functional-connectivity 0.1.3

Sensing functional connectivity in the brain, in Python

functional-connectivity implements a set of tools to detect and sense changes in a functional network from spike counts

This is the software repository behind the paper:

• Tzu-Chi Yen and Yi-Yun Ho, Mapping functional neuronal networks to behavioral states, in preparation (2024).

Read it on: arXiv.

• For full documentation, please visit this site.
• For general Q&A, ideas, or other things, please visit Discussions.
• For software-related bugs, issues, or suggestions, please use Issues.

Installation

functional-connectivity is available on PyPI:

pip install functional-connectivity

The dependencies needed to interact with Dandi are not installed by default. You will need to run:

• pip install --ignore-installed --no-binary=h5py h5py scipy numba

Development

Remember that ./docs contains the documentation of this library. You would need AWS credentials to be able to execute ./docs/deploy.sh.

Acknowledgement

The functional-connectivity library is supported by The Kavli Foundation. TCY wants to thank Rebecca Morrison (@rebeccaem) and Stephen Becker (@stephenbeckr) for inspirations.

We also want to thank the authors in these software implementations:

• cvxgrp/strat_models
• GalSha/GLASSO_Framework: arXiv (2023)
• tpetaja1/tvgl: KDD (2017), time-varying GGM using ADMM and Python 2.7.

License

functional-connectivity is open-source and licensed under the GNU Lesser General Public License v3.0.