map_fafbsegs_to_neuron: Find out what is already known about a neuron's connectivity...

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

Find out what is already known about a neuron's connectivity profile and connected FAFB segments

Description

Set the local path to the location where you have .zip files of FAFB segmented skeletons. This function also very roughly estimates whether fragment is microtubule containing, what Strahler order it is at, or if it is axonic or dendritic, if the neuron has this marked

Usage

map_fafbsegs_to_neuron(
  someneuronlist,
  node.match = 5,
  return.unmatched = FALSE,
  ...
)

Arguments

someneuronlist	a neuronlist or neuron object
node.match	how many nodes of each neuron in someneuronlist need to be within an auto segmented volume, for it to be said to match. These nodes all need to be consecutive, in the sense that they must be in the same segment or a branch from that segment. i.e. if a neuron matches with a volume 5 times at diverse points across it arbour, this is thought to be a non-match with a large, proximal auto-traced segment.
return.unmatched	defaults to FALSE. If TRUE, then a data frame of unmatched Point Numbers for the neuron in question are returned, and their Strahler order.
...	Additional arguments passed to fafbseg::brainmaps_xyz2id potentiallly including a volume identifier.

Volumes

You can choose which auto-segmentation to use by specifying an optional volume argument, which will be passed to fafbseg::brainmaps_xyz2id. By default the

Examples

## Not run: 
da2=read.neurons.catmaid("glomerulus DA2 right")
fafbseg::with_segmentation("20190805",{
autoseghits=map_fafbsegs_to_neuron(da2)
})
summary(autoseghits)

## End(Not run)

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