Open Software for Human Electrophysiology

This is a list of openly available software and code for working with electrophysiological data, including EEG, MEG, ECoG/iEEG, and LFP.

Table of Contents

• Overview
• General Purpose Tools
• Standalone Tools
• Plugins

Overview

This list is focused on re-usable tools for working with electrophysioligical data. Generally, this does not include code that is available for specific analysis on particular datasets (though these may be included where they are potentially useful for and licensed for re-use).

By 'open', here we mean that source code is provided and is released with a permissive license. Commercial products are not listed. Be sure to double check the license before using / modifying linked code. Note that some tools may require non-open dependencies (for example, Matlab tools are listed, but are not fully open).

General Purpose Tools

The following are general purpose platforms, with functionality including: loading data, preprocessing, visualization, standard analysis, and making figures.

MNE

MNE is a general purpose tool for processing, analyzing, and visualizing M/EEG data.

HomePage - Github - Paper

Neural Ensemble Tools

Neural Ensemble is an initiative for open-source software in neuroscience and includes a set of tools for managing and analyzing electrophysiology data.

neo is a tool for representing electrophysiology data, and reading neurophysiological file formats.

HomePage - Github

elephant is a tool for analyzing electrophysiological data.

HomePage - Github

Wonambi

Wonambi is a general purpose tool for processing, analyzing, and visualizing EEG data, including specific tools focused on sleep scoring and analysis.

HomePage - Github

NeuroKit2

NeuroKit2 is a tool for neurophysiological signal processing.

HomePage - Github

FieldTrip

FieldTrip is a general purpose tool for processing, analyzing, and visualizing M/EEG and iEEG/ECoG data.

HomePage - Github - Paper

BrainStorm

BrainStorm is a general purpose tool for processing, analyzing and visualizing focused primarily on MEG data, with additional support for EEG & ECoG data.

HomePage - Github - Paper

EEGLab

EEGLab is a general purpose tool for processing, analyzing, and visualizing EEG data.

HomePage - Paper

SPM

SPM is a general purpose toolbox for neuroimaging, including support for processing M/EEG data.

HomePage

NutMEG

NutMEG is a general purpose tool for processing, analyzing, and visualizing MEG data.

HomePage - Github - Paper

EEGUtils

EEGUtils is a general purpose tool for processing, analyzing, and visualizing EEG data.

HomePage - Github

EEGuana

EEGuana is a package for working with EEG data.

HomePage - Github

EEG.jl

EEG.jl is library for processing EEG data.

HomePage - Github

CarTool

CarTool is an EEG analysis toolbox.

HomePage - Paper

Standalone Tools

The following are standalone tools, independent of general software platforms, for specific purposes.

NeuroDSP

NeuroDSP is a package for calculating a broad range of measures on neural time series, including a range of time-domain measures such as waveform shape analyses.

Homepage - Github - Paper

FOOOF

FOOOF is a package for parameterizing neural power spectra.

Homepage - Github - Paper

ByCycle

ByCycle is a tool for cycle-by-cycle analyses of neural oscillations.

Homepage - Github - Paper

Frites: Framework for Information Theoretic analysis of Electrophysiological data and Statistics

FRITES is package for computing information-theoretic measures on human and electrophysiological data.

Homepage - Github

PTSA - Python Time Series Analysis

PTSA is package for time series analysis in Python, focused on analyzing electrophysiological data.

Homepage - Github

Spectral Connectivity

Spectral Connectivity is a package including a group of functional connectivity and coherence related measures.

HomePage - Github

Tensor PAC

TensorPAC is a tool for calculating phase-amplitude coupling measures, using tensors and parallel computing.

HomePage - Github - Paper

PACTools

PACTools is a package for calculating phase-amplitude coupling measures in neural time series.

HomePage - Github

PyEEG

PyEEG includes some implementations of information theoretic and complexity related measures for neural time series.

Github - Paper

ECoGTools

ECoGTools is a collection of tools for analyzing ECoG data.

Github

EELBrain

EELBrain is a tool for statistical analysis of M/EEG data

HomePage - Github

restingIAF

RestingIAF is a tool for estimating the peak individual alpha frequency.

Github - Paper

Phase Opposition Code

Phase Opposition is a collection of functions for calculating phase opposition measures.

HomePage - Paper

ADAM - Amsterdam Decoding and Modeling Toolbox

ADAM is a tool for encoding and decoding model analysis on M/EEG data.

Github - Paper

HERMES

HERMES is tool for estimating connectivity measures between M/EEG signals.

HomePage - Github - Paper

SEREEGA - Simulating Event-Related EEG Activity

SEREEGA is a package for simulating synthetic data that mimic event-related EEG activity.

Github - Paper

UNFOLD

Unfold is a tool for deconvolving overlapping EEG signals and for non-linear modeling.

HomePage - Github - Paper

ept-TFCE

ept-TFCE is a tool for statistical analysis of already preprocessed M/EEG data, focused mainly around the 'threshold-free cluster enhancement' method.

Github - Paper

ERP Reliability Analysis (ERA)

ERA is a tool for calculating reliability estimates for ERP data.

HomePage - Github - Paper

SynchSqueezing

SynchroSqueezing is a tool for time-frequency and time-scale analyses.

Github

AutoMagic

AutoMagic is a standardized toolbox for preprocessing EEG datasets.

Github - Paper

Multivariate Granger Causality Toolbox (MVGC)

The MVGC toolbox is designed to run Granger-causal analysis on multivariate time-series data.

HomePage - Code - Paper

OpenMEEG

OpemMEEG is a package for solving forward problems for EEG & MEG data.

HomePage - Github - Paper

Plugins

The following are plugins, designed primary for use with one of the aforementioned general purpose tools.

AutoReject

AutoReject is a tool for preprocessing M/EEG data, but algorithmically determining and applying rejection thresholds, with MNE.

HomePage - Github - Paper

MNE-BIDS

MNE-BIDS is a tool for creating BIDS compatible datasets with MNE.

HomePage - Github - Paper

PREP Pipeline (Standardized EEG preprocessing)

The PREP pipeline is a standardized processing tool for EEG data, using EEGLab.

HomePage - Github - Paper

ADJUST

ADJUST is an automatic artifact identification and removal tool, using EEGLab.

HomePage - Paper

ERPlab

ERPLab is a tool for event-related potential (ERP) analysis of EEG data, with EEGLab.

HomePage - Github - Paper

LIMO - Linear Modeling

LIMO is a tool for Linear Modeling of EEG data, with EEGLab.

HomePage - Github - Paper

SIFT - Source Information Flow Toolbox

SIFT is a tool for causality and information flow measures, with EEGLab.

HomePage

MPT - Measure Projection Toolbox

MPT is a tool for probabilistic multi-subject EEG independent component analysis, with EEGLab.

HomePage

Visualization Tools

The following are tools focused on visualizing neural data.

Visbrain

Visbrain is a tool for brain data visualization.

Homepage - Github

PyCortex

PyCortex is a tool for visualizing cortical surfaces.

Homepage - Github

Other Software Tools Lists

The Physionet project maintains a list of software available in the PhysioToolkit, which includes some software that can be used with electrophysiology data.