Hello Cellprofiler team,
I have several pictures with cells that have their nuclei labeled with DAPI, the cytoplasm with a different dye (Qdots) and another dye (Alexa 488) is present in some spots inside the nuclei. And I’m trying to get a pipeline which is capable of counting: number of labeled cells, number of labeled cells that contain the Alexa and number of unlabelled cells that also contain the Alexa. I’m not sure how to interpret the results given in the Default excel file, because I think it’s saying there are a lot of Alexa spots (much more than nuclei) and I would like it to associate the Alexa to the respective nuclei.
I also saw that in a simple pipeline (Load images, Resize, IDprimaryautomatic, ID secondary and Export to excel) just to count the number of labelled cells, the final results are always as many labeled cells as the number of nuclei when it was supposed to decrease in time.
I send two links for the folders with pictures and pipelines of both cases I referred here. I hope that you can take a look and find what I’m doing wrong. The first link is for the first decribed pipeline (three labels).
Thanks in advance!