Somehow I've come to be known as the tech savvy person in my lab, so they recently threw me into the deep end of the pool on using CellProfiler. For the first project I was successfully able to find and modify a pipeline to fit my needs. I was trying to quantify the area of glucagon in the pancreas, which was as simple as unmixing the stain colors. Then I did the same thing with insulin.
Now I've got a problem. I'm supposed to be finding the number of objects, and the area occupied by lipids in the liver. I thought I could handle it by unmixing colors again, but it's Masson's stain, which I can't seem to get to cooperate. The biggest problem (to me) is that the lipids are identified mostly by the absence of stain. I tried masking the stained area, but that hasn't seemed to work. I tried a custom filter, but couldn't get that to work.
My boss sent me some powerpoint slides with previously analyzed images, thinking it would help me reverse-engineer a pipeline (the original creator of the pipeline is no longer in our lab, and I can't get in touch with them to try and get it). The slides have only confused me more. I can't figure out how they got the binary image, or how they got the "outlines" image to only select the lipid objects, and not the larger objects like blood vessels and the like.
Could someone just give me a nudge in the right direction? I can't figure out what step I'm missing here.