pybioclip

Python package that simplifies using the BioCLIP foundation model.
https://github.com/imageomics/pybioclip

Category: Biosphere
Sub Category: Biodiversity Data Access and Management

Keywords

bioclip biology clip command-line-interface cv image-classification knowledge-guided taxonomy

Keywords from Contributors

clip taxonomy

Last synced: about 10 hours ago
JSON representation

Repository metadata

Python package and CLI that simplifies using the BioCLIP family of foundation models.

• Host: GitHub
• URL: https://github.com/imageomics/pybioclip
• Owner: Imageomics
• License: mit
• Created: 2024-03-28T20:12:01.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2026-08-15T02:04:32.000Z (15 days ago)
• Last Synced: 2026-08-19T16:34:33.062Z (11 days ago)
• Topics: bioclip, biology, clip, command-line-interface, cv, image-classification, knowledge-guided, taxonomy
• Language: Python
• Homepage: https://imageomics.github.io/pybioclip/
• Size: 7.15 MB
• Stars: 65
• Watchers: 3
• Forks: 14
• Open Issues: 17
• Releases: 14
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff
  • Zenodo: .zenodo.json
  • Copilot: .github/copilot-instructions.md

README.md

@inproceedings{gu2025bioclip,
  title={Bio{CLIP} 2: Emergent Properties from Scaling Hierarchical Contrastive Learning},
  author={Jianyang Gu and Samuel Stevens and Elizabeth G Campolongo and Matthew J Thompson and Net Zhang and Jiaman Wu and Andrei Kopanev and Zheda Mai and Alexander E. White and James Balhoff and Wasila Dahdul and Daniel Rubenstein and Hilmar Lapp and Tanya Berger-Wolf and Wei-Lun Chao and Yu Su},
  booktitle={The Thirty-ninth Annual Conference on Neural Information Processing Systems},
  year={2025},
  url={https://openreview.net/forum?id=yPC9zmkQgG}
}

@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}
}

@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}
}

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:
  - description: "The GitHub release URL of tag 2.1.5."
    type: url
    value: "https://github.com/Imageomics/pybioclip/releases/tag/2.1.5"
  - description: "The GitHub URL of the commit tagged with 2.1.5."
    type: url
    value: "https://github.com/Imageomics/pybioclip/tree/4ba2dbb4668728a9c0618c4ff6960ce1945d6ab6" # update on release
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: 2.1.5
date-released: '2026-04-20'
doi: 10.5281/zenodo.13151194

Owner metadata

• Name: Imageomics Institute
• Login: Imageomics
• Email:
• Kind: organization
• Description:
• Website: https://imageomics.osu.edu
• Location:
• Twitter: imageomics
• Company:
• Icon url: https://avatars.githubusercontent.com/u/77468321?v=4
• Repositories: 4
• Last ynced at: 2023-03-05T05:05:36.574Z
• Profile URL: https://github.com/Imageomics

GitHub Events

Total

• Create event: 60
• Delete event: 45
• Fork event: 4
• Gollum event: 19
• Issue comment event: 200
• Issues event: 81
• Member event: 1
• Pull request event: 76
• Pull request review comment event: 90
• Pull request review event: 177
• Push event: 288
• Release event: 6
• Watch event: 22

Last Year

• Create event: 20
• Delete event: 11
• Issue comment event: 46
• Issues event: 22
• Pull request event: 19
• Pull request review comment event: 4
• Pull request review event: 13
• Push event: 56
• Release event: 3
• Watch event: 7

Committers metadata

Last synced: 3 days ago

Committer domains:

• drycafe.net: 1

Issue and Pull Request metadata

Last synced: 1 day ago

Package metadata

• Total packages: 1
• Total downloads:
  • pypi: 7,051 last-month
• Total dependent packages: 0
• Total dependent repositories: 0
• Total versions: 15
• Total maintainers: 2

Dependencies

Score: 15.465152161808652