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Transform yakuba neurons or points to MANC space (or back)

Source: R/xform.R
xform_dyak2manc.Rd

xform_dyak2manc() maps objects in yakuba space onto the MANC template or, with inverse = TRUE, from MANC onto yakuba. Several alternative registrations are available; only the default ("tps1000") is used by nat.templatebrains::xform_brain().

Usage

xform_dyak2manc(
  x,
  method = c("tps1000", "manual", "ngscene", "tps1000_unshifted"),
  units = c("nm", "microns"),
  inverse = FALSE,
  ...
)

Arguments

x

An object compatible with nat::xform() (neuron, neuronlist, dotprops, surface, coordinate matrix etc).

method

Which registration to use (see details).

units

Coordinate units of x and of the returned object (in MANC space unless inverse = TRUE).

inverse

Whether to map from MANC to yakuba space.

...

Additional arguments passed to nat::xform().

See the transforms article for how the registrations and the offset were validated.

Value

A transformed object of the same kind as x, in the same units.

Details

The available methods are:

  • "tps1000" (default): a thin-plate spline with 1000 landmarks computed by Sebastian Cachero from a surface fitted to an earlier version of the yakuba data. That surface is offset by a pure translation from current yakuba coordinates, so points are first shifted by (-6.5, -7.1, -8.0) µm. The shift was estimated by fitting that surface to yakuba_neuropil_shell (precision ~1 µm); it reduces the mismatch between matched yakuba and MANC descending neurons and neuropils by several µm.

  • "tps1000_unshifted": the same registration without the shift, as used by yakuba versions before the correction. Provided for comparison and reproducibility; not recommended for new work.

  • "manual": a thin-plate spline defined by 100 landmarks placed by hand by Hiroshi Shiozaki.

  • "ngscene": a thin-plate spline from yakuba to the male CNS (malecnsum) defined by 21 landmark pairs from a clio neuroglancer scene, followed by the malecnsum to MANC bridging registration. Requires the suggested malecns package.

On descending neurons with a known MANC match (MDN, DNg13, DNa02) the mean distance to the matched MANC neuron was 5.6, 6.4, 7.7 and 8.9 µm for "tps1000", "manual", "ngscene" and "tps1000_unshifted", respectively.

Inverse thin-plate splines are computed by swapping the landmark sets, so round trips are approximate (~0.3 µm for "tps1000", a few µm for "manual").

All registrations are defined in microns; nm inputs are scaled before and after transformation. Requires the suggested Morpho package.

See also

yakuba_register_xforms()

Examples

if (FALSE) { # \dontrun{
mdn <- read_dyak_neurons("MDN")
mdn.manc <- xform_dyak2manc(mdn)
mdn.manc2 <- xform_dyak2manc(mdn, method = "manual")
plot3d(mdn.manc, col = "black")
plot3d(mdn.manc2, col = "red")
} # }