make.anatomical.model: Generate a neuroanatomical alpha shape from connector and/or...

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

Generate a neuroanatomical alpha shape from connector and/or tree node data

Description

implementation of the algorithm for clustering neurons by synapse location from Schlegel et al. (2016). Assumes neurons are scaled to microns.

Usage

make.anatomical.model(
  someneuronlist,
  substrate = c("connectors", "cable", "both"),
  maxdistance = 10000,
  groupsize = 100,
  alpha = 3000,
  auto.selection = T,
  chosen.points = NULL
)

Arguments

someneuronlist	a neuronlist or neuron object
substrate	whether to make the model based off of connectors, neuron cable or both
maxdistance	for automated cluster identification. Maximum distance at which nodes can be part of a cluster
groupsize	an integer number of nearest neighbours to find using nabor::knn()
alpha	a single value or vector of values for α, fed to alphashape3d::ashape3d. Selection is subsequently interactive
auto.selection	whether to try and remove points based on interactively chosen values for 'groupsize' and 'maxdistance'
chosen.points	whether to feed the function pre-chosen points. A matrix for 3D points
selection	whether or not to interactively select values for maxdistance and groupsize.
...	additional arguments passed to methods

Value

An alphashape object

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