Add kfb2zarr to Zarr converters

[camlloyd]

Adds kfb2zarr to the Zarr converters list. Converts KFBio whole slide images (.kfb, .kfbf) to OME-Zarr.

[github-actions]

Automated Review URLs

• Readthedocs

[camlloyd]

Any feedback is much appreciated!

[lubianat]

Thank you @camlloyd! PR looks good as far as I can tell. Just out of curiosity, would you have a bit more context on where kfb2zarr is used (or planned to be used) at the moment?

I'll ping @clbarnes for the Rust content

[camlloyd]

Might also be worth adding zarrs to Zarr readers & writers.

[clbarnes]

I can completely understand the choice to manage OME-Zarr metadata by handwriting JSON values instead of bringing in more dependencies, particularly in the context of one-shot writing, but I wondered whether you had come across https://crates.io/crates/ome_zarr_metadata for representing and validating OME-Zarr metadata?

The question of zarrs in the readers & writers section brings up whether we should really be listing and including raw zarr libraries as implied by the section titles. In my opinion that should be left to the zarr project and we should only concern ourselves with tools specific to OME-Zarr.

[camlloyd]

I can completely understand the choice to manage OME-Zarr metadata by handwriting JSON values instead of bringing in more dependencies, particularly in the context of one-shot writing, but I wondered whether you had come across https://crates.io/crates/ome_zarr_metadata for representing and validating OME-Zarr metadata?

Yes, that was my reasoning at the time, but your feedback was the push I needed - thank you!

kfb2zarr will use ome_zarr_metadata in the next release.

The question of zarrs in the readers & writers section brings up whether we should really be listing and including raw zarr libraries as implied by the section titles. In my opinion that should be left to the zarr project and we should only concern ourselves with tools specific to OME-Zarr.

Understood!

[camlloyd]

Thank you @camlloyd! PR looks good as far as I can tell. Just out of curiosity, would you have a bit more context on where kfb2zarr is used (or planned to be used) at the moment?

It's for users with KFBIO slide scanners who wish to open their whole slide images in tools such as QuPath, Napari etc (as OME-Zarr rather than .svs, .tiff, .dcm).

See:

1. https://forum.image.sc/t/how-to-open-kfbf-format-files-in-fiji/91249
2. https://forum.image.sc/t/does-qupath-support-kbf-format/40978

After yesterday's Open Bioimaging Practices Meetup, I would like to add this as a Fractal task.

If this use case is too specific for this list, I understand!

[lubianat]

Thanks @camlloyd for the context. It is specific, but that is fine AFAIK, as it is solving a documented need of the community. Thanks for that.

As long as there is a plan to maintain the converter for the near future, LGTM

[lubianat]

Hi @camlloyd, I am doing a refresh on the tool & data docs.
I have cherry-picked your changes there, I hope that is okay.

So this PR is superseded by #529

Thank you for the contributions!