I’m new to CellProfiler. I know what I want to do but not how to do it. I have fluorescent images of cells I’d like to count and may classify if I could. The issue is that I also have a lot of cellular debris which is the same size, shape, and intensity as my positive cells so I don’t want false positives.
I believe steps are 1) Threshold on the intensity to highlight objects versus the background. I think I’ve gotten this far.
2) Keep a certain size range but exclude anything smaller or larger. I think there is a way to hover over objects in the image to find their size, this would help me figure out the right size range to keep. I haven’t figured out how to do this yet.
3) Set some parameters around shape. Things that are circular are probably what I want but things linear are not. Also things rectangular or triangular are not. Thing that look like a bowling pin or a snowman with a body and a head are. So this is where it gets tricky, how do I keep some non circular things but not others.
Also, if it could keep track of how many were circular vs. bowling pin shaped that would be awesome.
- If I could do the first three steps approximately well then I think I could use analyst to train the system which are the positives and which are the false positives. Or maybe I don’t even have to do the first three steps, maybe I could skip right to the training. But, I haven’t been able to do anything in analyst.
I have images I could post and a pipeline I’ve started, but I’m not seeing how to attach them.
Thanks in advance for your help.