Tile an H&E image

This function takes an image of class magick-image and create a tile map. The size of each tile is 256x256 pixels and the number of zoom levels are determined from the automatically.

Usage

TileImage(
  im,
  sampleID = 1,
  outpath = NULL,
  maxZoomLevel = 4,
  maxImgWidth = 10000,
  nCores = detectCores() - 1,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

im

An image of class magick-image

sampleID

The section number to use. This number will be appended to the output files names

outpath

A string specifying an output directory to save the tiled image in.

maxZoomLevel

Max zoom level

maxImgWidth

Safety threshold to make sure that the zoom level doesn't get too deep.

nCores

Number of cores to use for threading

overwrite

If the the folder '<outpath>/viewer_data' already exists, it will be overwritten.

verbose

Print messages

Value

A character vector with the tile path

Author

Ludvig Larsson

Examples

# \donttest{

library(magick)
library(shiny)
library(leaflet)
#> 
#> Attaching package: ‘leaflet’
#> The following object is masked from ‘package:SeuratObject’:
#> 
#>     JS
#> The following object is masked from ‘package:Seurat’:
#> 
#>     JS

# Download hires image
he_img <- file.path("https://data.mendeley.com/public-files/datasets/kj3ntnt6vb/files",
                    "d97fb9ce-eb7d-4c1f-98e0-c17582024a40/file_downloaded")

# Load H&E image with magick
im <- image_read(he_img)

# tile image and return path to tiles
tile_res <- TileImage(im, outpath = tempdir(), nCores = 1, overwrite = TRUE)
#> ℹ Got an image of dimensions 2000x1882 for sample 1
#> →   Tiling image into 3 zoom levels
#> !   Replacing directory /private/var/folders/8r/bfm2m_q17znfk0m_8dt330tm0000gp/T/RtmpRVvGCP/viewer_data/tiles1
#> →   Creating tiles
#> →   Exporting tiles
#> →   Exporting meta data
#> !   Replacing file /private/var/folders/8r/bfm2m_q17znfk0m_8dt330tm0000gp/T/RtmpRVvGCP/viewer_data/image_info_1.json

# Create a simple viewer with leaflet
ui <- fluidPage(
  leafletOutput("map", height = 512, width = 512),
)

server <- function(input, output, session) {
  addResourcePath("mytiles", tile_res$tilepath)
  output$map <- renderLeaflet({
    leaflet(options = leafletOptions(preferCanvas = TRUE)) %>%
      addTiles(urlTemplate = "/mytiles/{z}/{x}_{y}.jpg",
               options = tileOptions(continuousWorld = TRUE,
                                     tileSize = "256",
                                     minZoom = 1,
                                     maxZoom = 3))
  })
}
if (interactive()) {
  shinyApp(ui, server)
}
# }