Read neuron skeletons via neuprint

Usage

read_fish_neurons(
  ids,
  connectors = FALSE,
  units = c("nm", "raw", "microns"),
  heal.threshold = Inf,
  conn = NULL,
  ...,
  dataset = fish_default_dataset()
)

Arguments

ids: Body ids in any form compatible with fish_ids.
connectors: Whether to fetch synaptic connections for the neuron (default FALSE in contrast to neuprint_read_neurons).
units: Units of the returned neurons: "nm" (default), "raw" (16 x 16 x 15 nm voxels) or "microns". Node radii are scaled by the x voxel size (16 nm) for "raw".
heal.threshold: The threshold for healing disconnected skeleton fragments. The default of Inf ensures that all fragments are joined together.
conn: Optional, a neuprint_connection object. Defaults to fish_neuprint to ensure that the query targets fish2.
...: Additional arguments passed to neuprint_read_neurons.
dataset: The name of the dataset as reported in Clio (default "fish2").

Value

A neuronlist object containing one or more neurons.

Details

Since September 2026 the fish2 neuprint server returns skeletons with coordinates and radii in nm (previously they were in 16 x 16 x 15 nm voxels). If the dataset metadata advertise a skeletonSize (nm per skeleton unit) this is used to calibrate the skeletons; otherwise they are assumed to be in nm.

Examples

# \donttest{
rgcsk3 <- read_fish_neurons(fish_ids("RGC")[1:3])
plot(rgcsk3, WithNodes=FALSE)

# }