neurodent 0.3.0

Rodent EEG analysis tools

NeuRodent 🐁

Presented at USRSE'25!

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.

Installation

NeuRodent can be installed via pip:

pip install 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 AnimalOrganizer and ExperimentPlotter for multi-animal comparison by genotype, session, or circadian cycle.

lro = LongRecordingOrganizer(data_path)
ao = AnimalOrganizer(lro)
war = 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!

@misc{https://doi.org/10.5281/zenodo.17051374,
  doi = {10.5281/ZENODO.17051374},
  url = {https://zenodo.org/doi/10.5281/zenodo.17051374},
  author = {Dong,  Joseph and Yongtaek Oh,   and Marsh,  Eric},
  title = {josephdong1000/PyEEG: 0.1.1},
  publisher = {Zenodo},
  year = {2025},
  copyright = {MIT License}
}