scverse / scverse/spatialdata

How to open the current Zarr based image data as OME-Zarr

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Python
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Description

As discussed in https://github.com/scverse/spatialdata/issues/803, the zarr based image data that is currently stored with spatialdata is not compatible with the current OME-Zarr spec and can thus not readily be opened with the current community eco-system for supporting OME-Zarr.

For simplicity I will call the currently saved image data SD-Zarrr (short for SpatialData-Zarr).
I would like to explore whether we could somehow make it possible to open SD-Zarr as OME-Zarr.

One idea that I have is to add another folder next to the images folder and call this extra folder ome-zarr. In that folder there would be sub-folders for the images stored in the images folder. These subfolders would only contain a .zgroup and .zattrs with a valid OME-Zarr multiscales where the paths to the resolution levels in the multiscales would then be, e.g. ../../images/img0/0. I don't know whether this would work? @bogovicj @joshmoore @bugraoezdemir

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading issue #803 and inspecting how the current SD-Zarr image data is stored. Investigate whether an additional ome-zarr folder with .zgroup and .zattrs can expose paths such as ../../images/img0/0 under the current OME-Zarr specification; done means the existing image data can be opened by the current OME-Zarr ecosystem.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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