Register a native LSM volume to JRC2018U via Elastix — lm_to_jrc2018u

Runs Elastix multi-resolution affine + B-spline to align a native-confocal NC82 volume to the JRC2018U_HR template, then applies the same transform to the matching GFP channel via transformix. Parameter files default to the package's inst/extdata/elastix_lm_to_jrc2018u/ bundle.

lm_to_jrc2018u_elastix(
  nc82,
  gfp,
  output_dir,
  template = NULL,
  param_files = NULL,
  elastix = "elastix",
  transformix = "transformix",
  threads = 8L,
  verbose = TRUE
)

Arguments

nc82: path to native NC82 NRRD (the registration moving image).
gfp: path to native GFP NRRD (same voxdims as nc82).
output_dir: directory for Elastix outputs (transform params, warped NC82, warped GFP).
template: path to JRC2018U template NRRD (the registration fixed image). Defaults to ~/templates/JRC2018_UNISEX_20x_HR.nrrd — override via options(neuronbridger.jrc2018u_template = ...).
param_files: length-2 character of Elastix parameter file paths (p_affine.txt, p_bspline.txt). Defaults to the package bundle.
elastix: path to the elastix binary.
transformix: path to the transformix binary.
threads: number of threads (Elastix default uses all).

Value

a list with nc82_jrc2018u (warped reference NRRD path), gfp_jrc2018u (warped GFP NRRD path), params (Elastix output directory), and final_metric (last metric value reported by Elastix).