imageomics-guide
Imageomics-focused guide to collaborative work, including GitHub and Hugging Face workflows.
Science Score: 52.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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✓Institutional organization owner
Organization imageomics has institutional domain (imageomics.osu.edu) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.1%) to scientific vocabulary
Keywords
Repository
Imageomics-focused guide to collaborative work, including GitHub and Hugging Face workflows.
Basic Info
- Host: GitHub
- Owner: Imageomics
- License: cc0-1.0
- Language: Python
- Default Branch: main
- Homepage: https://imageomics.github.io/Imageomics-guide/
- Size: 8.33 MB
Statistics
- Stars: 4
- Watchers: 6
- Forks: 0
- Open Issues: 17
- Releases: 2
Topics
Metadata Files
README.md
Imageomics Guide
Welcome to the Imageomics Guide!
Just joining or starting a new project? Check out the Imageomics Guide for guidance on conventions and best practices.
About the Guide
This guide started as an Imageomics Institute-internal wiki, focused on providing guidance and best practices for collaborative and interdisciplinary (computer science + biology) work. Recognizing that the topics and suggestions are broadly applicable to anyone working in similar or adjacent fields, we moved the vast majority to this guide. To increase accessibility for those less familiar with GitHub, we generated the website from our Markdown documents (which used to be wiki pages) with Material for MkDocs.
Please feel free to open an issue with any questions regarding the content of this guide.
Contributing
If you'd like to contribute to this guide, please read our Contributing Guidelines for information about our standards, development workflow, and submission process.
Testing
To test this site locally, first clone this repository, then create an environment with requirements.txt
pip install -r requirements.txt
and run mkdocs serve:
mkdocs serve
Then the site will run at http://127.0.0.1:8000/Imageomics-guide/.
History
This guide houses the information needed to get started with and use institute resources readily available to all members. However, most of its content is applicable to anyone working more broadly in the field of imageomics or adjacent fields of computer and data science, and it is tailored to help domain scientists bridging that gap. We further expanded development to include a more general template guide, the Collaborative Distributed Science Guide, for others wishing to develop a similar organization-specific guide (please see the template repository for more information). This solution was born out of the desire to do so for the AI and Biodiversity Change (ABC) Global Center while limiting duplicative updates between guides (Imageomics and ABC share some team members on this project).
Acknowledgments
This work was supported by both the Imageomics Institute and the AI and Biodiversity Change (ABC) Global Center. The Imageomics Institute is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under Award #2118240 (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). The ABC Global Climate Center is funded by the US National Science Foundation under Award No. 2330423 and Natural Sciences and Engineering Research Council of Canada under Award No. 585136. This guide draws on research supported by the Social Sciences and Humanities Research Council. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, Natural Sciences and Engineering Research Council of Canada, or Social Sciences and Humanities Research Council.
Owner
- Name: Imageomics Institute
- Login: Imageomics
- Kind: organization
- Website: https://imageomics.osu.edu
- Twitter: imageomics
- Repositories: 4
- Profile: https://github.com/Imageomics
Citation (CITATION.cff)
abstract: "Imageomics-focused guide to collaborative work, including GitHub and Hugging Face workflows."
authors:
- family-names: "Campolongo"
given-names: "Elizabeth G."
orcid: "https://orcid.org/0000-0003-0846-2413"
- family-names: "Thompson"
given-names: "Matthew J."
orcid: "https://orcid.org/0000-0003-0583-8585"
- family-names: Zhang
given-names: Net
orcid: "https://orcid.org/0000-0003-2664-451X"
- family-names: "Duan"
given-names: "Zoe"
orcid: "https://orcid.org/0000-0002-8547-5907"
- family-names: "Bradley"
given-names: "John"
orcid: "https://orcid.org/0000-0003-3858-848X"
- family-names: "Lapp"
given-names: "Hilmar"
orcid: "https://orcid.org/0000-0001-9107-0714"
cff-version: 1.2.0
date-released: "2025-08-29"
identifiers:
- description: "The GitHub release URL of tag v2.0.0."
type: url
value: "https://github.com/Imageomics/Imageomics-guide/releases/tag/v2.0.0"
- description: "The GitHub URL of the commit tagged with v2.0.0."
type: url
value: "https://github.com/Imageomics/Imageomics-guide/tree/48ee6c07a4ddfa453c85f8ad62f88e5c623f6a15"
keywords:
- imageomics
- metadata
- guide
- "best practices"
- "cheat-sheet"
- "command line cheat-sheet"
- "collaborative science"
- projects
- "collaborative workflows"
- standards
license: CC0-1.0
message: "If you find these docs helpful in your research, please cite them as below."
repository-code: "https://github.com/Imageomics/Imageomics-guide"
title: "Imageomics Guide"
version: "2.0.0"
references:
- authors:
- family-names: "Campolongo"
given-names: "Elizabeth G."
orcid: "https://orcid.org/0000-0003-0846-2413"
- family-names: "Thompson"
given-names: "Matthew J."
orcid: "https://orcid.org/0000-0003-0583-8585"
- family-names: Zhang
given-names: Net
orcid: "https://orcid.org/0000-0003-2664-451X"
- family-names: "Duan"
given-names: "Zoe"
orcid: "https://orcid.org/0000-0002-8547-5907"
- family-names: "Bradley"
given-names: "John"
orcid: "https://orcid.org/0000-0003-3858-848X"
- family-names: Eyriay
given-names: Iuliia
orcid: "https://orcid.org/0009-0007-1597-8684"
- family-names: Taylor
given-names: Graham
orcid: "https://orcid.org/0000-0001-5867-3652"
- family-names: "Lapp"
given-names: "Hilmar"
orcid: "https://orcid.org/0000-0001-9107-0714"
date-released: "2025-08-15"
doi:
license: CC0-1.0
repository-code: "https://github.com/Imageomics/Collaborative-distributed-science-guide"
title: "Collaborative Distributed Science Guide"
version: 1.0.0
doi: "10.5281/zenodo.16950875"
GitHub Events
Total
- Create event: 22
- Release event: 2
- Issues event: 37
- Watch event: 3
- Delete event: 19
- Member event: 3
- Issue comment event: 46
- Push event: 62
- Public event: 1
- Pull request review comment event: 35
- Pull request review event: 55
- Pull request event: 33
Last Year
- Create event: 22
- Release event: 2
- Issues event: 37
- Watch event: 3
- Delete event: 19
- Member event: 3
- Issue comment event: 46
- Push event: 62
- Public event: 1
- Pull request review comment event: 35
- Pull request review event: 55
- Pull request event: 33
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 23
- Total pull requests: 21
- Average time to close issues: 3 months
- Average time to close pull requests: 11 days
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 1.35
- Average comments per pull request: 0.14
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 23
- Pull requests: 21
- Average time to close issues: 3 months
- Average time to close pull requests: 11 days
- Issue authors: 4
- Pull request authors: 3
- Average comments per issue: 1.35
- Average comments per pull request: 0.14
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- egrace479 (20)
- thompsonmj (2)
- hlapp (2)
- gwtaylor (1)
Pull Request Authors
- egrace479 (17)
- NetZissou (4)
- thompsonmj (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v4 composite
- actions/setup-python v5 composite
- peaceiris/actions-gh-pages v4 composite
- mkdocs *
- mkdocs-glightbox *
- mkdocs-macros-plugin *
- mkdocs-material *
- mkdocs-material-extensions *