I am having some difficulties getting CP to recognize what I would consider to be fairly obvious cells. I am guessing that they are too close together (forming a clump that CP has a hard time separating), but cannot confirm this. As such, I am not entirely sure what to adjust for, since I do not know exactly what CP is having trouble with.
Here attached are a couple images (including a zoom with some of the cells that I am trying to identify) as well as the pipeline I am working with.
So far, the settings I am currently using produce the most accurate counts. I have tried using other declumping options (LoG) but they have not worked as well and for the sake of consistency across images in a same set, I would like to keep per-image analyses (i.e automatically counting different thresholds for each image) low.
Any suggestions as to why these cells are not being counted would be great.
Thank you for any help!
b431PIPE.cp (7.51 KB)