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Nested NGFF images can be written, not read #340
Description
When writing an image with a name which contains slashes, it is stored in a Zarr subgroup. However, the ome_zarr Reader does not descend into zgroups that do not match a spec, and thus returns no images to spatialdata._io.io_zarr._read_multiscale.
def test_read_spatialdata_with_nested_zgroups(tmp_path: str):
import numpy as np
sdata = SpatialData()
sdata.add_image(
name="slide1/well1/image",
image=Image2DModel.parse(np.random.random((2, 10, 10))),
)
path = Path(tmp_path) / "tmp.zarr"
sdata.write(path, overwrite=True)
# This should probably not raise:
# "ValueError: len(nodes) = 0, expected 1. Unable to read the NGFF file. Please report this bug and attach a minimal data example."
sdata_parsed = SpatialData.read(str(path))
assert len(sdata_parsed.images) == 1A work-around is to use a flat hierarchy with e.g. . delimiters instead of slashes.
This could be an upstream issue in ome_zarr, or SpatialData could forbid and validate that there are no slashes.
Activity
LucaMarconato commentedon Aug 23, 2023
Hi @aeisenbarth, thanks for reporting this. @giovp is working on an improvement of the IO and after that PR is merged we want to work on supporting parsing arbitrarily nested NGFF objects. We will keep in mind the case you mentioned and add a test for it.
aeisenbarth commentedon Aug 24, 2023
A use case that I was playing around with is to store high-content screening data using the NGFF Plate spec (currently not possible due to various issues).
It would look like:
where
image_nameis in our case the acquisition name (it is not clear to me whether ome-zarr-py means acquisitions or field of views, currently it only supports integer names).spatialdata.zarr/labelswithout images (ome-zarr-py cannot read plates of only labels).All in all, I think arbitrary nesting could be too complex and a Pandora's box.
LucaMarconato commentedon Aug 26, 2023
Thanks for providing the use case.
I think that this can be handled easily as we are using only portions of
ome-zarr-pyfor IO and we could read labels from anywhere without restrictions, also it would be possible to store images and labels in a mixed way without having to replicate the hierarchy, because we could drop the parent foldersimagesand `labels.This would be instead more problematic. Do you know already some plugin that can handle table annotations on such a merged Dask representation?
LucaMarconato commentedon Mar 23, 2024
With the new #501 we allow only element names that don't contain slashes. I will reintroduce the possibility to have slashes (writing nested hierarchies was initially not the intended behavior) in a PR for this more general issue: #398 (that we will try to make follow soon). Closing this issue as with the new incremental PR nested NGFF images won't be able to be written.