How to open the current Zarr based image data as OME-Zarr
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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