hemibrain_clean_skeleton: Remove erroneous branchlets to beautify neuron skeletons

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

Remove erroneous branchlets to beautify neuron skeletons

Description

Remove synapse-less branches from axons and dendrites, and clean up the primary neurite and primary dendrite (linker) of a neuron. Given neurons must have been split by either flow_centrality or hemibrain_flow_centrality. hemibrain_flow_centrality to re-root and split neurons into putative axons and dendrites. Optionally, it may also convert neurons from their raw voxel space (as they are stored in NeuPrint) to microns.

Usage

hemibrain_clean_skeleton(x, rval = c("pruned", "neuron", "points"), ...)

Arguments

x	a nat::neuronlist or nat::neuron object
rval	whether to return a pruned neuron, a neuron with the synapse-less branches set to Label = 0 or the PointNo for those branches.
...	methods passed to nat::nlapply.

Value

the neuron or neuron list object inputted, with centripetal flow centrality information added to neuron$d and a segregation index score. The neuron$d$Label now gives the compartment, where axon is Label = 2, dendrite Label = 3, primary dendrite Label = 4 and primary neurite Label = 7. Soma is Label = 1.

See Also

hemibrain_splitpoints, hemibrain_flow_centrality, hemibrain_precomputed_splitpoints, hemibrain_metrics,hemibrain_remove_bad_synapses

Examples

# Choose neurons
## In this case some antennal lobe local neurons
al.local.neurons = c("1702323386", "2068966051", "2069311379", "1702305987", "5812996027",
"1702336197", "1793744512", "1976565858", "2007578510", "2101339904",
"5813003258", "2069647778", "1947192569", "1883788812", "1916485259",
"1887177026", "2101348562", "2132375072", "2256863785", "5813002313",
"5813054716", "5813018847", "5813055448", "1763037543", "2101391269",
"1794037618", "5813018729", "2013333009")

# Only use first three neurons for documentation purposes
al.local.neurons=al.local.neurons[1:3]
# Get neurons
neurons = neuprintr::neuprint_read_neurons(al.local.neurons)

# Split  neurons
neurons = hemibrain_flow_centrality(neurons)

# Clean neurons
neurons.cleaned = hemibrain_clean_skeleton(neurons)

## Not run: 
# Plot the split to check it
nat::nopen3d()
nlscan_split(neurons.cleaned, WithConnectors = TRUE)

## End(Not run)

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