Setup
pizzarr does not depend on the raster package, but we use it for this demo to render an RGB array to an image using R.
install.packages("raster")Demo
library(pizzarr)
# The path to the root of the OME-NGFF Zarr store.
root <- system.file("extdata", "dog.ome.zarr", package="pizzarr")
# Open the OME-NGFF as a DirectoryStore.
store <- DirectoryStore$new(root)
g <- zarr_open_group(store)
# Using the OME metadata, get the path to the first resolution of the image pyramid.
attrs <- g$get_attrs()$to_list()
resolution_paths <- attrs$multiscales[[1]]$datasets[[1]]$path
first_resolution <- resolution_paths[[1]]
# Load the 3-dimensional array of RGB pixels (as a ZarrArray instance).
zarr_arr <- g$get_item(first_resolution)
print(zarr_arr$get_shape())
# [1] 3 500 750
# Load the 3-dimensional array of RGB pixels (as a NestedArray instance).
nested_arr <- zarr_arr$get_item("...")
# Extract the NestedArray contents as a base R array.
arr <- nested_arr$data
# Convert the base R array to a raster object.
arr_as_raster <- raster::as.raster(aperm(arr, c(2, 3, 1)) / 255.0)
# Plot the raster object.
raster::plot(arr_as_raster)