Display NGFF volume data in 3D Slicer

ngff.py

"""

Display zarr from s3 buckets for example data from here:
https://www.openmicroscopy.org/2020/11/04/zarr-data.html

exec(open("/Users/pieper/idc/ngff.py").read())

see also: /Volumes/GoogleDrive/My\ Drive/hacks/sardana.py
https://gist.github.com/pieper/10ee6add544633f4c75dbb293ef087bc

"""

import numpy

try:
    import ome_zarr
except:
    pip_install("ome-zarr")

import ome_zarr
import ome_zarr.io
import ome_zarr.reader

# idr0044 from https://www.openmicroscopy.org/2020/11/04/zarr-data.html
zarrEndpoint = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/4007801.zarr"

location = ome_zarr.io.parse_url(zarrEndpoint)

reader = ome_zarr.reader.Reader(location)

nodes = [node for node in reader()]
node = nodes[0]

level = len(node.data) - 3
timePoint = int(node.data[level].shape[0] / 2)

channel = 1
volume = node.data[level][timePoint][channel]

voxelType=vtk.VTK_UNSIGNED_SHORT
dimensions = list(volume.shape)
dimensions.reverse()

imageData = vtk.vtkImageData()
imageData.SetDimensions(dimensions)
imageData.AllocateScalars(voxelType, 1)

volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", "Zarr Volume")
volumeNode.SetAndObserveImageData(imageData)
volumeNode.CreateDefaultDisplayNodes()
volumeNode.CreateDefaultStorageNode()

array = slicer.util.arrayFromVolume(volumeNode)
array[:] = volume
slicer.util.arrayFromVolumeModified(volumeNode)