Modules/IdentifySecondary.m (376)
AnalyzeImagesButton_Callback in /Applications/CellProfiler/CellProfiler.m (4298)
gui_mainfcn in /Applications/CellProfiler/CellProfiler.m (6055)
CellProfiler in /Applications/CellProfiler/CellProfiler.m (55)

Also, I do have CP 2.0 on my computer, but for this specific task, I’m continuing that was started using CP 1.0, and I’d like to finish it using the same pipeline.

David, I’ll try to compile it, and see how it goes - Thanks!


It may not be sufficient, but the error sounds familiar and indicates that compiling this subfunction is necessary.