I am a new user of FIJI, and I am trying to run a Sholl analysis of interneurons in the spinal cord dorsal horn of mice. I have a simple black and white image of the neuron, with no noise in the background, yet whenever I try to run Sholl the program counts an extra line of intersections extending down from the soma.
I’ve tried this with a number of similar images, and on a number of versions of FIJI.
I should also note that I’m using the Sholl Analysis feature built into FIJI (the one listed under “Analysis”- not the separate plugin offered by the Ghosh lab).
Is there any way to get rid of this line so these intersections are not counted in the Sholl Results table?