SNT Sholl Analysis Annotations

image

I have been using the sholl analysis function of the simple neurite tracer plugin on 2D images of neurons. I use the color coded paths annotation with 16_colors LUT. I assume the color coding deals with number of intersections within a particular radius, but I cannot find the specifics. Does each color correspond to a particular number or range of intersections? Is there some other formula to determine the color coding of each path? Thanks!

Welcome to the forum @mscott!

The color coding will map the first entry in the lookup table to the lowest intersection count in the profile (typically 0 when parsing images directly, or 1 when parsing reconstructions), and the highest count to the last entry in the LUT. Mapping is linear. More details here: https://imagej.net/Sholl#Output_Options.

As a side note: color coding makes more sense with perceptually uniform lookup tables. See this example of a toy neuron mapped with the 16_colors and mpl-viiridis. With the former, the hue transitions from e.g., red>magenta>pink are quite confusing and contradict the expectation that warmer hues would reflect higher values.