Error message


I keep sending messages, sorry but I keep receiving the following error message:
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: Attempted to access OrigThreshold(1.339e+006); index out of bounds because numel(OrigThreshold)=1. in the IdentifyPrimAutomatic module, which is module #06 in the pipeline.

I managed to attach my pipeline and images this time :smile: I need to count how many nuclei there are with red cytoplasmic marker and in addition how many of those are labelled with a green marker.

I would be grateful if you can help me.

Thanks very much.


2010_Jan_PIPE.mat (1.91 KB)


This is an error that occurs when no objects are found using per-object thresholding. I’ve responded to the underlying issues in this post.