Third-party tools additions

[sbesson]

Potential candidate for adding to the list of third-party tools consuming Bio-Formats https://docs.openmicroscopy.org/bio-formats/latest/users/index.html

• R - https://github.com/aoles/RBioFormats
• Wolfram (incl. Mathematica) - https://github.com/WolframResearch/BioFormatsLink

[sbesson]

A few thoughts related to this issue and motivated by the discussions in #84.

The User information includes a lot of content about third-party integrations. Most of it has been inherited from a previous iteration of the Bio-Formats documentation over a decade ago which was maintained as a wiki. It is fair to say we haven't significantly expanded this section or even adjusted the workflow. As we are talking about additions/modification/deletions and there are growing discussions about the policy for community contributions, this feels fairly timely

There are a few issues with the way third-party tools are maintained in this documentation. Probably most of these stem from the fact that these integrations are neither developed nor tested by the Bio-Formats maintainer team.

• as noted in Review minimal MATLAB version #83, several of these integrations might be in a stale state because the integration or even the application itself is no longer developed, supported or maintained
• the content of these individual pages usually includes a description of the application as well as installation instructions for the integration and is hard to maintain

Moving forward, my inclination would be to extract this third-party tooling content from the reference Bio-Formats documentation as follows:

• define the set of user facing tool that are officially maintained, tested and supported. Currently, I would define these as the command-line utilities, the Fiji/ImageJ plugin and the MATLAB toolbox
• extract all the content of the user documentation that does not meet this criterion to a new location to be determined e.g. a GitHub repository and/or a website registering third-party Bio-Formats integrations. In its simplest form, this could start as a single Markdown table with linking to other pages giving additional content for the given applications
• define the rules for managing the content of this third-party tools registry. As per the above, I would vote for not puttig this responsibility to Bio-Formats maintainers. If this content lives under the OME organization, probably a minimal amount of review should happen. Or it could live under a separate organization.
• remove these items from the reference documentation and include a link to these third-party tools

There have been a few attempts at organizing community documentation in the past e.g. https://github.com/ome/community-docs. In a similar vein, for OMERO, several third-party integrations have been migrated to https://omero-guides.readthedocs.io/. We should definitely build on the successes and failures of these experiences and ideally find a solution that aligns with the management of the OME training materials /cc @jburel @pwalczysko