Local OME-NGFF Demo

library(pizzarr)

# The path to the root of the OME-NGFF Zarr store.
root <- pizzarr_sample("dog.ome.zarr")

# 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

# Plot the RGB image using base R rasterImage().
dm <- dim(arr)
plot.new()
plot.window(c(0, dm[3]), c(0, dm[2]), asp = 1)
rasterImage(aperm(arr, c(2, 3, 1)) / 255, 0, 0, dm[3], dm[2])