We believe in open science. Below are open-source tools, code, models, and resources that we use, develop, or recommend. We hope they are useful to other researchers, clinicians, students, and the broader community.

Lab Code & Software

  • GitHub: EpilepsyLab Github — code and analysis pipelines developed in the lab.
  • GitHub for SWISC: Sleep, Wake, and Epilepsy classifier for scoring mouse EEG/EMG recordings.

3D Models & Printing

Software Tools We Use

Open-source software and resources we rely on in our research:

  • MNE-Python — analysis of electrophysiological (EEG/MEG/SEEG) data.
  • FieldTrip — MATLAB toolbox for electrophysiology analysis.
  • FreeSurfer — neuroimaging analysis and cortical reconstruction.
  • FSL — neuroimaging analysis library.
  • Allen Mouse Brain Connectivity Atlas — open connectivity data we use for review prior to our circuit-tracing work.
  • Brainstorm — open source MATLAB software for MEG and iEEG analysis.
  • ERPLab — open source MATLAB software for ERP analysis.
  • eBrains — tools for computational neuroscience.
  • Virtual Brain project — European Virtual Brain Project.
  • Spike Interface — Python-based framework for handling spike data
  • Kilosort 4.0 — spike sorting for multiple electrode geometries
  • Spiking Circus — ideal sorting tool for tetrodes
  • OpenEphys
  • Intan — hardware and software for silicon probe or Intan recording
  • Spike GLX — software for Neuropixel probes
  • iEEG BIDS — BIDS framework for intracranial data
  • Spike 2.0 — proprietary chart recording and spike sorting
  • HIPPIE — High-dimensional Interpretation for Physiological Patterns in Intercellular Electrophysiology

Other Useful Pages

Data Repositories

Lab Data

Recommended Repositories

  • DABI
  • Dandy
  • Brain Data Science Platform
  • Open Science Framework
  • DRYAD