catmaid_find_likely_merge: Find the TODO tagged merge sites between a given neuron and...

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

Find the TODO tagged merge sites between a given neuron and the CATMAID database at large

Description

Find the location of tags in a CATMAID neuron, either as URLs to the location of a TODO tag in CATMAID or as a data.frame reporting the location and skeleton treenode locations of specified tags.

Usage

catmaid_find_likely_merge(
  TODO,
  skid = NULL,
  fafbseg = FALSE,
  min_nodes = 2,
  search.range.nm = 1000,
  pid = 1,
  conn = conn,
  ...
)

Arguments

TODO	a data.frame, as returned by catmaid_get_tag with tag = "TODO" (or a different tag indicative of a merge point) and url = FALSE
skid	the skeleton ID of a neuron for which merges are to be found. If NULL, the skeleton ID is taken as the rowname of the TODO data frame
fafbseg	whether or not to use fafbseg::read_brainmaps_meshes on the TODO tag locations and restrict possible merges to neurons within the search range and within the cognate auto-segmented volume
min_nodes	the minimum number of nodes a potential merger skeleton needs to have
search.range.nm	the maximum distance from which to search from the TODO point tag to find potential mergers
pid	project id. Defaults to 1
conn	CATMAID connection object, see ?catmaid::catmaid_login for details
...	methods passed to catmaid::catmaid_fetch

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