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osl-ephys

OHBA Software Library: Electrophysiological Data Analysis Toolbox

https://github.com/ohba-analysis/osl-ephys

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary

Keywords

eeg meg python
Last synced: 6 months ago · JSON representation ·

Repository

OHBA Software Library: Electrophysiological Data Analysis Toolbox

Basic Info
Statistics
  • Stars: 57
  • Watchers: 4
  • Forks: 11
  • Open Issues: 33
  • Releases: 19
Topics
eeg meg python
Created over 4 years ago · Last pushed 7 months ago
Metadata Files
Readme Contributing License Citation

README.md

OSL: Electrophysiological Data Analysis Toolbox

Tools for analysing electrophysiological (M/EEG) data.

Documentation: https://osl-ephys.readthedocs.io/en/latest/.

Installation

We recommend installing osl-ephys in a conda environment.

Conda / mamba

Miniforge (conda) can be installed with: wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" bash Miniforge3-$(uname)-$(uname -m).sh rm Miniforge3-$(uname)-$(uname -m).sh

Mamba (mamba) can be installed with: conda install -n base -c conda-forge mamba

osl-ephys

osl-ephys can be installed from source code in a conda environment using the following.

git clone https://github.com/OHBA-analysis/osl-ephys.git cd osl-ephys mamba env create -f envs/osle.yml conda activate osle pip install -e .

Note, on a headless server you may need to set the following environment variable: export PYVISTA_OFF_SCREEN=true

Oxford-specific computers

If you are installing on an OHBA workstation computer (hbaws) use: git clone https://github.com/OHBA-analysis/osl-ephys.git cd osl-ephys mamba env create -f envs/hbaws.yml conda activate osle pip install -e .

Or on the BMRC cluster: git clone https://github.com/OHBA-analysis/osl-ephys.git cd osl-ephys mamba env create -f envs/bmrc.yml conda activate osle pip install -e .

Remember to set the following environment variable: export PYVISTA_OFF_SCREEN=true

Removing osl-ephys

Simply remove the conda environment and delete the repository: conda env remove -n osle rm -rf osl-ephys

For developers

Install all the requirements: pip install -r requirements.txt

Run tests: cd osl_ephys pytest tests or to run a specific test: cd osl_ephys/tests pytest test_file_handling.py

Build documentation locally: sphinx-build -b html doc/source build Compiled docs can be found in doc/build/html/index.html.

Owner

  • Name: OHBA Analysis Group
  • Login: OHBA-analysis
  • Kind: organization
  • Location: Oxford Centre for Human Brain Activity, Warneford Hospital, Oxford, UK

Public repository for OHBA analysis group code

Citation (CITATION.cff) 

cff-version: 2.3.1
message: "If you use this software, please cite the software itself, as well as the paper listed in the preferred-citation field. osl-ephys is based on MNE-Python and the Source Recon module on FSL/FreeSurfer. Please cite these packages appropriately."
title: "osl-ephys"
version: 2.3.1
date-released: "2025-05-08"
commit: 2201385db8ed1f238b36361b6ea864d342c2293f
doi: 10.5281/zenodo.6875060
keywords:
  - MEG
  - magnetoencephalography
  - EEG
  - electroencephalography
  - electrophysiology
  - neuroimaging
  - data analysis
authors:
  - family-names: Quinn
    given-names: Andrew J.
    orcid: https://orcid.org/0000-0003-2267-9897
  - family-names: van Es
    given-names: Mats W.J.
    orcid: https://orcid.org/0000-0002-7133-509X
  - family-names: Gohil
    given-names: Chetan
    orcid: https://orcid.org/0000-0002-0888-1207
  - family-names: Woolrich
    given-names: Mark W.
    orcid: https://orcid.org/0000-0001-8460-8854
preferred-citation:
  title: "osl-ephys: a Python toolbox for the analysis of electrophysiology data"
  journal: "Frontiers in Neuroscience"
  type: article
  year: 2025
  volume: 19
  issue: 
  start: 1522675
  end: 
  doi: https://doi.org/10.3389/fnins.2025.1522675
  authors:
  - family-names: van Es
    given-names: Mats W.J.
    orcid: https://orcid.org/0000-0002-7133-509X
  - family-names: Gohil
    given-names: Chetan
    orcid: https://orcid.org/0000-0002-0888-1207
  - family-names: Quinn
    given-names: Andrew J.
    orcid: https://orcid.org/0000-0003-2267-9897
  - family-names: Woolrich
    given-names: Mark W.
    orcid: https://orcid.org/0000-0001-8460-8854

GitHub Events

Total
  • Create event: 33
  • Issues event: 30
  • Release event: 4
  • Watch event: 15
  • Delete event: 31
  • Issue comment event: 43
  • Push event: 126
  • Pull request review event: 6
  • Pull request review comment event: 5
  • Pull request event: 59
  • Fork event: 3
Last Year
  • Create event: 33
  • Issues event: 30
  • Release event: 4
  • Watch event: 15
  • Delete event: 31
  • Issue comment event: 43
  • Push event: 126
  • Pull request review event: 6
  • Pull request review comment event: 5
  • Pull request event: 59
  • Fork event: 3

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 11
  • Total pull requests: 28
  • Average time to close issues: 2 months
  • Average time to close pull requests: 18 days
  • Total issue authors: 5
  • Total pull request authors: 4
  • Average comments per issue: 0.73
  • Average comments per pull request: 0.25
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 11
  • Pull requests: 28
  • Average time to close issues: 2 months
  • Average time to close pull requests: 18 days
  • Issue authors: 5
  • Pull request authors: 4
  • Average comments per issue: 0.73
  • Average comments per pull request: 0.25
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • CarinaFo (6)
  • XinlingChen (3)
  • matsvanes (2)
  • Florenceck (1)
  • JizeZhangCS (1)
  • pwendiggensen (1)
  • cgohil8 (1)
  • aminkabir (1)
Pull Request Authors
  • matsvanes (16)
  • cgohil8 (12)
  • neurofractal (4)
  • AJQuinn (1)
Top Labels
Issue Labels
enhancement (1) bug (1) souce recon (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 49 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 2
pypi.org: osl-ephys

OHBA Software Library for the analysis of electrophysiological data

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 49 Last month
Rankings
Dependent packages count: 10.1%
Average: 33.6%
Dependent repos count: 57.0%
Maintainers (2)
cgohil8 matsvanes
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • anamnesis *
  • coverage *
  • file-tree *
  • flake8 *
  • fslpy *
  • glmtools *
  • h5py *
  • jinja2 *
  • matplotlib *
  • mne ==1.0.0
  • neurokit2 *
  • nibabel *
  • nilearn *
  • numba *
  • numpy *
  • numpydoc *
  • open3d ==0.9.0.0
  • opencv-python *
  • pandas *
  • pydata-sphinx-theme *
  • pytest *
  • pytest-cov *
  • pyyaml >=5.1
  • sails *
  • scikit-learn *
  • scipy *
  • setuptools >=41.0.1
  • sklearn *
  • sphinx ==4.0.2
  • sphinx_gallery *
  • tabulate *
  • yaml *
.github/workflows/osl-cicd-actions.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
setup.py pypi