manually_assign_labels: Manually assign the dendrite and axon to a neuron

In natverse/hemibrainr: Code for Working with Data from Janelia FlyEM's Hemibrain Project and the flywire data sets``

Manually assign the dendrite and axon to a neuron

Description

3D interactive functions to edit neurons in an rgl viewer, including re-assigned cable as being axon, dendrite, primary neurite, etc., choosing soma locations and pruning bits of cable as a user chooses.

Usage

manually_assign_labels(x, brain = NULL, is.cropped = FALSE, ...)

## S3 method for class 'neuron'
manually_assign_labels(x, brain = NULL, is.cropped = FALSE, ...)

## S3 method for class 'neuronlist'
manually_assign_labels(x, brain = NULL, is.cropped = FALSE, ...)

hemibrain_prune_online(x, brain = NULL, Label = NULL, lock = NULL, ...)

## S3 method for class 'neuron'
hemibrain_prune_online(x, brain = NULL, Label = NULL, lock = NULL, ...)

## S3 method for class 'neuronlist'
hemibrain_prune_online(x, brain = NULL, Label = NULL, lock = NULL, ...)

hemibrain_correctsoma(x, ...)

Arguments

x	a neuron/neuronlist object
brain	which brain to plot while splitting neuron.
is.cropped	logical. If TRUE, the user is asked whether the neuron being considered is complete or not.
...	additional arguments passed to plotting functions, namely plot3d_split
Label	the type of cable to be assigned/edited. Use standardise_labels to see how numbers convert to cable types.
lock	a vector of number representing cable types to lock (so that they cannot be edited interactively be a user). If NULL (default) no cable type is treated as locked. Locked cable will appear in green.

Value

The neuron/neuronlist object with axon/dendrite info assigned in SWC format to neuron$d

Examples

# Choose some neurons
exemplars = c("202916528", "1279775082",  "203253072",
             "326530038",  "203253253", "5813079341")

neurons = neuprintr::neuprint_read_neurons(exemplars)

neurons.flow = hemibrain_flow_centrality(neurons)

## Not run: 
# Plot the split to check it, correcting any errors
nat::nopen3d()
neurons.manual = manually_assign_labels(neurons.flow)

## End(Not run)

natverse/hemibrainr documentation built on Nov. 27, 2024, 9:01 p.m.