registerGiottoObjectListFiji: registerGiottoObjectListFiji

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

registerGiottoObjectListFiji

Description

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

Usage

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.