├── .nojekyll ├── styles.css ├── CNAME ├── .gitignore ├── janelia.jpg ├── template_image.png ├── review_process_image.png ├── posts.qmd ├── _data └── navigation.yml ├── index.qmd ├── file_formats.qmd ├── metadata.qmd ├── theme-dark.scss ├── .github └── workflows │ └── publish.yml ├── _quarto.yml ├── CONTRIBUTING.md ├── LICENSE ├── about.qmd ├── README.md ├── posts ├── title-metadata.html └── file_formats_introduction.qmd ├── docs └── site_libs │ └── quarto-html │ ├── quarto-syntax-highlighting-dark-8ea72dc5fed832574809a9c94082fbbb.css │ └── quarto-syntax-highlighting-549806ee2085284f45b00abea8c6df48.css ├── definitions.qmd └── REVIEW_PROCESS.md /.nojekyll: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /styles.css: -------------------------------------------------------------------------------- 1 | /* css styles */ 2 | -------------------------------------------------------------------------------- /CNAME: -------------------------------------------------------------------------------- 1 | datastandards.janelia.org 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # For macOS: 2 | .DS_Store 3 | 4 | # quarto: 5 | /_site/ 6 | /.quarto/ 7 | -------------------------------------------------------------------------------- /janelia.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JaneliaSciComp/JaneliaDataStandards/HEAD/janelia.jpg -------------------------------------------------------------------------------- /template_image.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JaneliaSciComp/JaneliaDataStandards/HEAD/template_image.png -------------------------------------------------------------------------------- /review_process_image.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JaneliaSciComp/JaneliaDataStandards/HEAD/review_process_image.png -------------------------------------------------------------------------------- /posts.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Posts" 3 | listing: 4 | contents: posts 5 | sort: "date desc" 6 | type: default 7 | categories: false 8 | --- 9 | -------------------------------------------------------------------------------- /_data/navigation.yml: -------------------------------------------------------------------------------- 1 | main: 2 | - title: "About" 3 | url: /about/ 4 | - title: "Posts" 5 | url: /posts/ 6 | - title: "File Formats" 7 | url: /file_formats/ 8 | - title: "Definitions" 9 | url: /definitions/ 10 | -------------------------------------------------------------------------------- /index.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Welcome!" 3 | --- 4 | 5 | :::{.column-page} 6 | This is a nascent project to unify bioimaging data conventions at HHMI's Janelia Research Campus. 7 | 8 | ![The Janelia Research Campus, Ashburn VA](janelia.jpg) 9 | ::: 10 | -------------------------------------------------------------------------------- /file_formats.qmd: -------------------------------------------------------------------------------- 1 | # Janelia's Bioimaging File Formats 2 | 3 | :::{.column-screen} 4 | 5 | ::: 6 | -------------------------------------------------------------------------------- /metadata.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Metadata: supported features" 3 | --- 4 | 5 | :::{.column-screen} 6 | 7 | ::: 8 | -------------------------------------------------------------------------------- /theme-dark.scss: -------------------------------------------------------------------------------- 1 | /*-- scss:defaults --*/ 2 | // Base document colors 3 | $body-bg: #181818; 4 | $body-color: white; 5 | $link-color: #75AADB; 6 | $popover-bg: #75aadb; 7 | 8 | // Code blocks 9 | $code-block-bg-alpha: -.8; 10 | 11 | // Navigation bar 12 | $navbar-bg: #181818; 13 | $navbar-hl: #75aadb; 14 | $navbar-fg: #75aadb; 15 | $dropdown-link-hover-color: #75aadb; 16 | -------------------------------------------------------------------------------- /.github/workflows/publish.yml: -------------------------------------------------------------------------------- 1 | on: 2 | workflow_dispatch: 3 | push: 4 | branches: main 5 | 6 | name: Quarto Publish 7 | 8 | jobs: 9 | build-deploy: 10 | runs-on: ubuntu-latest 11 | permissions: 12 | contents: write 13 | steps: 14 | - name: Check out repository 15 | uses: actions/checkout@v4 16 | 17 | - name: Set up Quarto 18 | uses: quarto-dev/quarto-actions/setup@v2 19 | 20 | - name: Render and Publish 21 | uses: quarto-dev/quarto-actions/publish@v2 22 | with: 23 | target: gh-pages 24 | env: 25 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 26 | -------------------------------------------------------------------------------- /_quarto.yml: -------------------------------------------------------------------------------- 1 | project: 2 | type: website 3 | 4 | execute: 5 | freeze: auto 6 | 7 | website: 8 | title: "Janelia Data Standards" 9 | navbar: 10 | tools: 11 | - icon: github 12 | href: https://github.com/JaneliaSciComp/JaneliaDataStandards 13 | left: 14 | - text: About 15 | href: about.qmd 16 | - text: Posts 17 | href: posts.qmd 18 | - text: File Formats 19 | menu: 20 | - text: Overview 21 | href: file_formats.qmd 22 | - text: Metadata features 23 | href: metadata.qmd 24 | - text: Definitions 25 | href: definitions.qmd 26 | 27 | format: 28 | html: 29 | theme: 30 | light: cosmo 31 | dark: [cosmo,theme-dark.scss] 32 | css: styles.css 33 | toc: false 34 | 35 | -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # How to contribute 2 | 3 | Thanks for considering contributing to Janelia's data standards! 4 | 5 | In order to keep things simple, please refrain from forking this repository. 6 | Instead, create a new branch with your changes in this repository and create a pull request against the main branch (or any other suitable branch). 7 | Alternatively, if your changes are small and reasonable, you may commit them to the main branch yourself. 8 | If you don't have edit rights in this repository but would like them, please contact Virginia Scarlett. 9 | 10 | Posts in a format suitable for [quarto](https://quarto.org), such as quarto markdown (.qmd) or a notebook (.ipynb) can be added to /posts/. 11 | Use the existing posts as a template, at least for the header block. Quarto will render these files to html, i.e., build the static site files. 12 | 13 | The workflow for submitting a PR (should you wish to do so) is as follows: \ 14 | Clone the repo > create your feature branch > do some work > Optionally do `quarto preview` to host the site locally and see it in your browser > `git commit` and `git push` as usual. 15 | 16 | To preview the site or build it locally, you will need quarto installed on your computer. Neither of these is strictly necessary, since a GitHub action should render the site files remotely for you. Changes may take up to 20 minutes to be reflected on the website. 17 | 18 | The rendered site pages are automatically stored in, and deployed from, the gh-pages branch, so please do not modify that branch. 19 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | BSD 3-Clause License 2 | 3 | Copyright (c) 2023, Howard Hughes Medical Institute 4 | 5 | Redistribution and use in source and binary forms, with or without 6 | modification, are permitted provided that the following conditions are met: 7 | 8 | 1. Redistributions of source code must retain the above copyright notice, this 9 | list of conditions and the following disclaimer. 10 | 11 | 2. Redistributions in binary form must reproduce the above copyright notice, 12 | this list of conditions and the following disclaimer in the documentation 13 | and/or other materials provided with the distribution. 14 | 15 | 3. Neither the name of the copyright holder nor the names of its 16 | contributors may be used to endorse or promote products derived from 17 | this software without specific prior written permission. 18 | 19 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 20 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 21 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 22 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 23 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 24 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 25 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 26 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 27 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 28 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 29 | -------------------------------------------------------------------------------- /about.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "About Janelia Data Standards" 3 | --- 4 | ## Purpose 5 | 6 | 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. 7 | 8 | **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. 9 | 10 | ## Style 11 | 12 | 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. 13 | 14 | ## Contributing 15 | 16 | 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. 17 | 18 | ## Structure 19 | 20 | This effort is in its infancy. Ultimately, the project is expected to consist of four components: 21 | 22 | - Written articles. 23 | - An accessible and easily readable website that hosts the articles. 24 | - A glossary and/or thesaurus. 25 | - A directory of example data that the public can view and browse. 26 | 27 | We appreciate the community’s interest in this social experiment. 28 | 29 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Janelia Data Standards 2 | [https://datastandards.janelia.org/](https://datastandards.janelia.org) 3 | 4 | ## Purpose 5 | 6 | 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. 7 | 8 | **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. 9 | 10 | ## Style 11 | 12 | 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. 13 | 14 | ## Contributing 15 | 16 | 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. 17 | 18 | ## Structure 19 | 20 | This effort is in its infancy. Ultimately, the project is expected to consist of four components: 21 | 22 | - Written articles. 23 | - An accessible and easily readable website that hosts the articles. 24 | - A glossary and/or thesaurus. 25 | - A directory of example data that the public can view and browse. 26 | 27 | We appreciate the community’s interest in this social experiment. 28 | 29 | -------------------------------------------------------------------------------- /posts/title-metadata.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | $if(by-affiliation/first)$ 4 |
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