I am trying to generate a pipeline that select the cells with high cytosolic staining specifically and then measure those cells’ nucleus and cytosolic signal intensity.
Since not all the cells have the cytosolic marker or not even signal intensity, I have tried to “Threshold” the signal followed by IdentifyPimaryObjectes with the Hole filled option checked in hoping to identify the cytosolic marker positive cells then we could identifysecondaryobject. Somehow my pipeline could not capture the cytosolic marker positive cells easily…
Here are several representative pics: https://www.dropbox.com/sh/gobhaxe1wn1wb3w/AAB4UPoDuqHJarx8o8c3LS82a?dl=0
in which green is the cytosolic marker, blue is dapi, and red is another nucleus staining.
I am wondering if my algorithm design is correct or not or is there any better way to do this?