registerGiottoObjectList#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/image_registration.R#L223

Description#

Wrapper function for registerGiottoObjectListFiji and registerGiottoObjectListRvision

Usage#

registerGiottoObjectList(
  gobject_list,
  spat_unit = NULL,
  method = c("fiji", "rvision"),
  image_unreg = "image",
  image_reg_name = "image",
  image_list = NULL,
  save_dir = NULL,
  spatloc_unreg = "raw",
  spatloc_reg_name = "raw",
  fiji_xml_files,
  fiji_registered_images,
  scale_factor = NULL,
  allow_rvision_autoscale = TRUE,
  verbose = TRUE
)

Arguments#

Argument

Description

gobject_list

List of gobjects to register

spat_unit

spatial unit

method

Method used to align gobjects. Current options are either using FIJI register_virtual_stack_slices output or rvision

image_unreg

Gobject image slot to use. Defaults to ‘image’ (optional)

image_reg_name

Arbitrary image slot name for registered images to occupy. Defaults to replacement of ‘image’ slot (optional)

image_list

RVISION - under construction

save_dir

RVISION - under construction

spatloc_unreg

Unregistered spatial locations to align. Defaults to ‘raw’ slot (optional)

spatloc_reg_name

Arbitrary name for registered spatial locations. Defaults to replacement of ‘raw’ slot (optional)

fiji_xml_files

Filepaths to FIJI registration XML outputs

fiji_registered_images

Registered images output by FIJI register_virtual_stack_slices

scale_factor

Scaling to be applied to spatial coordinates

allow_rvision_autoscale

Whether or not to allow rvision to automatically scale the images when performing image registration

verbose

Be verbose

Value#

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