Hello, I am a student and new to the forum community. I am having some difficulties when it comes to performing Sholl analyses in the Simple Neurite Tracer program. I have traced select astrocytes using an .AVI file of a z-stack I took on a confocal microscope. I have selected the center of analysis by highlighting the first path and using CTRL+SHIFT to follow the path to the desired center of analysis. I then go ahead and use the CTRL+SHIFT+ALT prompt to initialize the Sholl analysis. All the paths traced are selected in the analysis, and I step a radius step size to a desired 3.65 pixels. The analysis runs perfectly fine, however, I am getting variable results (i.e. number of intersections). I have included screenshots to roughly demonstrate my process and the parameters I am setting. Is it an issue of my images having a lot of background that vary from slice to slice in the Z-stack? Is it possible that some of the processes extends tangentially to the sampling circles, making it so that a single process is contributing to multiple intersections? Would anyone have suggestions to help me achieve consistent and accurate measurements?
Thank you kindly,