A Python package to quantify and visualize 3D cardiomyocyte orientation in heart imaging datasets

Cardiotensor is a user-friendly and memory-efficient toolkit designed for analyzing the orientation of cardiomyocyte fibers in large heart imaging datasets. It uses advanced image processing techniques to help researchers to accurately quantify 3D cardiomyocyte orientations with high efficiency.

Cardiotensor is published as a Python package and can be installed with pip, ideally by using a virtual environment. Open up a terminal and install cardiotensor with:

pip install cardiotensor

Cardiotensor's documentation is available at josephbrunet.fr/cardiotensor/

Have a look at our simple example that runs you through all the commands of the package

This package uses the structure-tensor package to calculate the structure tensor, extending its capabilities for cardiac imaging.

This project is licensed under the MIT License. See the LICENSE file for details.

Contributions are welcome! If you encounter a bug or have suggestions for new features:

• Report an Issue: Open an issue in the repository.
• Submit a Pull Request: Fork the repository, make changes, and submit a pull request.

For major changes, please discuss them in an issue first.

For questions, feedback, or support, please contact the maintainers at [j.brunet@ucl.ac.uk].

If you use Cardiotensor in your research, please cite:

Brunet, J., Chestnutt, L., Chourrout, M., Dejea, H., Sabarigirivasan, V., Lee, P. D., & Cook, A. C. "Cardiotensor: A Python Library for Orientation Analysis and Tractography in 3D Cardiac Imaging." Journal of Open Source Software 11(121) (2026): 9720. 🗎

@article{Brunet2026,
  doi={10.21105/joss.09720},
  url={https://doi.org/10.21105/joss.09720},
  year={2026},
  publisher={The Open Journal},
  volume={11},
  number={121},
  pages={9720},
  author={Brunet, Joseph and Chestnutt, Lisa and Chourrout, Matthieu and Dejea, Hector and Sabarigirivasan, Vaishnavi and Lee, Peter D. and Cook, Andrew C.},
  title={Cardiotensor: A Python Library for Orientation Analysis and Tractography in 3D Cardiac Imaging},
  journal={Journal of Open Source Software}
}

Brunet, J., Cook, A. C., Walsh, C. L., Cranley, J., Tafforeau, P., Engel, K., Arthurs, O., Berruyer, C., Burke O'Leary, E., Bellier, A., et al. "Multidimensional analysis of the adult human heart in health and disease using hierarchical phase-contrast tomography." Radiology 312(1) (2024): e232731. 🗎