Wraps the bundled Python helper
inst/python/lsm_to_nrrd.py (uses tifffile + SimpleITK)
to extract channel 0 (GFP) and channel 1 (NC82) into two
.nrrd files with proper voxdims metadata. Channel order is
assumed; for any LSM cohort that swaps the order, pass the channel
indices via ... (forwarded as --gfp-channel /
--nc82-channel).
lsm_to_nrrd(input, output_dir, prefix = NULL, python = NULL, verbose = TRUE)path to the source .lsm file.
directory where <stem>_nc82.nrrd and
<stem>_gfp.nrrd are written; created if missing.
optional output stem (default = input file basename).
path to a Python interpreter with tifffile +
SimpleITK installed; defaults to whichever reticulate
would use.
a length-2 named character of c(nc82 = ..., gfp = ...)
absolute paths to the written NRRDs.