create_skeleton_from_nrrd: Create a skeleton from a skeletonised neuron saved as a .Nrrd...

In alexanderbates/catnat: Analyse neuronal morphology and connectivity (extends catmaid and nat)

Create a skeleton from a skeletonised neuron saved as a .Nrrd file

Description

Skeletonise a neuron in Fiji and then use this function to retrieve it as a skeleton

Usage

create_skeleton_from_nrrd(
  files,
  connection.distance = 25,
  k = "all",
  distance.steps = 0.5,
  ...
)

Arguments

files	paths to saved .Nrrd files that have been skeletonised in Fiji
connection.distance	maximal connection distance between points
k	value used in nearest neighbours search to identify close points and draw lines between them
distance.steps	each round of the algorithm connects the closest points to the start point / leaf node, that are within the search range, starting at distance.steps and increasing by this amount to the maximal connection.distance
...	additional arguments passed to methods.

Value

A neuronlist object

alexanderbates/catnat documentation built on Sept. 5, 2023, 4:51 a.m.