fafbseg_join_connectors_in_ngl_volumes: Join free connectors in a CATMAID instance to skeletons if...

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

Join free connectors in a CATMAID instance to skeletons if they share a Google Brainmaps volume

Description

Join free connectors (the up or downstream nodes of a connector are joined, but only where this point belongs to a skeleton of 1 node) in a CATMAID instance to skeletons if they share a Google Brainmaps volume

Usage

fafbseg_join_connectors_in_ngl_volumes(
  x,
  direction = c("presynapses", "postsynapses", "both"),
  maybe.connected,
  connector.range.nm = 1000,
  node.match = 5,
  pid = 1,
  conn = NULL,
  ...
)

Arguments

x	a neuronlist object or skeletons IDs / names / annotations that can be read by catmaid::catmaid_skids
direction	whether to seek to assign connectors upstream of neurons specified by maybe.connected, or connections downstream, or both.
maybe.connected	the skeleton IDs for neurons whose connectors (both incoming and outgoing) may be considered
connector.range.nm	the range in nm within which to search for a treenode ID to attach the connector
node.match	number of nodes a neuron from x must have within a brainmaps 3D volume, for the volume to be considered to belong to this neuron
pid	project id. Defaults to 1
conn	CATMAID connection object, see ?catmaid::catmaid_login for details
...	methods passed to catmaid::catmaid_fetch and catmaid::catmaid_get_treenode_detail

Value

makes joins in the specified CATMAID instance, but also returns a list of URLs for the locations at which joins have been made

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