Simple Neurite Trace and Sholl analysis

Dear all,
I am trying to use Simple Neurite Trace to measure microglia process total length, totoal area, number of processes and intersections. Raw data is a Z stack individual microglia. I get some results, but the operation interface has some parameters that I do not know what it means, and do not know how to set parameters.

  • What does mean ? What should be based on to set the value, or say that can be the default?

  • What does Fill out mean? Does the result it give exactly total area? How to set threshold value ?

  • When sholl ananlysis for tracing of stack, what is ? I have attached different analysis results of different values.
    The distance value means the distance from the starting point?

I am new to imageJ, thanks for your help.


  1. On Hessian’s Sigma/Multiplier: These define the scale of the structures you want to trace. You can grasp their meaning in an intuitive manner by using the “Pick Sigma Visually” option

  2. On Sholl’s radius step size: See A value of zero, simply means “smallest possible size” (as defined by the voxel dimensions).

  3. In “Distance from (X,Y,Z)”, X,Y,Z refer to the point coordinates you chose as center of analysis

  4. On filling: see (accessed from within SNT: Help>Filling out processes)

Simple Neurite Tracer (SNT), and all the options available in the program can be a bit overwhelming, but the truth is that it is a complex program and you will need to dedicate a bit of your time to read the existing documentation (including the original publication). If something is unclear, do let us know, or better: go ahead and improve it. Any changes on the wiki are always reversible.