I have been trying to perform a sholl analysis on approximately 40 images, containing roughly 20 microglia per image. I have been trying to do this manually per microglia, but quickly noticed that when you save to a folder, it overwrites the previous .csv table present in the folder (i was hoping it would add onto it).
I have read the FAQ and as many other sources as I could find, but it’s not really clear to me how i’m supposed to be processing multiple microglia in a single image. I have tried drawing all the tracings and focal points (soma) in an image, but then i’m not sure how to make it run sholl analyses on each marked soma point without also calculating intersections for processes/dendrites that don’t belong to that soma.
Some extra info:
I’m doing max intensity projections of Z-stacks, and i’ve been manually drawing the traces along the processes, and using a single focal point to mark the soma (all within the SNT plug-in).
I will have many more images to process, but I only have about 2 months left on my internship.
Thank you very much for reading, I hope you can help me out.