Metadata-Version: 2.4
Name: pybioclip
Version: 2.1.5
Summary: Python package that simplifies using the BioCLIP foundation model.
Project-URL: Documentation, https://imageomics.github.io/pybioclip/
Project-URL: Issues, https://github.com/Imageomics/pybioclip/issues
Project-URL: Source, https://github.com/Imageomics/pybioclip
Author-email: John Bradley <johnbradley2008@gmail.com>
License-Expression: MIT
License-File: LICENSE
Classifier: Development Status :: 5 - Production/Stable
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: >=3.10
Requires-Dist: open-clip-torch
Requires-Dist: pandas
Requires-Dist: prettytable
Requires-Dist: torch
Requires-Dist: torchvision
Provides-Extra: docs
Requires-Dist: mkdocs; extra == 'docs'
Requires-Dist: mkdocs-material; extra == 'docs'
Requires-Dist: mkdocs-material-extensions; extra == 'docs'
Requires-Dist: mkdocstrings-python; extra == 'docs'
Description-Content-Type: text/markdown

# pybioclip

[![DOI](https://zenodo.org/badge/778988552.svg)](https://doi.org/10.5281/zenodo.13151194)

[![PyPI - Version](https://img.shields.io/pypi/v/pybioclip.svg)](https://pypi.org/project/pybioclip)
[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pybioclip.svg)](https://pypi.org/project/pybioclip)

-----

Command line tool and python package to simplify using [BioCLIP](https://imageomics.github.io/bioclip-2/) (current and earlier versions), 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](https://imageomics.github.io/pybioclip/) for requirements, installation instructions, and tutorials.

## License

`pybioclip` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.

## Citation

To cite this repository, please use the citation provided by _Cite this repository_ in the sidebar, which uses the information in the `CITATON.cff` file. If you need a citation with a version-specific DOI, you can obtain this by following the Zenodo DOI badge at the top of this file.

Unless you selected (via `--model`) a model different from the default (which is now BioCLIP 2), please also cite the BioCLIP 2 paper:
```bibtex
@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}
}
```

If you selected the original BioCLIP model (using `--model`), please cite the original BioCLIP paper:
```bibtex
@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:
```bibtex
@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}
}
```
