Metadata-Version: 2.1
Name: functional-connectivity
Version: 0.1.2
Summary: Sensing functional connectivity in the brain, in Python
Author-email: Tzu-Chi Yen <tzuchi.yen@colorado.edu>
Project-URL: repository, https://github.com/junipertcy/functional-connectivity
Project-URL: documentation, https://docs.netscied.tw/functional-connectivity/index.html
Keywords: functional-connectivity,convex-optimization,keywords-TBD
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development :: Libraries
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: urllib3==1.26.9
Requires-Dist: matplotlib==3.8.0
Requires-Dist: numpy==1.26.1
Requires-Dist: scikit-learn==1.3.2
Requires-Dist: numba==0.58.1
Requires-Dist: loky==3.4.1
Requires-Dist: xarray==2023.10.1
Requires-Dist: jupyterlab==4.0.7
Requires-Dist: nwbwidgets==0.11.3
Requires-Dist: dandi==0.57.0
Requires-Dist: h5py==3.10.0
Provides-Extra: dev
Requires-Dist: pytest==7.4.3; extra == "dev"
Requires-Dist: click==8.1.7; extra == "dev"
Requires-Dist: sphinx==7.2.6; extra == "dev"

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[![PyPI](https://img.shields.io/pypi/v/functional-connectivity)](https://pypi.org/project/functional-connectivity/)
[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![license](https://img.shields.io/badge/license-LGPL-green.svg?style=flat)](https://github.com/junipertcy/functional-connectivity/blob/master/LICENSE)


**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](https://arxiv.org/) or [PRX Life](https://journals.aps.org/prxlife/).

* For full documentation, please visit [this site](https://docs.netscied.tw/functional-connectivity/index.html).
* For general Q&A, ideas, or other things, please visit [Discussions](https://github.com/junipertcy/functional-connectivity/discussions).
* For software-related bugs, issues, or suggestions, please use [Issues](https://github.com/junipertcy/functional-connectivity/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:
* SOMETHING


Development
-----------
Remember that `./docs` contains [the documentation](https://docs.netscied.tw/functional-connectivity/index.html) 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](https://www.kavlifoundation.org/). 
The authors want to thank Rebecca Morrison and Stephen Becker ([@stephenbeckr](https://github.com/stephenbeckr)) for inspirations. 

We also want to thank the authors in these software implementations:
* [cvxgrp/strat_models](https://github.com/cvxgrp/strat_models)
* [GalSha/GLASSO_Framework](https://github.com/GalSha/GLASSO_Framework): [arXiv (2023)](https://arxiv.org/abs/2205.10027)
* [tpetaja1/tvgl](https://github.com/tpetaja1/tvgl): [KDD (2017)](https://dl.acm.org/doi/10.1145/3097983.3098037), 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](https://www.gnu.org/licenses/lgpl-3.0.en.html).
