I am currently using the simple neurite tracer plugin on Fiji. I have just finished reconstructing about 100 cells and I am now attempting to analyze two sets of said cells in an effort to determine and quantify key differences between them such that they can be distinguished from one another.
To do this I have started with a simple Sholl Analysis in order to get their raw and smooth X and Ys. I would also like to quantify other characteristics about the cells such as total um, branch point # average, average branch point distribution, etc.
If anyone knows how I can do this through Sholl Analysis or perhaps another analysis program/plugin this would be greatly appreciated! Also, any and all other quantification characteristic ideas are always welcome!