I’m wracking my head on how to count the nuclei, stained with dapi, that are included in the area of the green stained fibroblast smac+. I have two image for field: one is the dapi image with all the nuclei and the second one is the image with all the fibroblast smac+. I tried to create a pipeline that polish the smac+ image, that is really clumped, and use the polished image as a mask to apply over the image containing all the DAPI nuclei. With this method i managed to select and count only the nuclei that i’m interested in. But… there is always a “but”… The image is so clumped and with cells on different levels that the morph and threshold modules sometimes miss the “lighter” colored cells and, if i try to lower the threshold, cp take in too much “noise”.
fibroblastGREEN-DAPI_counter.cppipe (24.0 KB)
Maybe you can suggest other approach to this counting procedure or help me adjust my pipeline!
Thank You for the help!