registerGiottoObjectListFiji

Function to spatially align gobject data based on FIJI image registration.

registerGiottoObjectListFiji(
  gobject_list,
  spat_unit = NULL,
  image_unreg = "image",
  image_reg_name = "image",
  image_replace_name = "unregistered",
  registered_images = NULL,
  spatloc_unreg = "raw",
  spatloc_reg_name = "raw",
  spatloc_replace_name = "unregistered",
  xml_files,
  scale_factor = NULL,
  verbose = TRUE
)

Arguments

gobject_list

list of gobjects to register

spat_unit

spatial unit

image_unreg

name of original unregistered images. Defaults to "image" (optional)

image_reg_name

arbitrary name for registered images to occupy. Defaults to replacement of "image" (optional)

image_replace_name

arbitrary name for any images replaced due to image_reg_name argument (optional)

registered_images

registered images output by FIJI register_virtual_stack_slices

spatloc_unreg

spatial locations to use. Defaults to "raw" (optional)

spatloc_reg_name

name for registered spatial locations. Defaults to replacement of "raw" (optional)

spatloc_replace_name

arbitrary name for any spatial locations replaced due to spatloc_reg_name argument (optional)

xml_files

atomic vector of filepaths to xml outputs from FIJI register_virtual_stack_slices

scale_factor

vector of scaling factors of images used in registration vs spatlocs

verbose

be verbose

Value

list of registered giotto objects where the registered images and spatial locations