List contributions

This is a list of open-source project, tools, and resources, maintained by the NTH community. This list is non-exhaustive. If you are missing useful resources in the list, please suggest your contributions through the github page!

Open Source Hardware

• OpenEphys - Community project for modular, customizable open-source electrophysiology acquisition hardware and software.

• OpenNerve - A versitile implantable pulse generator (IPG) and a large library of leads for stimulation, recording, and biomarker sensing. Developed by the Center for Autonomic Nerve Recording and Stimulation Systems (CARSS)

• OpenNIRScap – A Wearable Functional Near-Infrared Spectroscopy (fNIRS) based Brain Interface

• OpenStim - A low-cost electrical stimulator for experimental stimulation electrophysiology based on the Arduino platform

Open Data Repositories & Platforms

• OpenNeuro - A free and open platform for validating and sharing BIDS-compliant MRI, PET, MEG, EEG, and iEEG data.

• DANDI Archive - An archive of cellular neurophysiology data including electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experiments.

• The EBRAINS Knowledge Graph - A database to find and share neuroscientific data, software and models (part of the Human Brain Project ecosystem).

• Neurodata Without Borders - A data standard and software ecosystem for neurophysiology and behavioral data.

• CRCNS - A marketplace and discussion forum for sharing tools and data in neuroscience. Funded by the Collaborative Research in Computational Neuroscience program.

• Pennsieve – A cloud-based platform for scientific data management, analysis and publication

Signal Acquisition, Streaming & Real-Time Processing

• BrainFlow - A library intended to obtain, parse and analyze EEG, EMG, ECG and other kinds of data from biosensors.

• Timeflux - A free and open-source framework for the acquisition and real-time processing of biosignals.

• BioSPPY - A toolbox for biosignal processing written in Python. The toolbox bundles together various signal processing and pattern recognition methods geared torwards the analysis of biosignals.

• EEGsynth - An open-source Python codebase that provides a real-time interface between (open-hardware) devices for electrophysiological recordings (e.g. EEG, EMG and ECG) and analogue and digital devices (e.g. MIDI, OSC and analogue synthesizers). This allows one to use electrical brain/body activity to flexibly control devices in real-time.

Experiments, BCIs & Closed-Loop Frameworks

• PsychoPy – An open-source package for running psychophysics experiments in Python.

• EEG-ExPy - A collection of classic EEG experiments, implemented in Python.

• OpenVibe - A software platform that enables to design, test and use Brain-Computer Interfaces (BCIs).

• bcikit - Modular analysis of biosensor data streams, with visualization component, especially designed for EEG signals.

• EEG-Notebooks - A collection of classic EEG experiments, implemented in Python and Jupyter notebooks.

• Mother of all BCI Benchmarks (MOABB) - A comprehensive benchmark of popular Brain-Computer Interface (BCI) algorithms applied on an extensive list of freely available EEG datasets.

Data Analysis & Neuroimaging

• FreeSurfer – An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.

• MNE-Python – Open-source Python package for exploring, visualizing, and analyzing human neurophysiological data: MEG, EEG, sEEG, ECoG, NIRS, and more.

• NiPy – An ecosystem of python packages for the analysis of neuroimaging data.

• BrainSuite – A collection of open-source software tools that enable largely automated processing of magnetic resonance images (MRI) of the human brain.

• FSL (FMRIB Software Library) – a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data.

• Brainstorm – A collaborative, open-source application dedicated to the analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology.

• EEGLAB – An interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data.

• Chronux – An open-source software package for the analysis of neural data.

• NeuroDSP - A collection of approaches for applying digital signal processing, and related algorithms, to neural time series.

Modeling & Computational Resources

• Open Source Brain – A platform for sharing data and analysis techniques in neuroscience and collaboratively developing computational models of neural systems.

• ModelDB - An accessible location for storing and efficiently retrieving computational neuroscience models.