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Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

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ome-ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

Editing

Specifications are written in markdown, or technically bikeshed -- a markdown document, with special extensions understood by the bikeshed tool. The bikeshed tool is run on-commit via the spec-prod github action, generating the familiar "spec looking" ReSpec format. ReSpec is just html with a javascript ReSpec library.

Specification files end with the .bs file extension. The github action runs on commit to automatically convert to respec/html, via bikeshed.

Learn more about bikeshed

Reviewing

Commits on GitHub can be viewed using web services from the W3C:

New version

  • Make new changes to latest/index.bs
  • Update changelog at the bottom of latest/index.bs
  • Find references to previous version and in most cases, bump to the current version.

JSON schemas

For each top-level metadata key of the OME-NGFF specification, JSON schemas are maintained for each version of the specification and stored under $VERSION/schemas/ or latest/schemas/. Tests validating these schemas must be implemented to follow principles of the JSON schema test suite and stored under $VERSION/tests/ or latest/tests/ to allow their execution on each CI build.

All official example snippets must also be extracted and managed as separate JSON files under $VERSION/examples/ or latest/examples/, validated by the appropriate schema by adding a .config.json file specifying the JSON schema to use and included in the specification document using the include-code directive.

The official OME-NGFF JSON schemas are published under https://ngff.openmicroscopy.org//schemas/<schema_name>.schema using the Spec prod GitHub action. When a new JSON schema is introduced, this action needs to be reviewed to update the deployment script and allow the publication of the schema.

Release process

  • copy latest/index.bs to $VERSION/index.bs
  • copy latest/copyright.include to $VERSION/copyright.include
  • update the head matter in the $VERSIONed file
    • Use: Status: w3c/CG-FINAL
    • Update URL:
    • Use the following Status Text:: "This is the $VERSION release of this specification. Migration scripts will be provided between numbered versions. Data written with the latest version (an "editor's draft") will not necessarily be supported."
  • update the footer matter in the $VERSIONed file
    • Version in the citation block including release date
  • Update https://github.com/ome/spec-prod for the new version

Citing

Please see https://ngff.openmicroscopy.org/latest#citing for the latest citation.

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  • Bikeshed 88.8%
  • Python 10.4%
  • Other 0.8%