https://janeliascicomp.github.io/JaneliaDataStandards/
The Janelia Data Standards group was formed by bioimaging developers who have encountered specific, practical bioimaging data dilemmas for which there is little or no guidance from international community standards. Janelia is excited about international standardization efforts, particularly OME-NGFF. Janelia is contributing to OME-NGFF and is rooting for its success. However, such efforts are not enough, since research experiments may often outpace or even diverge from contemporary community standards. The essays in this collection are meant to fill that gap.
This website is Janelia’s bioimaging developers’ manifesto. It is a collection of essays written by developers, for developers, on the advanced technical challenges they’ve encountered. It records the choices Janelia’s developers have made when encountering exotic data, so that those encountering similar situations can make consistent choices.
The articles in this collection will be vetted, and their conclusions authoritative, for Janelia’s purposes. Where swift, unambiguous decisions are needed, such decisions will be made. The rationale behind those decisions will be explained, and they will become standard practice at Janelia. Contributors are encouraged to remain pragmatic, to describe their use cases, and to share their example data. That being said, where applicable, developers should speak to the abstract design principles that drove their choices.
This project aims to develop conventions that Janelians need to do their work, and to disseminate those conventions across Janelia. It is not this group’s goal to create a comprehensive textbook, nor to create an international standard. However, as this project matures, contributions to and from the community may be considered. Individuals outside of Janelia who are interested in writing an article should create a GitHub issue to explore this possibility before investing time in it. It is this group’s hope that the rapidly evolving conventions developed here may ultimately, gradually, be considered for incorporation into the OME-NGFF standard as well.
This effort is in its infancy. Ultimately, the project is expected to consist of four components:
- Written articles.
- An accessible and easily readable website that hosts the articles.
- A glossary and/or thesaurus.
- A directory of example data that the public can view and browse.
We appreciate the community’s interest in this social experiment.