catmaid_update_radius: Update radius information for tree nodes in a CATMAID...

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

Update radius information for tree nodes in a CATMAID instance

Description

Update radius information for tree nodes in a CATMAID instance. A locked neuron cannot be edited until it is unlocked.

Update radius information for skeletons in a CATMAID instance using Peter Li's segmentation of FAFB-v14. Brainmaps API access required

Usage

catmaid_update_radius(tnids, radii, pid = 1, conn = NULL, ...)

fafbseg_update_node_radii(
  x,
  max.dist = 2000,
  method = c("nearest.mesh.point", "ray.cast"),
  pid = 1,
  conn = NULL,
  ...
)

Arguments

tnids	the treenode ids to edit
radii	a vector the same length as tnids, giving the new radius for each treenode id in that vector
pid	project id. Defaults to 1
conn	CATMAID connection object, see ?catmaid::catmaid_login for details
...	methods passed to catmaid::catmaid_fetch
x	the treenode ids to edit
max.dist	the radius is calculated as the mean distance of the nearest 10 mesh vertices for a 3D volume to a each treenode the mesh encompasses. Max.dist sets the maximum distance fro which to search for the ten closest nodes. If exceeded, the radius is set to max.dist.
method	whether to use raycast (casts 10 rays perpendicular to the path of the neuron for each point, slower but more accurate) or the nearest point on the bounding mesh, to estimate node radius

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