Pipeline for stained pon cross section drn counting

Hello everyone,

I am new to CellProfiler and trying to figure out how to count the amount of stained dorsal raphe nucleus (black spot near the cerebral aquaduct) in the image below. I tried the basic pipeline (ColorToGrey and then indentifyprimaryobject to locate the nucleus), yet not very successful (The autofluorescence is a problem, though we already dimmed it as much as possible).

Thanks for all the input in advance!