Pre-process hemibrain skeletons

Call hemibrain_reroot on neurons read from the hemibrain neuprintr project, that have no marked soma, and hemibrain_remove_bad_synapses on all neurons. Does not prune synapses from soma positions / along the primary neurite, but does remove synapses outside of the hemibrain volume.

hemibrain_skeleton_check(
  x,
  meshes = hemibrainr::hemibrain.surf,
  min.nodes.from.soma = 100,
  min.nodes.from.pnt = 5,
  OmitFailures = FALSE,
  ...
)

Arguments

x	a `nat::neuronlist` or `nat::neuron` object. It is assumed that this neuron has been read in by `neuprintr::neuprint_read_neurons` or possibly `catmaid::read.neurons.catmaid`.
meshes	a list/a single object of class `mesh3d` or `hxsurf`. Defaults to `hemibrain.surf`. See examples for alternatives.
min.nodes.from.soma	the minimum number of nodes (geodesic distance) a synapse can be from the soma. Synapses closes than this will be removed. For comparable results across neurons, recommended to use `nat::resample` on your neurons before using.
min.nodes.from.pnt	the minimum number of nodes (geodesic distance) a synapse can be from a point along the primary neurite. Synapses closes than this will be removed.
OmitFailures	Whether to omit neurons for which FUN gives an error. The default value (NA) will result in nlapply stopping with an error message the moment there is an error.
...	methods sent to `nat::nlapply`

Value

a nat::neuronlist or nat::neuron object

Examples

# \donttest{
# Choose some known trouble makers
ids = c("5813056323", "579912201", "5813015982", "973765182", "885788485",
"915451074", "5813032740", "1006854683", "5813013913", "5813020138",
"853726809", "916828438", "5813078494", "420956527", "486116439",
"573329873", "5813010494", "5813040095", "514396940", "665747387",
"793702856", "451644891", "482002701", "391631218", "390948259",
"390948580", "452677169", "511262901", "422311625", "451987038"
)

# just use a subset for documentation purposes
ids=ids[1:3]

# Read in these neurons
neurons = neuprintr::neuprint_read_neurons(ids)
if (FALSE) {
# Get all the roi meshes
hemibrain.rois = hemibrain_roi_meshes()
## Using this as the argument for 'meshes' will also
## give you the ROI for each point and synapse in a neuron's skeleton!!

# Re-root
neurons.checked = hemibrain_skeleton_check(neurons, meshes = hemibrain.rois)
}

# Alternatively, we can do this faster using a single surface model for the
# whole hemibrain

neurons.checked = hemibrain_skeleton_check(neurons, meshes = hemibrain.surf)
#> Re-rooting 1 neurons without a soma
#> Removing synapses outside the hemibrain neuropil volume for 3 neurons
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated
#> Warning: invalid factor level, NA generated

if (FALSE) {
# Let's check that this worked
nat::nopen3d()
for(n in neurons.checked){
     clear3d();
     message(n$bodyid)
     plot3d(n,col="brown",lwd=2)
     points3d(nat::xyzmatrix(n$connectors),col="black")
     spheres3d(nat::xyzmatrix(n)[nat::rootpoints(n),],radius=500, alpha=0.5)
     p = readline("Done? ")
}
}# }

Arguments

Value

See also

Examples