Spectral Connectivity

Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU - Published in JOSS (2022)

https://github.com/eden-kramer-lab/spectral_connectivity

Science Score: 98.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 16 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: joss.theoj.org, zenodo.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

brain-connectivity canonical-coherence coherence connectivity-measures electrophysiology frequency-domain global-coherence multitaper neuroscience phase-lag-index python spectral-granger-causality spectrogram

Scientific Fields

Mathematics Computer Science - 40% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Frequency domain estimation and functional and directed connectivity analysis tools for electrophysiological data

Basic Info

Host: GitHub
Owner: Eden-Kramer-Lab
License: gpl-3.0
Language: Python
Default Branch: master
Homepage:
Size: 31.9 MB

Statistics

Stars: 129
Watchers: 3
Forks: 45
Open Issues: 9
Releases: 12

Topics

Created over 8 years ago · Last pushed 7 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

README.md

spectral_connectivity

What is spectral_connectivity?

spectral_connectivity is a Python software package that computes multitaper spectral estimates and frequency-domain brain connectivity measures such as coherence, spectral granger causality, and the phase lag index using the multitaper Fourier transform. Although there are other Python packages that do this (see nitime and MNE-Python), spectral_connectivity has several differences:

it is designed to handle multiple time series at once
it caches frequently computed quantities such as the cross-spectral matrix and minimum-phase-decomposition, so that connectivity measures that use the same processing steps can be more quickly computed.
it decouples the time-frequency transform and the connectivity measures so that if you already have a preferred way of computing Fourier coefficients (i.e. from a wavelet transform), you can use that instead.
it implements the non-parametric version of the spectral granger causality in Python.
it implements the canonical coherence, which can efficiently summarize brain-area level coherences from multielectrode recordings.
easier user interface for the multitaper fourier transform
all function are GPU-enabled if cupy is installed and the environmental variable SPECTRAL_CONNECTIVITY_ENABLE_GPU is set to 'true'.

Tutorials

See the following notebooks for more information on how to use the package:

Usage Example

```python from spectral_connectivity import Multitaper, Connectivity

Compute multitaper spectral estimate

m = Multitaper(timeseries=signals, samplingfrequency=samplingfrequency, timehalfbandwidthproduct=timehalfbandwidthproduct, timewindowduration=0.060, timewindowstep=0.060, starttime=time[0])

Sets up computing connectivity measures/power from multitaper spectral estimate

c = Connectivity.from_multitaper(m)

Here are a couple of examples

power = c.power() # spectral power coherence = c.coherencemagnitude() weightedphaselagindex = c.weightedphaselagindex() canonicalcoherence = c.canonicalcoherence(brainarea_labels) ```

Documentation

See the documentation here.

Citation

For citation, please use the following:

Denovellis, E.L., Myroshnychenko, M., Sarmashghi, M., and Stephen, E.P. (2022). Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU. JOSS 7, 4840. 10.21105/joss.04840.

Implemented Measures

Functional

coherency
canonical_coherence
imaginary_coherence
phaselockingvalue
phaselagindex
weightedphaselag_index
debiasedsquaredphaselagindex
debiasedsquaredweightedphaselag_index
pairwisephaseconsistency
global coherence

Directed

directedtransferfunction
directed_coherence
partialdirectedcoherence
generalizedpartialdirected_coherence
directdirectedtransfer_function
group_delay
phaselagindex
pairwisespectralgranger_prediction

Package Dependencies

spectral_connectivity requires:

python
numpy
matplotlib
scipy
xarray

See environment.yml for the most current list of dependencies.

Installation

bash pip install spectral_connectivity

bash conda install -c edeno spectral_connectivity

Developer Installation

If you want to make contributions to this library, please use this installation.

Install miniconda (or anaconda) if it isn't already installed. Type into bash (or install from the anaconda website):

bash wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; bash miniconda.sh -b -p $HOME/miniconda export PATH="$HOME/miniconda/bin:$PATH" hash -r

Clone the repository to your local machine (.../spectral_connectivity) and install the anaconda environment for the repository. Type into bash:

bash conda env create -f environment.yml conda activate spectral_connectivity pip install -e .

Recent publications and pre-prints that used this software

Detection of Directed Connectivities in Dynamic Systems for Different Excitation Signals using Spectral Granger Causality https://doi.org/10.1007/978-3-662-58485-9_11
Network Path Convergence Shapes Low-Level Processing in the Visual Cortex https://doi.org/10.3389/fnsys.2021.645709
Subthalamic–Cortical Network Reorganization during Parkinson's Tremor https://doi.org/10.1523/JNEUROSCI.0854-21.2021
Unifying Pairwise Interactions in Complex Dynamics https://doi.org/10.48550/arXiv.2201.11941
Phencyclidine-induced psychosis causes hypersynchronization and disruption of connectivity within prefrontal-hippocampal circuits that is rescued by antipsychotic drugs https://doi.org/10.1101/2021.02.03.429582
The cerebellum regulates fear extinction through thalamo-prefrontal cortex interactions in male mice https://doi.org/10.1038/s41467-023-36943-w

Owner

Name: Eden-Kramer Lab
Login: Eden-Kramer-Lab
Kind: organization
Email: tzvi@bu.edu

Website: https://eden-kramer-lab.github.io/
Repositories: 39
Profile: https://github.com/Eden-Kramer-Lab

Tools for analysis of neural data

JOSS Publication

Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU

Published

December 13, 2022

DOI

10.21105/joss.04840

Volume 7, Issue 80, Page 4840

Authors

Eric L. Denovellis

Howard Hughes Medical Institute - University of California, San Francisco, San Francisco, California, United States of America, Departments of Physiology and Psychiatry, University of California, San Francisco, San Francisco, California, United States of America, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, California, United States of America

Maxym Myroshnychenko

National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, United States of America

Mehrad Sarmashghi

Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America

Emily P. Stephen

Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America, Center for Systems Neuroscience, Boston University, Boston, Massachusetts, United States of America

Editor

Elizabeth DuPre

Citation (CITATION.cff)

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
title: 'Eden-Kramer-Lab/spectral_connectivity'
doi: 10.5281/zenodo.10023078
authors:
  - family-names: Denovellis
    given-names: Eric
    orcid: https://orcid.org/0000-0003-4606-087X
    affiliation: Howard Hughes Medical Institute - University of California, San Francisco, San Francisco, California, United States of America
  - family-names: Myroshnychenko
    given-names: Maxym
    affiliation: National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, United States of America
    orcid: https://orcid.org/0000-0001-7790-257X
  - family-names: Sarmashghi
    given-names: Mehrad
    affiliation: Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America
    orcid: https://orcid.org/0000-0002-7976-6636
  - family-names: Stephen
    given-names: Emily
    affiliation: Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America
    orcid: https://orcid.org/0000-0003-1978-9622

title: Eden-Kramer-Lab/spectral_connectivity
version: v1.1.2
date-released: 2023-10-17
repository-code: https://github.com/Eden-Kramer-Lab/spectral_connectivity
license: GPL-3.0

preferred-citation:
  type: article
  authors:
  - family-names: Denovellis
    given-names: Eric
    orcid: https://orcid.org/0000-0003-4606-087X
    affiliation: Howard Hughes Medical Institute - University of California, San Francisco, San Francisco, California, United States of America
  - family-names: Myroshnychenko
    given-names: Maxym
    affiliation: National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, United States of America
    orcid: https://orcid.org/0000-0001-7790-257X
  - family-names: Sarmashghi
    given-names: Mehrad
    affiliation: Division of Systems Engineering, Boston University, Boston, Massachusetts, United States of America
    orcid: https://orcid.org/0000-0002-7976-6636
  - family-names: Stephen
    given-names: Emily
    affiliation: Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America
    orcid: https://orcid.org/0000-0003-1978-9622
  doi: "10.21105/joss.04840"
  journal: "Journal of Open Source Software"
  month: 12
  title: "Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU"
  issue: 80
  volume: 7
  year: 2022

GitHub Events

Total

Issues event: 2
Watch event: 7
Issue comment event: 6
Push event: 1
Pull request review comment event: 2
Pull request review event: 3
Pull request event: 2
Fork event: 1

Last Year

Issues event: 2
Watch event: 7
Issue comment event: 6
Push event: 1
Pull request review comment event: 2
Pull request review event: 3
Pull request event: 2
Fork event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 366
Total Committers: 9
Avg Commits per committer: 40.667
Development Distribution Score (DDS): 0.115

Past Year

Commits: 8
Committers: 1
Avg Commits per committer: 8.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Eric Denovellis	e**s@g**m	324
Mehrad Sarmashghi	5****m	16
Leo Scholl	l**l@g**m	8
Max Myroshnychenko	m**s@g**m	7
Emily Stephen	e**4@g**m	6
Stefan Appelhoff	s**f@m**g	2
Patrick F. Bloniasz	7****p	1
Danylo Ulianych	d**a@g**m	1
Andrew Quinn	a**1@g**m	1

Committer Domains (Top 20 + Academic)

mailbox.org: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 39
Total pull requests: 20
Average time to close issues: 8 months
Average time to close pull requests: 23 days
Total issue authors: 13
Total pull request authors: 8
Average comments per issue: 1.46
Average comments per pull request: 1.95
Merged pull requests: 18
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: about 2 months
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 4.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

edeno (11)
sappelhoff (10)
EtienneCmb (4)
emilyps14 (3)
AJQuinn (3)
mkkubins (1)
christian-oreilly (1)
xiaolongwu0713 (1)
saarangp (1)
mschart (1)
mgm248 (1)
olivercliff (1)
KaetzelLab (1)

Pull Request Authors

mmyros (7)
emilyps14 (4)
MehradSm (2)
leoscholl (2)
dizcza (2)
sappelhoff (2)
AJQuinn (1)
bloniaszp (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 615 last-month

Total dependent packages: 3
Total dependent repositories: 3
Total versions: 16
Total maintainers: 1

pypi.org: spectral-connectivity

Frequency domain functional and directedconnectivity analysis tools for electrophysiologicaldata

Homepage: https://github.com/Eden-Kramer-Lab/spectral_connectivity
Documentation: https://spectral-connectivity.readthedocs.io/en/latest/
License: GPL-3.0
Latest release: 1.1.2
published over 2 years ago

Versions: 16
Dependent Packages: 3
Dependent Repositories: 3
Downloads: 615 Last month

Rankings

Dependent packages count: 4.8%

Forks count: 6.4%

Stargazers count: 6.8%

Average: 7.5%

Dependent repos count: 9.0%

Downloads: 10.4%

Maintainers (1)

edeno

Last synced: 4 months ago

Dependencies

docs/requirements-docs.txt pypi

numpydoc *
sphinx *
sphinx_rtd_theme *

.github/workflows/PR-test.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
conda-incubator/setup-miniconda v2 composite
coverallsapp/github-action master composite
styfle/cancel-workflow-action 0.6.0 composite

.github/workflows/linting.yml actions

actions/checkout v2 composite
psf/black stable composite

setup.py pypi

environment.yml conda

black
coveralls
flake8
jupyter
jupyterlab
matplotlib
nitime
numpy >=1.11
numpydoc
pytest >=2.7.1
pytest-cov
scipy
setuptools
sphinx
sphinx-autoapi
sphinx-copybutton
xarray

Spectral Connectivity

Science Score: 98.0%

Keywords

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

spectral_connectivity

What is spectral_connectivity?

Tutorials

Usage Example

Compute multitaper spectral estimate

Sets up computing connectivity measures/power from multitaper spectral estimate

Here are a couple of examples

Documentation

Citation

Implemented Measures

Package Dependencies

Installation

Developer Installation

Recent publications and pre-prints that used this software

Owner

JOSS Publication

Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: spectral-connectivity

Rankings

Maintainers (1)

Dependencies