produce an array from selected image in a spatialdata zarr store

produce an array from selected image in a spatialdata zarr store

rast_zarr(
  zpath,
  xlim = c(19000, 22000),
  ylim = c(8000, 8500),
  image_name = "he_image",
  target_width = 800
)

Arguments

zpath

path to zarr store

xlim

extent of interest, 'horizontal' axis

ylim

extent of interest, 'vertical' axis

image_name

character(1)

target_width

numeric(1)

Value

R array dimensions nx x ny x 3 suitable for use with EBImage

Examples

# \donttest{
if (dir.exists("lungdata.zarr")) {
  nn = rast_zarr("lungdata.zarr")
  if (requireNamespace("EBImage")) {
     ii = EBImage::Image(nn, colormode="Color")
     EBImage::display(ii) # to browser for zoom/pan
  } else message("Install EBImage to run this code.")
}
# }