hemibrain_read_neurons: Read neurons from the hemibrain connectome project

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

Read neurons from the hemibrain connectome project

Description

Read neurons from the hemibrain connectome project. This function uses the package neuprintr to read neurons. It then uses 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_read_neurons(
  x = NULL,
  local = FALSE,
  microns = FALSE,
  reroot = TRUE,
  remote = TRUE,
  googlesheet = FALSE,
  remove.bad.synapses = FALSE,
  clean = FALSE,
  ...
)

scale_neurons(x, scaling = (8/1000), ...)

hemibrain_neurons(
  x = NULL,
  local = FALSE,
  brain = c("JRCFIB2018Fraw", "JRCFIB2018F", "FAFB14", "JFRC2", "JRC2018F", "FCWB"),
  mirror = FALSE,
  dotprops = FALSE,
  swc = FALSE,
  zip = FALSE,
  folder = "hemibrain_neurons/"
)

Arguments

x	a vector of bodyids that can be read from 'https://neuprint.janelia.org/'.
local	FALSE or path. By default (FALSE) data is read from options()$remote_connectome_data), but the user can specify an alternative path.
microns	convert dimensions from raw voxels into microns (template brain: JRCFIB2018F, else JRCFIB2018Fraw).
reroot	logical, whether or not somas should be re-rooted. Note that if FALSE, re-rooting occurs anyway via hemibrain_flow_centrality. However, setting this argument to TRUE
remote	logical. Whether not to use hemibrain_neurons to try to read neurons stored on the hemibrainr google drive, and mounted with either rclone or google filestream.
googlesheet	logical, whether or not manually checked somas should be read from the Google Sheet
remove.bad.synapses	whether or not to run hemibrain_remove_bad_synapses on neurons pulled from neuPrint.
clean	whether or not to set synapse-less branches to Label = 0.
...	arguments passed to neuprintr::neuprint_read_neurons, hemibrain_remove_bad_synapses and hemibrain_flow_centrality
scaling	the factor by which neuron coordinates in raw voxel space should be multiplied. The default scales to microns.
brain	the brainspace in which hemibrain neurons have been registered. Defaults to raw voxel space for the hemibrain project.
mirror	logical, whether or not to read neurons that have been mirrored (i.e. flipped to the 'other' brain hemisphere).
dotprops	logical. Whether or not to retrieve a nat::dotprops object, i.e. vector cloud representations of neurons for NBLASTing. The dotprops object will be in JRC2018FIBF micron space.
swc	logical. When using neurons with hemibrain_neurons from the Google drive, whether to read .swc files (if TRUE), or a neuronlistfh object (default).
zip	logical. If TRUE then nat::neuronlistz is used to read neurons from a .zip archive. Otherwise, nat::neuronlistfh is used to read neurons from a .rds file with a linked 'data' folder. The .zip method is preferred. Both methods load a dynamic neuronlist, which only loads skeleton data into memory at the point where it is processed.
folder	the sub-folder in which to look for a nat::neuronlistfh .rds file and its data, representing hemibrain neurons. The function will look for this folder in the location: hemibrainr:::good_savedir(local=local), by default the mounted Google drive (options()$remote_connectome_data) or locally ((options()$hemibrain_data))

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_somas, hemibrain_precomputed_splitpoints, hemibrain_metrics,hemibrain_remove_bad_synapses ,hemibrain_get_meta,flywire_neurons

Examples

## Not run: 

# 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")

# Get neurons
neurons = hemibrain_read_neurons(al.local.neurons)

# Plot the split to check it
nat::nopen3d()
nlscan_split(neurons, WithConnectors = TRUE)

## End(Not run)

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