flywire_annotations_for_synapses: Generate a CSV of neuron synapses to import to a flywire...

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

Generate a CSV of neuron synapses to import to a flywire annotation layer

Description

Generate a CSV of neuron synapses to import to a flywire annotation layer

Usage

flywire_annotations_for_synapses(
  fw.ids,
  direction = c("inputs", "outputs", "both"),
  partners = NULL,
  db = flywire_neurons(WithConnectors = TRUE),
  keep.dist.nm = 500,
  cleft_scores.thresh = 75,
  sample = 250,
  write.csv = TRUE,
  csv.path = getwd(),
  volume = NULL,
  ...
)

flywire_annotation_csv(
  xyz,
  write.csv = TRUE,
  csv.path = getwd(),
  description = "top_nt",
  csv.name = "flywire_points_annotations.csv"
)

flywire_verified_synapses(
  fw.ids,
  direction = c("inputs", "outputs", "both"),
  partners = NULL,
  csv.path = getwd(),
  csv.name = "annotations.csv",
  write.csv = TRUE
)

Arguments

fw.ids	character vector, a vector of valid flywire IDs
direction	whether to get presynapses, postsynapses or both.
partners	character vector else not used i NULL. A vector of valid flywire IDs for postsynaptic neurons to keep. Synapses to other postsynaptic targets are filtered out.
db	a neuronlist of flywire neurons with synapses attached
keep.dist.nm	numeric, minimum distance in nm that one synapse can be from another. One random synapse is chosen from groups of proximal synapses. To deactivate, enter NULL.
cleft_scores.thresh	numeric, cleft_score threshold for synapse inclusion
sample	numeric, the number of synapses to choose from both the dendrite and axon of each neuron in fw.ids
write.csv	logical, whether or not to write a .csv output file, ready for import into flywire for each neuron. They will be named using the pattern "flywire_<fw.id>_synapse_annotations.csv" and written to csv.path.
csv.path	Output path for CSV files (defaults to current working directory)
volume	if NLLL there is no subsetting. If a mesh3d object, only points inside this volume are chosen.
...	further arguments passed to fafbseg::flywire_partners, when db is NULL.
xyz	a data.frame of xyz coordinates in flywire voxel space -to write as a flywire annotation .csv file. Can contains other columns.
description	the column in xyz to use for the Description field of the final .csv.
csv.name	the name of the .csv file to be saved

Examples

## Not run: 
csv = flywire_annotations_for_synapses(fw.id = "720575940616046363",
direction = "inputs",
partners = c("720575940628113292",
"720575940610903062",
"720575940611661805",
"720575940628115084",
"720575940612337575",
"720575940618976297",
"720575940619059497",
"720575940616852894",
"720575940629359076",
"720575940632437856",
"720575940624804248",
"720575940613725708"),
db = NULL, keep.dist.nm = NULL, cleft_scores.thresh = 0, sample = NULL)

## End(Not run)

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