sholl_analysis: Perform a Sholl analysis on neuron skeletons

In natverse/nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

Perform a Sholl analysis on neuron skeletons

Description

Functions for Sholl analysis of neuronal skeletons

Usage

sholl_analysis(
  x,
  start = colMeans(xyzmatrix(x)),
  starting.radius = radius.step,
  ending.radius = 1000,
  radius.step = ending.radius/100
)

## S3 method for class 'neuron'
sholl_analysis(
  x,
  start = colMeans(xyzmatrix(x)),
  starting.radius = radius.step,
  ending.radius = 1000,
  radius.step = ending.radius/100
)

## S3 method for class 'neuronlist'
sholl_analysis(
  x,
  start = colMeans(xyzmatrix(x)),
  starting.radius = radius.step,
  ending.radius = 1000,
  radius.step = ending.radius/100
)

Arguments

x	a neuron or neuronlist object
start	the origin from which spheres are grown for the Sholl analysis
starting.radius	the radius of the first sphere. Defaults to the radius step
ending.radius	the radius of the last sphere. If NULL the distance to the furthest dendritic point from the start point is taken
radius.step	the change in radius between successive spheres. Defaults to one 100th of the radius of the ending sphere

Value

a data.frame of spheres radii and the number of dendritic intersections at each radius

Examples

## Not run:  
# Calculate how much some neurons overlap with one another
## Example requires the package nat.flybrains
Cell07PNs_sholl = sholl_analysis(x = Cell07PNs, radius.step = 1, ending.radius = 100)
head(Cell07PNs_sholl[[1]])

## End(Not run) 

natverse/nat documentation built on Feb. 19, 2024, 7:19 a.m.