fafb_segs_stitch_volumes: Get neuron volumes and stitch them into a cohesive neuron, or...

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

Get neuron volumes and stitch them into a cohesive neuron, or neuronal compartment

Description

Stitch together volumes for a single neuron, based on the Google FAFB segmentation by Peter Li. If the neuron given has its microtubules marked (catnat::mark.microtubules), Strahler orders (catnat::assign_strahler) or axon/dendrite (catnat::flow.centrality) then this information can be used to estimate a volume that over these neuronal sub-compartments.

Visualise neuron meshes or point clouds, retrieved and downsampled from the Google brainmaps segmentation by Peter Li.

Usage

fafb_segs_stitch_volumes(
  neuron,
  volumes = NULL,
  map = TRUE,
  voxelSize = 50,
  downsample.factor = 12,
  downsample.volumes = TRUE,
  soma = TRUE,
  node.match = 4,
  smooth = FALSE,
  resample.neuron = TRUE,
  resample.volume = FALSE,
  smooth.type = c("taubin", "laplace", "HClaplace", "fujiLaplace", "angWeight",
    "surfPreserveLaplace"),
  lambda = 0.5,
  mu = -0.53,
  delta = 0.1,
  conn = NULL,
  ...
)

neuronvolume3d(
  neuronvolume,
  type = c("volume", "points"),
  split = c("whole", "split", "soma", "primary neurite", "axon", "dendrite",
    "microtubule", "primary dendrite"),
  alpha = 0.3,
  WithConnectors = TRUE,
  synapse.radius = 500,
  cols = c(neuron = "grey", dendrite = "cyan", soma = "magenta", primary.neurite =
    "purple", primary.dendrite = "chartreuse", axon = "orange", microtubule = "green",
    twig = "brown")
)

Arguments

neuron	a neuron object that matches the volumes given
volumes	a list of mesh3d objects, retrieved using fafbseg::read_brainmaps_meshes
map	if TRUE, instead of using the volumes argument, map_fafbsegs_to_neuron and fafbseg::read_brainmaps_meshes are used to retrieve Google 3D segmentations as mesh3d objects
voxelSize	a single number, which is used to downsample the starting meshes, resample neuron, and choose an alpha value for alphashape3d::ashape3d()
downsample.factor	after the Google volumes have been resampled uniformly at voxelSize, points are randomly removed from the neuron cloud (no.points=no.points/downsample.factor) in order to make alphashape generation by alphashape3d::ashape manageable
downsample.volumes	downsample the volume pulled from the brainmaps API by xovelsize.
soma	if TRUE, the soma (root point for neuron) will be identified
node.match	how many nodes of each neuron in someneuronlist, need to be within a 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. need be in the volumetric Google FAFB segmentation for a Neuroglancer fragment, for that fragment to be returned
smooth	if TRUE, the final mesh will be smoothed, using
resample.neuron	if TRUE, neuron is resampled (nat:resample), stepsize = voxelSize
resample.volume	if TRUE, the final mesh3D object is uniformly resampled using Rvcg::vcgUniformRemesh, voxelSize = voxelSize
smooth.type	character: select smoothing algorithm. Available are "taubin", "laplace", "HClaplace","fujiLaplace", "angWeight" (and any sensible abbreviations). See Rvcg::vcgSmooth
lambda	numeric: parameter for Taubin smooth. See Rvcg::vcgSmooth
mu	numeric:parameter for Taubin smooth. See Rvcg::vcgSmooth
delta	numeric: parameter for Scale dependent laplacian smoothing and maximum allowed angle (in radians) for deviation between normals Laplacian (surface preserving). See Rvcg::vcgSmooth
conn	CATMAID connection
...	methods passed to Rvcg functions: vcgUniformRemesh, vcgSmooth, vcgClost
neuronvolume	an object of class neuronvolume, as returned by catnat::fafb_segs_stitch_volumes
type	whether to plot meshes of a point cloud
split	whether to plot the whole neuron or some subset of it
alpha	mesh transparency
WithConnectors	whether or not to plot synaptic connectors using spheres3D()
synapse.radius	radius information passed to rgl:spheres3d
cols	colours for different parts of the neuron

Value

a 'neuronvolume' object, with the same structure as a neuron object (see the nat package), but which contains a mesh3D object for the neuron and other volume related data as a list at neuron$volume

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