[ENH] Add OME-Zarr as a supported format for imaging data

[kabilar]

Fix #1704

cc @satra @balbasty @ayendiki

[kabilar]

I fixed most of the CI failures. The remaining 2 failures appear unrelated.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.07%. Comparing base (308395f) to head (827e536).

Additional details and impacted files

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##           master    #2392   +/-   ##
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  Coverage   83.07%   83.07%           
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  Files          22       22           
  Lines        1696     1696           
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  Hits         1409     1409           
  Misses        287      287           

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[effigies]

I support this. It is in line with the decision made at the Copenhagen 2023 meeting which was: HDF5 and Zarr are preferred formats for new multi-dimensional data.

It looks like we dropped the ball on the wording in #1614, but I do think the decision should hold, nonetheless.

[yarikoptic]

I thought to scream "duplication is evil!" but apparently we do not really disclose much in microscopy section about OME or NGFF

❯ git grep -i -e OME.Zarr -e ngff -- src/modality-specific-files/microscopy.md
src/modality-specific-files/microscopy.md:file's header. Further, OME-ZARR (sometimes referred to as OME-NGFF or NGFF) has been developed to provide improved
src/modality-specific-files/microscopy.md:-   [OME-ZARR/NGFF](https://ngff.openmicroscopy.org/latest/) (`.ome.zarr` directories)

but then we should at least take an opportunity to point to this section here from within that microscopy.md section. attn @bids-standard/bep031

[kabilar]

Good idea. I have just pushed a commit.

[yarikoptic]

I wonder if some schema-level check /could/should be added here based on some characteristics of the volume(s) -- e.g. any dimension having over 1k elements?

[effigies]

Could: yes

checkname:
  issue: ...
  selectors:
    - type(nifti_header) != 'null'
  checks:
    - max(nifti_header.shape) <= 1000

Should: 🤷🏻

[kabilar]

Thanks. I don't feel too strongly here, but if we do add a check let's use level: warning.

[yarikoptic]

That's shaping up nicely! Please complement with a PR against bids-examples which would demo some fake dataset with .ome.zarr . FWIW -- here I am creating one but scripting so I could easily recreate etc

[kabilar]

That's shaping up nicely! Please complement with a PR against bids-examples which would demo some fake dataset with .ome.zarr . FWIW -- here I am creating one but scripting so I could easily recreate etc

Thanks @yarikoptic. There was already a bids-examples dataset with an .ome.zarr so I pushed a commit that references it.