I am a new user of the CellProfiler. I am trying to use it to quantify the membrane staining intensity and the intensity ratio of membrane vs cytoplasm. But as I run the pipeline, I got two problems.
First, let me describe my pipeline. Load the images; IndentifyPrimAutomatic(which is Nuclear); Identify Secondary(the whole cell); ExpandOrShrink(I shrunken 1 pixel from the secondary(which is the whole cell) and defined the shrunken object as Cytoplasm; IdentifyTertiarySubregion(the larger object is the whole cell, the smaller object is Cytoplasm and the subregion is defined as membrane); MeasureObjectIntensity(measure the whole cell, Cytoplasm and membrane). When I use this pipeline to run a test on one image, it worked fine. But even through the IntegratedIntensity is different from the three measurement, the MeanIntensity is the same. This is my first question. Why I got the same MeanIntensity over the three measurements?
After I tested the pipeline, I run this pipeline with more images. I got the second problem here. At the cycle 2, the Cytoplasm measurement couldn’t run through because of an error. Matlab says the error is: subscripted assignment dimension mismatch in the MeasureObjectIntensity module. The problem only accures with the cytoplasm measurement. If I take the Cytoplasm Measurement of from the module, pipeline runs through fine. Could you please help me with that problem as well? How can I solve this problem?

Thanks for your help.



I will contact you through e-mail. Please send your image and pipeline and I will take a look.