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 23 hours ago
JSON representation

Repository metadata

Python package that simplifies using the BioCLIP foundation model.

• Host: GitHub
• URL: https://github.com/imageomics/pybioclip
• Owner: Imageomics
• License: mit
• Created: 2024-03-28T20:12:01.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-11-27T19:53:20.000Z (28 days ago)
• Last Synced: 2025-11-30T08:59:10.579Z (26 days ago)
• Topics: bioclip, biology, clip, command-line-interface, cv, image-classification, knowledge-guided, taxonomy
• Language: Python
• Homepage: https://imageomics.github.io/pybioclip/
• Size: 4.27 MB
• Stars: 56
• Watchers: 3
• Forks: 10
• Open Issues: 13
• Releases: 10
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff
  • Zenodo: .zenodo.json

README.md

@software{Bradley_pybioclip_2025,
author = {Bradley, John and Lapp, Hilmar and Campolongo, Elizabeth G.},
doi = {10.5281/zenodo.13151194},
month = sept,
title = {{pybioclip}},
version = {2.1.1},
year = {2025}
}

@article{gu2025bioclip,
      title = {{B}io{CLIP} 2: Emergent Properties from Scaling Hierarchical Contrastive Learning}, 
      year = {2025},
      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 M Dahdul and Daniel Rubenstein and Hilmar Lapp and Tanya Berger-Wolf and Wei-Lun Chao and Yu Su},
      eprint={2505.23883},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url={https://arxiv.org/abs/2505.23883},
}

@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:
  - type: doi
    value: 10.5281/zenodo.13151194
  - description: "The GitHub release URL of tag 2.1.1."
    type: url
    value: "https://github.com/Imageomics/pybioclip/releases/tag/2.1.1"
  - description: "The GitHub URL of the commit tagged with 2.1.1."
    type: url
    value: "https://github.com/Imageomics/pybioclip/tree/04d1f293fa353396a317e07598c8a019dd6af5f8"
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: 2.1.1
date-released: '2025-09-17'
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"

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

• Fork event: 4
• Create event: 49
• Release event: 5
• Issues event: 74
• Watch event: 20
• Delete event: 35
• Member event: 1
• Issue comment event: 190
• Push event: 261
• Gollum event: 19
• Pull request event: 71
• Pull request review comment event: 87
• Pull request review event: 174

Last Year

• Create event: 35
• Release event: 4
• Issues event: 51
• Watch event: 16
• Delete event: 27
• Member event: 1
• Issue comment event: 126
• Push event: 141
• Pull request review comment event: 32
• Pull request review event: 92
• Pull request event: 50
• Fork event: 4

Committers metadata

Last synced: 2 days ago

Committer domains:

• drycafe.net: 1

Issue and Pull Request metadata

Last synced: 21 days ago

Package metadata

• Total packages: 1
• Total downloads:
  • pypi: 261 last-month
• Total dependent packages: 0
• Total dependent repositories: 0
• Total versions: 10
• Total maintainers: 2

Score: 11.88570207845486