Hello! I’ve been using the count speckles pipeline to count my nuclear foci. I think I’ve gotten it to a point that it is useful but I’m still having problems with how it detects the actual foci. I know it has to do with thresholding and size of the foci but I’ve tried to figure it out by reading all the foci entries and looking at some of your tutorials but I’m still lost.
Here is my pipeline. I haven’t changed much from the original one (although I’ve tested a bunch of different parameters but I got lost, hence why I’m here)
FociTest1.cpproj (598.5 KB)
Here are two of my images
This image should have very few speckles, but I get a massive number. Also, I do not understand what the image below is showing me. I the window named outlined all the speckles and then the one labeled RAD51Foci just the ones that pass the test?
Any help is greatly appreciated! As I said I read most of the other posts that had to do with Foci, but clearly I’m missing something!