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Mirror BANC Connectome Points

Source: R/xform.R
banc_mirror.Rd

This function mirrors 3D points in the BANC (Buhmann et al. Adult Neural Connectome) coordinate system by transforming to JRC2018F, mirroring, and transforming back.

Usage

banc_mirror(
  x,
  banc.units = c("nm", "um", "raw"),
  subset = NULL,
  inverse = FALSE,
  transform_files = NULL,
  method = c("tpsreg", "elastix", "navis_elastix_xform"),
  ...
)

Arguments

x

An object containing 3D points (must be compatible with nat::xyzmatrix).

banc.units

Character string specifying the banc.units of the input points. Must be one of "nm" (nanometers), "um", or "raw" (BANC raw banc.units). Default is "nm".

subset

Optional. A logical vector or expression to subset the input object.

inverse

Logical. Not used in this function, kept for compatibility with banc_to_JRC2018F.

transform_files

Optional. A vector of two file paths for custom transform files. If NULL, uses default files.

method

Character string specifying the transformation method. Must be either "elastix" or "tpsreg". Default is "elastix".

...

Additional arguments passed to nat.templatebrains::mirror_brain.

Value

The input object with mirrored 3D points.

Details

This function performs mirroring of BANC points by first transforming them to the JRC2018F coordinate system, applying the mirroring operation, and then transforming them back to BANC. It can use either Elastix transforms or thin-plate spline registration for the coordinate system transformations.

See also

banc_to_JRC2018F for the underlying transformation function. nat.templatebrains::mirror_brain for the mirroring operation in JRC2018F space.

Examples

if (FALSE) { # \dontrun{
# Example using saved tpsreg
banc_neuropil.surf.m <- banc_mirror(banc_neuropil.surf, method = "tpsreg")
clear3d()
banc_view()
plot3d(banc_neuropil.surf, alpha = 0.5, col = "lightgrey")
plot3d(banc_neuropil.surf.m, alpha = 0.5, col = "green")

# Example using custom Elastix transforms
choose_banc()
rootid <- "720575941626035769"
neuron.mesh <- banc_read_neuron_meshes(rootid)

# Show neuron in BANC neuropil
banc_view()
plot3d(neuron.mesh, col = "red")
plot3d(banc_neuropil.surf, alpha = 0.1, col = "lightgrey")

# Show only the portion in the brain
neuron.mesh.brain <- banc_decapitate(neuron.mesh, invert = TRUE)

# Mirror in BANC space
neuron.mesh.mirror <- banc_mirror(neuron.mesh.brain,
transform_files = c("brain_240721/BANC_to_template.txt",
 "brain_240721/template_to_BANC.txt"))
plot3d(neuron.mesh.mirror, col = "cyan")
} # }