Functions for Sholl analysis of neuronal skeletons

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

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

# S3 method for 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

if (FALSE) { # 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]]) }