Mirror Aedes neurons or points to the opposite side of the brain

aedes_mirror() mirrors objects supported by nat::xform(), including neurons, neuronlists, dotprops and coordinate matrices.

Usage

aedes_mirror(
  x,
  method = c("tps", "landmarks", "symmetric"),
  units = c("nm", "microns"),
  subset = NULL,
  landmarks = NULL,
  raw = TRUE,
  url = .aedes_mirror_landmarks_url,
  vd = NULL,
  ...
)

Arguments

x: An object to mirror.
method: Mirror method. "tps" uses the bundled aedes_aedesSym_1000_tps.rds registration to map into Aedes symmetric space, flip across the X axis, then map back to original Aedes space. "landmarks" uses paired landmarks in the original Aedes space.
units: Coordinate units for x and the returned object. The symmetric registration is defined in microns; nm inputs are scaled before and after transformation.
subset: Optional subset passed to nat::xform(), for example when transforming selected elements of a neuronlist.
landmarks: Optional landmark data with pointA and pointB entries. When NULL, landmarks are read from url using fafbseg::ngl_annotations().
raw: Whether landmark coordinates are in raw voxel space. When FALSE, landmark coordinates are assumed to be in units.
url: Neuroglancer URL containing paired mirror landmarks.
vd: Optional voxel dimensions in nm. Advanced use; when NULL and raw = TRUE, these are detected automatically.
...: Additional arguments passed to nat::xform().

Value

A transformed object of the same kind as x.

Details

Mirroring requires the suggested Morpho package at runtime.

Examples

if (FALSE) { # \dontrun{
sk <- with_aedes(fafbseg::read_l2skel(aedes_ids("class:DNa")[1]))
sk.mirror <- aedes_mirror(sk, units = "nm")

plot3d(sk, col = "grey")
plot3d(sk.mirror, col = "red", add = TRUE)

dps <- with_aedes(fafbseg::read_l2dp(aedes_ids("class:DNa")))
dps.mirror <- aedes_mirror(dps, units = "microns")
} # }