pybioclip
Python package that simplifies using the BioCLIP foundation model.
Science Score: 65.0%
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
Found 2 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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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 (10.9%) to scientific vocabulary
Repository
Python package that simplifies using the BioCLIP foundation model.
Basic Info
- Host: GitHub
- Owner: Imageomics
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://imageomics.github.io/pybioclip/
- Size: 3.51 MB
Statistics
- Stars: 36
- Watchers: 3
- Forks: 7
- Open Issues: 6
- Releases: 8
Metadata Files
README.md
pybioclip
Command line tool and python package to simplify using BioCLIP, including for taxonomic or other label prediction on (and thus annotation or labeling of) images, as well as for generating semantic embeddings for images. No particular understanding of ML or computer vision is required to use it. It also implements a number of performance optimizations for batches of images or custom class lists, which should be particularly useful for integration into computational workflows.
Documentation
See the pybioclip documentation website for requirements, installation instructions, and tutorials.
License
pybioclip is distributed under the terms of the MIT license.
Citation
Our code (this repository):
@software{Bradley_pybioclip_2025,
author = {Bradley, John and Lapp, Hilmar and Campolongo, Elizabeth G.},
doi = {10.5281/zenodo.13151194},
month = jul,
title = {{pybioclip}},
version = {2.0.0},
year = {2025}
}
BioCLIP paper:
@inproceedings{stevens2024bioclip,
title = {{B}io{CLIP}: A Vision Foundation Model for the Tree of Life},
author = {Samuel Stevens and Jiaman Wu and Matthew J Thompson and Elizabeth G Campolongo and Chan Hee Song and David Edward Carlyn and Li Dong and Wasila M Dahdul and Charles Stewart and Tanya Berger-Wolf and Wei-Lun Chao and Yu Su},
booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
year = {2024}
}
Also consider citing the BioCLIP code:
@software{bioclip2023code,
author = {Samuel Stevens and Jiaman Wu and Matthew J. Thompson and Elizabeth G. Campolongo and Chan Hee Song and David Edward Carlyn},
doi = {10.5281/zenodo.10895871},
title = {BioCLIP},
version = {v1.0.0},
year = {2024}
}
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)
cff-version: 1.2.0
title: pybioclip
message: If you use this software, please cite both the conference paper from references section and the software itself.
type: software
authors:
- given-names: John
family-names: Bradley
- given-names: Hilmar
family-names: Lapp
- family-names: Campolongo
given-names: "Elizabeth G."
identifiers:
- type: doi
value: 10.5281/zenodo.13151194
- description: "The GitHub release URL of tag 2.0.0."
type: url
value: "https://github.com/Imageomics/pybioclip/releases/tag/2.0.0"
- description: "The GitHub URL of the commit tagged with 1.3.2."
type: url
value: "https://github.com/Imageomics/pybioclip/tree/c318c6c9f2bc75c4da6ac060927623de69331344"
repository-code: 'https://github.com/Imageomics/pybioclip'
url: 'https://github.com/Imageomics/pybioclip'
abstract: Python package and command line tool that simplifies using the BioCLIP foundation model.
keywords:
- clip
- biology
- CV
- imageomics
- animals
- species
- images
- taxonomy
- "rare species"
- "endangered species"
- "evolutionary biology"
- multimodal
- "knowledge-guided"
- python
- "command line"
- bioclip
- plants
- fungi
- genus
- "image classification"
license: MIT
version: 2.0.0
date-released: '2025-07-30'
references:
- type: conference-paper
title: "BioCLIP: A Vision Foundation Model for the Tree of Life"
authors:
- family-names: Stevens
given-names: Samuel
- family-names: Wu
given-names: Jiaman
- family-names: Thompson
given-names: "Matthew J."
- family-names: Campolongo
given-names: "Elizabeth G."
- family-names: Song
given-names: "Chan Hee"
- family-names: Carlyn
given-names: "David Edward"
- family-names: Dong
given-names: Li
- family-names: Dahdul
given-names: "Wasila M"
- family-names: Stewart
given-names: Charles
- family-names: "Berger-Wolf"
given-names: Tanya
- family-names: Chao
given-names: "Wei-Lun"
- family-names: Su
given-names: Yu
version: 1.0.0
doi: "10.5281/zenodo.10895871"
date-released: "2024-03-29"
GitHub Events
Total
- Fork event: 4
- Create event: 42
- Release event: 3
- Issues event: 62
- Watch event: 15
- Delete event: 35
- Member event: 1
- Issue comment event: 157
- Push event: 239
- Gollum event: 19
- Pull request event: 61
- Pull request review comment event: 87
- Pull request review event: 168
Last Year
- Fork event: 4
- Create event: 42
- Release event: 3
- Issues event: 62
- Watch event: 15
- Delete event: 35
- Member event: 1
- Issue comment event: 157
- Push event: 239
- Gollum event: 19
- Pull request event: 61
- Pull request review comment event: 87
- Pull request review event: 168
Committers
Last synced: 6 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| John Bradley | j****8@g****m | 69 |
| Hilmar Lapp | h****p@d****t | 4 |
| Matt Thompson | 3****j | 2 |
| Sreejith Menon | 1****8 | 1 |
| Elizabeth Campolongo | 3****9 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 56
- Total pull requests: 127
- Average time to close issues: 23 days
- Average time to close pull requests: 5 days
- Total issue authors: 11
- Total pull request authors: 7
- Average comments per issue: 2.32
- Average comments per pull request: 1.3
- Merged pull requests: 103
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 38
- Pull requests: 89
- Average time to close issues: 14 days
- Average time to close pull requests: 5 days
- Issue authors: 9
- Pull request authors: 5
- Average comments per issue: 2.76
- Average comments per pull request: 1.43
- Merged pull requests: 70
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- johnbradley (26)
- hlapp (11)
- thompsonmj (9)
- work4cs (2)
- nblumoe (2)
- quitmeyer (1)
- smenon8 (1)
- Link7808 (1)
- yanis-falaki (1)
- egrace479 (1)
- Jordan-Pierce (1)
Pull Request Authors
- johnbradley (101)
- thompsonmj (9)
- hlapp (8)
- Copilot (3)
- yanis-falaki (2)
- egrace479 (2)
- smenon8 (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 197 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 8
- Total maintainers: 2
pypi.org: pybioclip
Python package that simplifies using the BioCLIP foundation model.
- Documentation: https://imageomics.github.io/pybioclip/
- License: mit
-
Latest release: 2.0.0
published 7 months ago