3.1 Load images

With the Seurat object created, we are ready to load the H&E images from the file paths provided in the infoTable. The LoadImages() function allow you to load the images into the Seurat object and will automatically save a scaled down version of each image that you can use for plotting.

se <- LoadImages(se, time.resolve = FALSE, verbose = TRUE)

## Loading images for 2 samples: 
##   Reading ../data/V19D02-087_B1/spatial/tissue_hires_image.png for sample 1 ... 
##   Scaling down sample 1 image from 1979x2000 pixels to 400x404 pixels 
##   Reading ../data/V19T26-013_A1/spatial/tissue_hires_image.png for sample 1 ... 
##   Scaling down sample 2 image from 2000x2000 pixels to 400x400 pixels

ImagePlot(se, method = "raster", type = "raw", annotate = FALSE)

Figure 3.1: Raw H&E images