Create spatraster image from G4X jp2 image file

Create a SpatRaster object (package terra) using Visium image file

load_g4x_img(
  seurat = NULL,
  img_path = NULL,
  rm_old_img = F,
  return.seurat = T,
  max_dim = 2000
)

Arguments

seurat: a Seurat object containing G4X data
img_path: character string indicating the path of the H&E image to be used. If set to NULL, the function will look for any image path 'img' stored in tools slot
rm_old_img: boolean, whether or not removing any Image object already loaded in the Seurat object (Images())
return.seurat: boolean, whether returning the input Seurat file with the raster object stored in the tools slot (TRUE) or the raster object alone (FALSE). Default value is TRUE
max_dim: numeric value indicating the ideal maximum pixel dimension accepted for Visium H&E image. If image size is bigger than this value, a scale factor will be applied to lower image pixel resolution/size up to the defined maximum value

Seurat object with the new raster image stored in the misc slot or the raster image alone, depending on the return.seurat parameter

This function will use G4X H&E image file to create a SpatRaster image for downstream analysis and visualization.