Convert xyz locations to root or supervoxel ids

Convert xyz locations to root or supervoxel ids

Usage

banc_xyz2id(
  xyz,
  rawcoords = FALSE,
  root = TRUE,
  integer64 = FALSE,
  fast_root = TRUE,
  method = c("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

root

Whether to return the root id of the whole segment rather than the supervoxel id.

integer64

Whether to return ids as integer64 type (more compact but a little fragile) rather than character (default FALSE).

fast_root

Whether to use a fast but two-step look-up procedure when finding roots. This is strongly recommended and the alternative approach has only been retained for validation purposes.

method

Whether to use the spine transform-service API or cloudvolume for lookup. "auto" is presently a synonym for "spine".

...

additional arguments passed to pbapply when looking up multiple positions.

Value

A character vector of segment ids, NA when lookup fails.

Details

This used to be very slow because we do not have a supervoxel field on spine.

I am somewhat puzzled by the voxel dimensions for banc. Neuroglancer clearly shows voxel coordinates of 4.3x4.3x45. But in this function, the voxel coordinates must be set to 4.25 in x-y to give the correct answers.

See also

flywire_xyz2id

Other banc-ids: banc_cellid_from_segid(), banc_ids(), banc_islatest(), banc_latestid(), banc_leaves(), banc_rootid()

Examples

if (FALSE) { # \dontrun{
# a point from neuroglancer, should map to 648518346498932033
banc_xyz2id(cbind(438976,985856,215955), rawcoords=FALSE)
} # }