Attach synapses to flywire neuron skeletons

Attach the appropriate input and output synapses to each flywire neuron skeleton in a neuronlist.

Usage

flywire_neurons_add_synapses(
  x,
  connectors = NULL,
  cloudvolume.url = NULL,
  method = c("auto", "spine", "sqlite"),
  remove_autapses = TRUE,
  cleft.threshold = 0,
  Verbose = TRUE,
  transmitters = FALSE,
  local = NULL,
  ...
)

# S3 method for neuron
flywire_neurons_add_synapses(
  x,
  connectors = NULL,
  cloudvolume.url = NULL,
  method = c("auto", "spine", "sqlite"),
  remove_autapses = TRUE,
  cleft.threshold = 0,
  Verbose = TRUE,
  transmitters = FALSE,
  local = NULL,
  ...
)

# S3 method for neuronlist
flywire_neurons_add_synapses(
  x,
  connectors = NULL,
  cloudvolume.url = NULL,
  method = c("auto", "spine", "sqlite"),
  remove_autapses = TRUE,
  cleft.threshold = 0,
  Verbose = TRUE,
  transmitters = FALSE,
  local = NULL,
  ...
)

flywire_synapse_annotations(
  x,
  file = NULL,
  scale = 1/c(4, 4, 40),
  sample = NULL,
  best = TRUE,
  cleft.threshold = 30,
  remove_autapses = TRUE,
  local = NULL,
  cloudvolume.url = NULL
)

Arguments

x

a nat::neuronlist for flywire neurons in the FlyWire or FAFB14 brainspace. These skeletons can be created using skeletor, or retrieved using hemibrainr::flywire_neurons. When using flywire_synapse_annotations this can be a data.frame of synapses, e.g. from flywire_ntpred that need to be formatted as FlyWire annotations.

connectors

a data.frame of FAFB synapses, with XYZ coordinates, to attach to x. If NULL (default) synapses are fetched, as in flywire_partners.

cloudvolume.url

The segmentation source URL for cloudvolume. Normally you can ignore this and rely on the default segmentation chosen by choose_segmentation

method

Whether to use a local SQLite database or remote spine service for synapse data. The default auto uses a local database when available (45GB but faster).

remove_autapses

whether to remove autapses (defaults to TRUE).

cleft.threshold

select only synaptic connections exceeding this confidence threshold (default of 0 uses all synapses; values in the range 30-100 seem to make sense).

Verbose

Whether to print status messages

transmitters

if TRUE also attempt to retrieve neurotransmitter predictions from Eckstein et al. 2020, for the flywire neuron in question.

local

path to SQLite synapse data. Evaluated by fafbseg:::local_or_google. Work in progress. Default is to download this data and place it in ~/projects/JanFunke.

...

methods sent to nat::nlapply.

file

when using flywire_synapse_annotations, the file path to which to output a .csv. If NULL, a data.frame formatted like a annotations CSV for FlyWire, is returned.

scale

a scale factor applied to the XYZ coordinates for synapses. Default moves them from nanometre FlyWire space to raw voxel FlyWire space, which is most appropriate for FlyWire annotations.

sample

if an integer, this is the number of synapses that are sampled from x.

best

logical. If TRUE and sample is an integer, then the synapses with the highest cleft scores are chosen, 1:sample.

Value

A nat::neuronlist object, where each neuron in the neuronlist has a data.frame of synapses at neuron$connectors.

See also

Other automatic-synapses: flywire_adjacency_matrix(), flywire_ntplot(), flywire_ntpred(), flywire_partners()

Examples

# \donttest{
if (FALSE) {
choose_segmentation("flywire")
nx=xform_brain(elmr::dense_core_neurons, ref="FlyWire", sample="FAFB14")
xyz = xyzmatrix(nx)
ids = unique(flywire_xyz2id(xyz[sample(nrow(xyz),100),]))
neurons = skeletor(ids, brain = elmr::FAFB14.surf)
neurons.syns = flywire_neurons_add_synapses(neurons, transmitters = TRUE)
neurons.syns[,]

# Plot in 3D
library(catmaid)
nopen3d()
plot3d(neurons.syns, WithConnectors = TRUE)

# Axon-dendrite split
library(hemibrainr)
neurons.flow = flow_centrality(neurons.syns,
  polypre = TRUE,
  mode = "centrifugal")
clear3d()
plot3d_split(neurons.flow, WithConnectors = TRUE,
transmitter = TRUE,
radius = 1000, soma = 4000)

# Save .csv of synapses as FlyWire annotations
flywire_synapse_annotations(ids[1], file="annotations1.csv",
cleft.threshold=30)

# And similar, from a neuronlist
syns = hemibrainr::hemibrain_extract_synapses(neurons.flow,
.parallel = TRUE, OmitFailures = TRUE)
flywire_synapse_annotations(syns, file="annotations2.csv",
cleft.threshold=30)

}
# }