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Load images

load-images.Rd

Load H&E images (or any other custom images) required for visualization methods in semla.

Usage

LoadImages(object, ...)

# S3 method for default
LoadImages(object, image_height = 400, pad_info = NULL, verbose = TRUE, ...)

# S3 method for Seurat
LoadImages(object, image_height = 400, verbose = TRUE, ...)

Arguments

object

An object

...

Arguments passed to other methods

image_height

An integer specifying the height of the down-scaled images

pad_info

A tibble with information about how the image should be padded

verbose

print messages

Value

An object with images in raster format

default method

If a character vector of image paths are provided, the images will be loaded, then down-scaled based on image_height and returned as a list of raster objects. Only JPEG and PNG images are supported.

Seurat

If a Seurat object is provided, the images will be loaded as raster objects and stored inside the Staffli object that is located in the tools slot.

See also

Other pre-process: LoadAndMergeMatrices(), LoadAnnotationCSV(), LoadImageInfo(), LoadScaleFactors(), LoadSpatialCoordinates(), ReadVisiumData(), UpdateImageInfo()

Other pre-process: LoadAndMergeMatrices(), LoadAnnotationCSV(), LoadImageInfo(), LoadScaleFactors(), LoadSpatialCoordinates(), ReadVisiumData(), UpdateImageInfo()

Examples


library(semla)

# Get paths for example images
mousebrain_jpg <- system.file("extdata/mousebrain", 
                              "spatial/tissue_lowres_image.jpg", 
                              package = "semla")
mousecolon_jpg <- system.file("extdata/mousecolon", 
                              "spatial/tissue_lowres_image.jpg", 
                              package = "semla")

rasters <- LoadImages(c(mousebrain_jpg, mousecolon_jpg))
#> 
#> ── Loading H&E images ──
#> 
#> ℹ Loading image from /private/var/folders/91/twz8ld_x3f98sr9yc2hq9xpn47blx2/T/RtmpQDm3p7/temp_libpathed1b712617f8/semla/extdata/mousebrain/spatial/tissue_lowres_image.jpg
#> ℹ Scaled image from 600x565 to 400x377 pixels
#> ℹ Loading image from /private/var/folders/91/twz8ld_x3f98sr9yc2hq9xpn47blx2/T/RtmpQDm3p7/temp_libpathed1b712617f8/semla/extdata/mousecolon/spatial/tissue_lowres_image.jpg
#> ℹ Scaled image from 541x600 to 400x444 pixels
#> ℹ Saving loaded H&E images as 'rasters' in Seurat object

# Save graphical parameters
oldpar <- par(no.readonly = TRUE)

# plot images
par(mfrow = c(1, 2), mar = c(0, 0, 0, 0))
for (rst in rasters) {
  plot(rst)
}


# Reset graphical parameters
par(oldpar)


library(semla)

# Load example Visium data
se_mbrain <- readRDS(system.file("extdata/mousebrain", "se_mbrain", package = "semla"))
se_mcolon <- readRDS(system.file("extdata/mousecolon", "se_mcolon", package = "semla"))
se_merged <- MergeSTData(se_mbrain, se_mcolon)

# Load images
se_merged <- LoadImages(se_merged)
#> 
#> ── Loading H&E images ──
#> 
#> ℹ Loading image from /private/var/folders/91/twz8ld_x3f98sr9yc2hq9xpn47blx2/T/RtmpQDm3p7/temp_libpathed1b712617f8/semla/extdata/mousebrain/spatial/tissue_lowres_image.jpg
#> ℹ Scaled image from 600x565 to 400x377 pixels
#> ℹ Loading image from /private/var/folders/91/twz8ld_x3f98sr9yc2hq9xpn47blx2/T/RtmpQDm3p7/temp_libpathed1b712617f8/semla/extdata/mousecolon/spatial/tissue_lowres_image.jpg
#> ℹ Scaled image from 541x600 to 400x444 pixels
#> ℹ Saving loaded H&E images as 'rasters' in Seurat object