napari-ome-zarr plugin does not recognize the data created by example correctly? #486
Description
Hi all, I just run this script (latest ome-zarr-py, napari-ome-zarr and napari installed):
import numpy as np
import zarr
import napari
from ome_zarr.format import FormatV04
from ome_zarr.io import parse_url
from ome_zarr.writer import write_image, write_plate_metadata, write_well_metadata
path = "test_ngff_plate.zarr"
row_names = ["A", "B"]
col_names = ["1", "2", "3"]
well_paths = ["A/2", "B/3"]
field_paths = ["0", "1", "2"]
# generate data
mean_val = 10
num_wells = len(well_paths)
num_fields = len(field_paths)
size_xy = 128
size_z = 20
rng = np.random.default_rng(0)
data = rng.poisson(mean_val, size=(num_wells, num_fields, size_z, size_xy, size_xy)).astype(np.uint8)
# write the plate of images and corresponding metadata
store = parse_url(path, mode="w").store
root = zarr.group(store=store)
write_plate_metadata(root, row_names, col_names, well_paths)
for wi, wp in enumerate(well_paths):
row, col = wp.split("/")
row_group = root.require_group(row)
well_group = row_group.require_group(col)
write_well_metadata(well_group, field_paths)
for fi, field in enumerate(field_paths):
image_group = well_group.require_group(str(field))
write_image(
image=data[wi, fi], group=image_group, axes="zyx", storage_options=dict(chunks=(1, size_xy, size_xy))
)
viewer = napari.Viewer()
viewer.open(path, plugin="napari-ome-zarr")
napari.run()What I do not understand is how I now "browse the different wells"? The data shown seem to only have 20 z-planes but this is it?
