First of all, thanks for the CellProfiler development team. CellProfiler is a amazing image tool that saves me heaps of time when need to deal with many images.
I am currently trying to differentiate two cell types based on their intensity differences from two channels (i.e. Alexa594 and DAPI) after using certain probes. By using CP, I was able to extract intensity information from each channels for each identified objects in a given image. We could clearly see two populations when plotting MeanIntensity_Alexa594 against MeanIntensity_DAPI (Please see attached scatter plot). May I ask if there is a way to assign different colors to the objects that being classified to either two populations?
I have tried Pair of Measurements within ClassifyObjects, however, 1) the options list there (i.e. Mean, Median and Custom) could not reveal the relationship we observed from the scatterplot. 2) I also got error message “Error while processing ClassifyObjects: boolean index did not match indexed array along dimension 0; dimension is 2271 but corresponding boolean dimension is 2270”.
I attached a sample data and the pipeline. I am running CP 313 on MacOS 10.13.1, java version “1.8.0_152”.
I really appreciate if you may help me for this question.
Archive.zip (3.7 MB)