Read Aedes L2 skeletons

Thin Aedes-aware wrapper around fafbseg::read_l2skel(). Optionally reroots each skeleton to its soma, cascading through a configurable set of methods.

Usage

read_aedes_neurons(
  ids,
  units = c("nm", "raw", "microns"),
  reroot = TRUE,
  method = c("auto", "flytable", "nucleus", "l2+mesh", "l2", "mesh", "none"),
  mesh = aedes::aedes_neuropil_mesh,
  chunksize = 20L,
  cl = NULL,
  OmitFailures = TRUE,
  previous = NULL,
  version = NULL,
  timestamp = NULL,
  ...
)

Arguments

ids

Root IDs or a FlyTable query string compatible with aedes_ids().

units

Units of the returned skeletons (default "nm").

reroot

Whether to reroot the returned neurons.

method

Reroot strategy passed through to aedes_soma_position(). With "auto" (the default) each neuron is handled by the first source that succeeds in the cascade: FlyTable soma_xyz → FlyWire nucleus → "l2+mesh" (a combined L2-attribute + neuropil signed-distance score for any neuron that has no FlyTable or nucleus soma; only used if a mesh is available). Restrict to a single value to disable the cascade. "none" skips rerooting (equivalent to reroot = FALSE).

mesh

A mesh3d for the neuropil. Defaults to the packaged aedes_neuropil_mesh. Pass NULL to disable mesh-based fallback in "auto"; "l2+mesh" and "mesh" error without a mesh.

chunksize, cl

Forwarded to aedes_soma_position() – batch size for L2 attribute fetches and optional parallel cluster for chunk processing.

OmitFailures

Passed to fafbseg::read_l2skel().

previous

Optional nat::neuronlist() from an earlier call. Neurons whose names match requested root ids are reused so only missing skeletons are read. previous is expected to be in nm coordinates.

version, timestamp

Optional CAVE materialisation selectors.

...

Additional arguments passed to fafbseg::read_l2skel().

Value

A nat::neuronlist() of L2 skeletons. When rerooted, each neuron's data slot gains soma_source ("flytable", "nucleus", "l2+mesh", "l2", "mesh", or NA), n_nuclei (count of distinct-position nucleus candidates considered, or NA), and nucleus_id (the nuclei_v1_aedes primary key of the chosen row, or NA). n_nuclei > 1 indicates the chosen nucleus was one of several at distinct positions for that root id; see aedes_soma_position() for the full candidate list.

See also

aedes_soma_position(), aedes_neuropil_mesh

Examples

if (FALSE) { # \dontrun{
dns <- read_aedes_neurons("class:DNa")
dns <- read_aedes_neurons("class:DNa", method = "flytable") # no fallback
dns <- read_aedes_neurons("class:DNa", reroot = FALSE)
} # }