View source: R/image_registration.R
registerGiottoObjectListFiji | R Documentation |
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
)
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 |
list of registered giotto objects where the registered images and spatial locations
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