Manually align an image (e.g. H&E, Immuno) to a SM SpaMTP dataset

Usage

AddSMImage(
  image_path,
  SpaMTP,
  fov = "fov",
  grey.scale = 0.5,
  plot.greyscale = FALSE,
  seed = 123,
  n.spots = NULL,
  ...
)

image_path: Character string defining the full path of the image to align.
SpaMTP: SpaMTP Seurat object to align the image to.
fov: Character string defining the image fov that contains the SM data coordinates (default = "fov").
grey.scale: Numeric value defining the grey scale to use for generating a tissue mask from the provided image (default = 0.5).
plot.greyscale: Boolean indicating whether to display the grey scale plot used to generate the tissue mask (default = FALSE).
seed: Integer value defining the seed to use for calculating random fake gene values for aligning the image (default = 123).
n.spots: Integer specifying the number of fake spots to generate for the aligned image. If NULL the number of spots will match that of the SpaMTP object provided (default = NULL).
...: Additional inputs used by the AlignSpatialOmics function. Please see documentation or call ?AlignSpatialOmics for more infomation.

A SpaMTP Seurat object with the provided image aligned to the SM data. The image is stored in the @image$slice1 slot.

# AddSMImage(image_path = "../HnE_image.png", SpaMTP = SpaMTP_obj)