Transform Points between BANC Connectome and JRC2018F Template Brain

This function transforms 3D points between the BANC (Buhmann et al. Adult Neural Connectome) coordinate system and the D. melanogaster template brain JRC2018F coordinate system.

Usage

banc_to_JRC2018F(
  x,
  region = c("brain", "vnc"),
  banc.units = c("nm", "um", "raw"),
  subset = NULL,
  inverse = FALSE,
  transform_file = NULL,
  method = c("tpsreg", "elastix", "navis_elastix_xform")
)

Arguments

x

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

region

Whether this transform is for the JRC2018F brainspace (default) ot the JRCVNC2018F VNC template (only alternative).

banc.units

Character string specifying the units of the BANC space data (input or output, depending on the inverse argument). 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. If TRUE, performs the inverse transformation (JRC2018F to BANC). Default is FALSE.

transform_file

Optional. Path to a custom transform file. If NULL, uses default files.

method

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

Value

The input object with transformed 3D points.

Details

This function applies either an Elastix transform or a thin-plate spline registration to convert points between the BANC and JRC2018F coordinate systems. It handles unit conversions as necessary.

The default transformation files are included with the package and are located in the 'inst/extdata/brain_240721' directory.

See also

elastix_xform for the underlying Elastix transformation function. banc_raw2nm and banc_nm2raw for unit conversion functions.

Examples

if (FALSE) { # \dontrun{
### BRAIN EXAMPLE ####
# Transform points from BANC to JRC2018F
transformed_points <- banc_to_JRC2018F(points, banc.units = "nm")

# Use a custom transform file
custom_transformed <- banc_to_JRC2018F(points, transform_file = "path/to/custom/transform.txt")

# Where the default transform files are located:
banc_to_JRC2018F_file <- system.file(file.path("extdata","brain_240721"),
"BANC_to_template.txt", package="bancr")
JRC2018F_to_banc_file <- system.file(file.path("extdata","brain_240721"),
"template_to_BANC.txt", package="bancr")

### VNC EXAMPLE ####
library(malevnc)
library(nat.jrcbrains)
nat.jrcbrains::register_saalfeldlab_registrations()

# Get DNa02 axons from the MANC project
DNa02s=read_manc_meshes('DNa02')
plot3d(JRCVNC2018U)

# Transform into JRCVNC2918F
## nb convert from nm to microns
DNa02s.jrcvnc2018f=xform_brain(DNa02s/1e3, reference = "JRCVNC2018F", sample="MANC")
plot3d(DNa02s.jrcvnc2018f, co = "red")
plot3d(JRCVNC2018F)

# Transform into the BANC
DNa02s.banc <- banc_to_JRC2018F(DNa02s.jrcvnc2018f, region="VNC", method="tpsreg")
open3d()
plot3d(DNa02s.banc, co = "blue")
plot3d(banc_vnc_neuropil.surf)

} # }