Find Aedes root or supervoxel (leaf) IDs for XYZ locations

Usage

aedes_xyz2id(
  xyz,
  rawcoords = FALSE,
  voxdims = aedes_voxdims(),
  cloudvolume.url = NULL,
  root = TRUE,
  timestamp = NULL,
  version = NULL,
  stop_layer = NULL,
  integer64 = FALSE,
  method = c("auto", "cloudvolume", "spine"),
  ...
)

Arguments

xyz: One or more xyz locations as an Nx3 matrix or in any form compatible with xyzmatrix including neuron or mesh3d surface objects.
rawcoords: whether the input values are raw voxel indices or in nm
voxdims: voxel dimensions in nm used to convert raw coordinates. The default value uses the flywire_voxdims function to identify the value for the current segmentation (usually with success).
cloudvolume.url: URL for CloudVolume to fetch segmentation image data. The default value of NULL chooses the flywire production segmentation dataset.
root: Whether to return the root id of the whole segment rather than the supervoxel id.
timestamp: An optional timestamp as a string or POSIXct, interpreted as UTC when no timezone is specified.
version: An optional CAVE materialisation version number. See details and examples.
stop_layer: Which layer of the chunked graph to stop at. The default NULL is equivalent to layer 1 or the full root id. Coarser layer 2 IDs can be a useful intermediate for some operations.
integer64: Whether to return ids as integer64 type (more compact but a little fragile) rather than character (default FALSE).
method: Lookup method: "auto" and "spine" use the Aedes transform service; "cloudvolume" delegates to fafbseg::flywire_xyz2id().
...: Additional arguments passed to backend helpers.

Value

A vector of segment IDs (character or integer64).

Details

Method auto (which maps to spine) should be much faster for look ups with many points, especially points in the same region of space.

Examples

if (FALSE) { # \dontrun{
aedes_xyz2id(c(24606, 12450, 5798), rawcoords = TRUE, root = FALSE)
} # }