Draft BEP031

[mariehbourget]

@jcohenadad
This is a draft PR of BEP031 for review and approbation on our side only.
Once it is completed, I will open a PR on the main BIDS repo.

I recommend using mkdocs to see the rendered version of the doc.

The two files to review are:
src/04-modality-specific-files/10-microscopy.md --> will appear under Modality specific files/Microscopy in the rendered doc.
src/schema/entities.yaml --> will appear under Appendix/Entities in the rendered doc.

Other files do not need review at this point.

In the final version (after community review), the tables and the file tree examples will be generated automatically via macros and specific yaml files. I was asked to do "manual" tables and examples to minimize the number of changed files and facilitate community review.

A few remaining points to address, details in comments in the 10-microscopy.md file.

• If we have a paper, add the link in Citing BIDS
• Complete BIDS-examples and add their names
• Add other links to relevant dataset examples
  • update our ADS dataset
  • it would be great to have a "real" OMETIFF dataset.
• Finalize "chunks" figure
• StationName metadata description --> to check with maintainers
• BodyPart metadata description --> to check with maintainers
• Check matrix definition "Array of arrays of number" --> according to this "In JSON, array values must be of type string, number, object, array, boolean or null." and this "Matrices in JavaScript Object Notation (JSON) are represented in this list of lists.". So an array of arrays of numbers is allowed. --> to check with the maintainers.
• Make sure JSON example is "plausible" (confirmed with NanoZoomer spec here).
• Recommended participant data section may changed
• Add "photo" example
• Check with maintainers if make_filetree macro should be used before on only after community review.

Note: I converted this PR from "draft" to "ready for review" only because I had problems pushing new commits to the branch when in "draft". Not sure why.

[mariehbourget]

Hi @jcohenadad,
If you wish to review, the files src/04-modality-specific-files/10-microscopy.md and src/schema/entities.yaml are complete and will be submitted as a PR to the main BIDS-repo next week.

[jcohenadad]

LGTM!