NeuRodent 🐁

A Python package for standardizing rodent EEG analysis and figure generation. Various EEG formats are loadable and features are extracted in parallel. Also includes a Snakemake workflow for automated analysis.

Presented at USRSE'25!

Installation

NeuRodent can be installed via pip or conda:

pip install neurodent

or

conda install -c conda-forge neurodent

For pipeline support, development setup, and other installation options, check out the full installation guide.

Usage

Visit the full documentation for more how-tos and examples: https://josephdong1000.github.io/neurodent

• Quickstart
• Tutorials
• API documentation

Overview

NeuRodent loads multi-format EEG data (LongRecordingAnalyzer → AnimalOrganizer) and computes features over windows (WindowAnalysisResult) and population spiking (FrequencyDomainSpikeAnalysisResult). Results feed into AnimalPlotter and ExperimentPlotter for multi-animal comparison by genotype, session, or circadian cycle.

from neurodent import (
    LongRecordingOrganizer,
    AnimalOrganizer,
    AnimalAnalyzer,
    ExperimentPlotter,
)

lro = LongRecordingOrganizer(data_path)
ao = AnimalOrganizer(lro)
war = AnimalAnalyzer(ao).compute_windowed_analysis(features=["rms", "psdband", "cohere"])
ep = ExperimentPlotter([war])
ep.plot_feature("rms", groupby="genotype")

A companion Snakemake workflow automates the full pipeline with cluster support.

Snakemake Workflow

The pipeline follows the Snakemake Workflow Catalog standardized layout, with workflow/Snakefile as the single entry point.

# Deploy via snakedeploy
pip install snakedeploy
snakedeploy deploy-workflow https://github.com/josephdong1000/neurodent . --tag <version>

# Run manually
snakemake --snakefile workflow/Snakefile --configfile config/config.yaml

Acknowledgements

This project benefited from insights and best practices described in Peter K. G. Williams’s One Good Tutorial.

Citation

If you find NeuRodent useful, please cite our work!

@software{dong2026neurodent,
  author    = {Dong, Joseph P. and Oh, Yongtaek and Marsh, Eric D.},
  title     = {NeuRodent},
  year      = {2025},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.15780751},
  url       = {https://doi.org/10.5281/zenodo.15780751},
  license   = {MIT}
}

Machine-readable citation metadata is also available in CITATION.cff.

Community & Governance

• Contributing: CONTRIBUTING.md
• Support: SUPPORT.md
• Code of Conduct: CODE_OF_CONDUCT.md