I am trying to quantify the number of neurons in different subregions of the hippocampus which is stained by NeuN. I encountered two problems: 1. the contrast is not consistent in my image so the CellProfiler is picking up some background stuffs that are not neurons (like below). 2. I want to count how many neurons in a confined area, not the whole image, how can I draw that out? I tried using ‘IdentifyObjectsManually’ along with ‘IdentifyPrimaryObjects’ but it is not working. Thank you!
I am attaching some of my original images:
[orinigal images removed on request]
The pipelines I am using: NeuN IHC trial 8.12.2019.cppipe (22.4 KB)