Better support for visualising highly multiplexed images

This is a tracking issue for some of the current issues when having a SpatialImage of circa >10 channels in SpatialData:

• Vizarr, Avivator, Vitessce fail when loading SpatialImage
  • Test: Non-ome test datasets fail, except when subsetted to 3 channels. Test datasets with ome work.
  • Solution: add ome.channels in NGFF metadata (See #230, posthoc fix code here)
• Loading a SpatialData object from disk with ome.channels NGFF metadata fails
  • Test: ome test datasets fails on SpatialData.read
  • Solution: fix channel parsing in io_raster.py maybe? (Also see #230)
• Show scale bar when viewing image
  • Not in Vitessce though it has support, is present in vtk.js
  • Vitessce scalebar currently defaults to 1 pixel = 1 micron
  • Solution: add physical units to metadata instead of ‘unit’ when writing SpatialData (See #357, #120, #30; NGFF spec on units)
• vtk.js viewer does not work for ImageElement if the name doesn’t end in .zarr
  • Test: non vtk datasets fail, vtk dataset works
  • Solution: create issue at vtk.js (See https://github.com/Kitware/itk-vtk-viewer/issues/719)
• bug in animated-cell viewer when data does not have Z and/or T channel
  • All datasets without z or t channel fail
  • Solution: create issue at animated-cell (See https://github.com/allen-cell-animated/website-3d-cell-viewer/issues/172)

Test datasets at https://dl01.irc.ugent.be/spatial/proteomics/macsima_liver/ome_test/

Combinations of 4 different options. Ideally, SpatialData outputs ome+transform NGFF images by default and this can be read in by all viewers of OME-NGFF.

3c: subset to only 3 channels instead of 10
ome: add ome channels metadata (can no longer be read in by SpatialData)
transform: add microns transformation (but still with unit: ‘unit’) (only option that passes NGFF validator)
vtk: added .zarr suffix to image

HumanLiverH35.zarr NGFF validator
HumanLiverH35_3c.zarr NGFF validator
HumanLiverH35_ome.zarr NGFF validator
HumanLiverH35_vtk.zarr NGFF validator
HumanLiverH35_microns.zarr NGFF validator
HumanLiverH35_3c_ome.zarr NGFF validator
HumanLiverH35_3c_vtk.zarr NGFF validator
HumanLiverH35_3c_microns.zarr NGFF validator
HumanLiverH35_ome_vtk.zarr NGFF validator
HumanLiverH35_ome_microns.zarr NGFF validator
HumanLiverH35_vtk_microns.zarr NGFF validator
HumanLiverH35_3c_ome_vtk.zarr NGFF validator
HumanLiverH35_3c_ome_microns.zarr NGFF validator
HumanLiverH35_3c_vtk_microns.zarr NGFF validator
HumanLiverH35_ome_vtk_microns.zarr NGFF validator
HumanLiverH35_3c_ome_vtk_microns.zarr NGFF validator

Start by reproducing the listed failures with the linked HumanLiverH35 test datasets and inspect spatialdata_io/readers/_utils/_utils.py and io_raster.py, especially the ome.channels and physical-unit metadata paths. Compare the results with the NGFF validator and the affected viewers; done means the unchecked loading, visualization, and scale-bar cases work without breaking SpatialData.read.