This may be a very simple question, and it might have been answered already, but I’m very new to ImageJ/computer analysis software in general and would appreciate any pointers. I have samples of rat brain tissue that have been prepared through fluorescent in-situ hybridization to tag mRNA. My goal is to create a macro that automatically counts how many particles of tagged mRNA are in each cell of the sample. However, due to staining artifacts and background fuzziness, I am having issues isolating the particles, as well as developing a good way of segmenting the cells from background/each other.
Again, any help is appreciated!