I hope someone can help me with a few questions I have about using the Sholl analysis plugin.
I am trying to run the Sholl on 3D reconstructed images of GFAP stained sections. As you see in the image, there is many cells per image, and sometimes they overlap.
Can I run the analysis on images with many cells (can the software distinguish the end of the arbors even if it was overlapping with another cell’s arbors)? Or do I have to use the ROI for each cell and run it separately?
What does the “number of samples” in the settings refer to? Does it refer to the number of cells inside radius?
Can I run multiple cells at the same time using the ROI?
I need help and would really appreciate it!
Thanks in advance,