Update tools and datasets

[lubianat]

This PR addresses documentation gaps outlined in multiple issues

(1) The data page is restructured in significant ways:

• Data resources are now categorized, similarly to the tools page

• There are small paragraphs describing the sets of resources, as well as a general introduction

• Information on size and number of OME-Zarr files in each resource is removed (it is unmaintainable and often hard/impossible to verify). Without a way to check it, there is a risk of misinforming the reader and the numbers get brittle. Some of them were clearly outdated.

(2) A new ecosystem page is created, covering the projects that did not fit on tools or data`

(3) The PR is also collecting new tools and resources, so they are not spread in many small PRs (cited in the commits individually).

and

(4) it sets the OME logo as a favicon (closes #532)

This PR supersedes

• Add documentation for 'atlas'-type resources #512
• Add kfb2zarr to Zarr converters #525

Points to clear out:

• creation and naming of "/ecosystem"
• use of the OME logo (assuming ok, as this is under the OME org)
• use of the proxy "https://tiago.bio.br?links?go={shortcut}" as a way to circumvent huge neuroglancer URLS that break sphinx). Are there any better solutions?

as this ended up being somewhat large, cc @ome/ngff-docs

[github-actions]

Automated Review URLs

• Readthedocs

[lubianat]

last commits
close #496

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/ngff-weekly-dev-update-thread/110810/107

[m-albert]

Hi @lubianat, I just read your post on image.sc and thought I'd suggest adding multiview-stitcher under "Other tools and libraries". Disclaimer: I'm the main developer of the tool.

Name	Link	Description
multiview-stitcher		Interoperable Python package for aligning, fusing, and stitching large 2D/3D image datasets, with first-class support for OME-Zarr workflows.

Thank you :)

[lubianat]

@m-albert thanks! I added you as a co-author (after some struggle), hopefully that is okay

[m-albert]

@lubianat Amazing, thank you Tiago 🙏

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/tissuumaps-vs-ome-zarr/120430/4

[lubianat]

maybe the bat-signal @ome/ngff-docs works?

[joshmoore]

Looks like there's a table issue

[jo-mueller]

Huggingface logo seems a bit out of proportion :)

[jo-mueller]

In some instances I think it would be nice to directly link to the actual project, i.e., link to biofile finder rather than its gh page?

[erickmartins]

maybe the bat-signal @ome/ngff-docs works?

Did not ping me on github notifications, but sent me an email notification. Arguably a me problem.

[govekk]

Rendering libraries table in Tools is broken

Otherwise thanks for doing the work to keep this up to date!

[lubianat]

Thanks all! Nice that the ping worked, even if in unexpected ways for some.

I'll fix the formating issues

In some instances I think it would be nice to directly link to the actual project, i.e., link to biofile finder rather than its gh page?

on that @jo-mueller, I agree generally. I do have a secret plan of scraping those github ids to get some metrics, I'll see if I can figure out a way to link both in a clean way.

I think having repository + docpage/website can work cleanly. I'll give it a shot