I’m new to immunohistochemistry, and I’ve been trying to develop an automated counting system for a group of interneurons within the mouse striatum. In short, I would like to be able to identify the number of neurons within a slice and obtain their xy coordinates.
I have tried a number of online methods on the images I have obtained but none appear to satisfactorily identify all the neurons, or they appear to highlight some of the processes that are also highly stained. Part of the issue is the high background noise that I’ve gotten with the antibody. I’m not very sure what to settings to adjust to make some of the methods found online to work, so any help would be very much appreciated. I would be happy to provide an example image.