get_connected_skeletons: Retrieving CATMAID neuron skeletons connected to query...

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

Retrieving CATMAID neuron skeletons connected to query skeletons

Description

Gets neurons downstream/upstream of a query set of skeletons from a CATMAID database

Usage

get_connected_skeletons(
  someneuronlist,
  X = c(upper = 1e+08, lower = 0),
  Y = c(upper = 1e+08, lower = 0),
  Z = c(upper = 1e+08, lower = 0),
  min_nodes = 1000,
  max_nodes = NULL,
  min_synapses = 4,
  prepost = NULL,
  soma = T,
  exclude.skids = NULL,
  ...
)

Arguments

someneuronlist	a 3D shape, neuronlist or neuron object that has been plotted in 3D whose coordinates can be accessed with nat::xyzmatrix()
X	The upper and lower bounds for acceptable X coordinates
Y	The upper and lower bounds for acceptable Y coordinates
Z	The upper and lower bounds for acceptable Z coordinates
min_nodes	Minimum number of nodes wanted in returned neuronlist
max_nodes	Maximum number of nodes wanted in returned neuronlist
min_synapses	Minimum number of synapses required from/to any neuron of the query group
prepost	Whether to return downstream neurons (0), upstream neurons (1) or both (NULL)
soma	Whether returned neurons must have a soma or not. Defaults to T.
exclude.skids	skids of neurons
...	additional arguments passed to methods.

Details

CATMAID access required.

Value

A neuronlist object

See Also

skeleton_connectivity_matrix

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