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cedalion

fNIRS analysis toolbox

https://github.com/ibs-lab/cedalion

Science Score: 44.0%

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

  • ✓
    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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    DOI references
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    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary
Last synced: 8 months ago · JSON representation ·

Repository

fNIRS analysis toolbox

Basic Info
  • Host: GitHub
  • Owner: ibs-lab
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 351 MB
Statistics
  • Stars: 41
  • Watchers: 4
  • Forks: 21
  • Open Issues: 21
  • Releases: 2
Created over 2 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

cedalion - fNIRS analysis toolbox

To avoid misinterpretations and to facilitate studies in naturalistic environments, fNIRS measurements will increasingly be combined with recordings from physiological sensors and other neuroimaging modalities. The aim of this toolbox is to facilitate this kind of analyses, i.e. it should allow the easy integration of machine learning techniques and provide unsupervised decomposition techniques for multimodal fNIRS signals.

Documentation

The documentation contains installation instructions as well as several example notebooks that illustrate the functionality of the toolbox. For discussions and help you can visit the cedalion forum on openfnirs.org

Development environment

To create a conda environment with the necessary dependencies run:

$ conda env create -n cedalion -f environment_dev.yml

Afterwards activate the environment and add an editable install of cedalion to it: $ conda activate cedalion $ pip install -e . $ bash install_nirfaster.sh CPU # or GPU

This will also install Jupyter Notebook to run the example notebooks.

If conda is too slow consider using the faster drop-in replacement mamba. If you have Miniconda or Anaconda you can install mamba with: ''' $ conda install mamba -c conda-forge ''' and then create the environment with $ mamba env create -n cedalion -f environment_dev.yml Please note: If this does not socceed there is another route to go: Install the libmamba solver ''' $ conda install -n base conda-libmamba-solver ''' and then build the environment with the --solver=libmamba $ conda env create -n cedalion -f environment_dev.yml --solver=libmamba

How to cite Cedalion

A paper for the toolbox is currently in the making. If you use this toolbox for a publication in the meantime, please cite us using GitHub's "Cite this repository" feature in the "About" section. If you want to contact us or learn more about the IBS-Lab please go to https://www.ibs-lab.com/

Owner

  • Name: IBS-Lab
  • Login: ibs-lab
  • Kind: organization

Intelligent Biomedical Sensing (IBS) Lab at BIFOLD, TU Berlin

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Intelligent Biomedical Sensing (IBS) Lab"
- family-names: "Cedalion Developers"
title: "Cedalion Python Toolbox"
version: 1.0.0
date-released: 2024-09-08
url: "https://github.com/ibs-lab/cedalion"

GitHub Events

Total
  • Create event: 64
  • Release event: 2
  • Issues event: 7
  • Watch event: 13
  • Delete event: 45
  • Issue comment event: 41
  • Push event: 341
  • Pull request review comment event: 19
  • Pull request review event: 30
  • Pull request event: 92
  • Fork event: 11
Last Year
  • Create event: 64
  • Release event: 2
  • Issues event: 7
  • Watch event: 13
  • Delete event: 45
  • Issue comment event: 41
  • Push event: 341
  • Pull request review comment event: 19
  • Pull request review event: 30
  • Pull request event: 92
  • Fork event: 11

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 9
  • Total pull requests: 93
  • Average time to close issues: 4 days
  • Average time to close pull requests: 15 days
  • Total issue authors: 6
  • Total pull request authors: 15
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.38
  • Merged pull requests: 49
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 62
  • Average time to close issues: 2 days
  • Average time to close pull requests: 14 days
  • Issue authors: 4
  • Pull request authors: 14
  • Average comments per issue: 0.17
  • Average comments per pull request: 0.24
  • Merged pull requests: 29
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Hadi-Borjkhani (2)
  • dboas (2)
  • JulesPad (2)
  • avolu (1)
  • ptrhbt (1)
  • harmening (1)
Pull Request Authors
  • harmening (20)
  • jccutler (13)
  • avolu (10)
  • dboas (10)
  • emiddell (9)
  • ahns97 (9)
  • lauracarlton (8)
  • thomasfischer11 (4)
  • shakiba93 (3)
  • jackybehrendt12 (2)
  • TCodina (1)
  • huppertt (1)
  • shankell212 (1)
  • bilal-siddique6 (1)
  • fangq (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels
bug (4) enhancement (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 111 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
pypi.org: cedalion

A fNIRS analysis framework

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 111 Last month
Rankings
Dependent packages count: 8.9%
Average: 29.7%
Dependent repos count: 50.4%
Maintainers (1)
emiddell
Last synced: 8 months ago