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Neuroscience

GitHub repository ↗ synced 2026/8/9

Curated list of awesome neuroscience libraries, software and any content related to the domain.

Neuroscience is the study of how the nervous system develops, its structure, and what it does. Neuroscientists focus on the brain and its impact on behavior and cognitive functions. Traditionally, neuroscience has been seen as a branch of biology, but it has grown to encompass a wide range of interdisciplinary fields that work together toward elucidating brain function at multiple levels of investigation.

Awesome

Programming

Software, libraries and frameworks for development purposes.

Python

Nengo

Library for creating and simulating large-scale brain models.

Nitime

Timeseries analysis for neuroscience data.

Nilearn

Module for performing statistical learning/machine learning on NeuroImaging data.

DIPY

Toolbox for analysis of MR diffusion imaging.

MNE-Python

Community-driven software for processing time-resolved neural signals including electroencephalography (EEG) and magnetoencephalography (MEG).

NiBabel

Provides read and write access to some common medical and neuroimaging file formats.

PsychoPy

Package for running psychology and neuroscience experiments. It allows for creating psychology stimuli in Python.

Brian2

Free, open source simulator for spiking neural networks.

expyriment

Platform-independent lightweight Python library for designing and conducting timing-critical behavioural and neuroimaging experiments.

DeepLabCut

Markerless pose estimation toolkit for animal behavior analysis using transfer learning with deep neural networks.

CaImAn

Computational toolbox for large-scale calcium imaging data analysis, including motion correction, source extraction, and deconvolution.

Elephant

Library for the analysis of electrophysiology data, providing tools for spike train statistics, signal processing, and connectivity analysis.

NEURON

Simulation environment for modeling individual neurons and networks of neurons, widely used in computational and systems neuroscience.

Nipype

Workflow engine providing a uniform Python interface to existing neuroimaging packages (FSL, FreeSurfer, AFNI, SPM, ANTs) and flexible pipeline composition.

PyNWB

Python API for reading and writing Neurodata Without Borders (NWB) files, the community standard data format for cellular-based neurophysiology data.

fMRIPrep

Robust preprocessing pipeline for fMRI data that adapts to nearly any dataset and produces analysis-ready outputs with minimal manual intervention.

AllenSDK

Toolkit for accessing and processing data from the Allen Institute for Brain Science, including the Allen Brain Atlas and Allen Brain Observatory.

Suite2p

Pipeline for cell detection and signal extraction from large-scale two-photon calcium imaging recordings.

Neo

Package for representing electrophysiology data in Python, with readers for a wide range of neurophysiology file formats.

Monty

Sensorimotor learning framework based on the thousand brains theory of the neocortex.

PyNoetic

A Modular Python Framework for No-Code Development of EEG Brain-Computer Interfaces supporting end-to-end BCI design.

  • BindsNET - Package for simulating spiking neural networks for reinforcement & machine learning.
  • SpikeInterface - Framework designed to unify spike-sorting technologies
  • NiMARE - NiMARE is a Python package for neuroimaging meta-analyses

Matlab

Brain Dynamics Toolbox

Open software for simulating dynamical systems in neuroscience.

BrainStorm

Open-source application dedicated to the analysis of brain recordings (MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology).

EEGLAB

Interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data.

FieldTrip

Toolbox for MEG and EEG analysis.

Psychtoolbox-3

Free set of Matlab and GNU Octave functions for vision and neuroscience research.

SPM

Free and open source software for the analysis of brain imaging data sequences (fMRI, PET, SPECT, EEG, MEG).

C++

Brayns

Minimalistic visualiser that can perform ray-traced rendering of neurons. Ray-tracing can help to highlight areas of neural circuits where cells touch each other and where synapses are being created leading to a better understanding of how individual cells and subsequently the brain functions.

JavaScript

Brainbrowser

Library exposing set of web-based 3D visualization tools primarily targetting neuroimaging.

jsPsych

Library for creating and running behavioural experiments in a web browser.

R

nat: NeuroAnatomy Toolbox

Package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

brainGraph

Package for performing graph theory analyses of brain MRI data.

Resources

Interesting resources related to neuroscience.

Ebooks

Neuroscience Online

Open-access electronic textbook and interactive courseware covering neuroscience in depth. Provided by the Department of Neurobiology and Anantomy at the University of Texas Medical School at Houston.

Computational Cognitive Neuroscience

Text which provides an in-depth introduction to the main ideas in the computational cognitive neuroscience, a field which aims to understand the brain by using biologically based computational models.

Neuronal Dynamics

Open-access electronic textbook that covers computational and theoretical neuroscience. Provided by École Polytechnique Fédérale de Lausanne (EPFL).

Andy's Brain Book

Book companion to [Andy's Brain Blog](https://www.andysbrainblog.com/). Provides an introduction to working in a Unix environment, fMRI analysis, and commonplace neuroimaging tools and topics.

NiPraxis

Textbook for the [NiPraxis course](https://nipraxis.org/), covers fundamental concepts in neuroimaging analysis and how they relate to the wider world of statistics, engineering and computer science. Learn how to work with data and code to get a deeper understanding of how fMRI methods work, how they can fail, how to fix them, and how to develop new methods.

Blogs

Neuroskeptic

[Discover magazine](http://discovermagazine.com/)'s neuroscience blog which offers a look at the latest developments in neuroscience, psychiatry and psychology through a critical lens.

Andy's Brain Blog

A large collection of articles, tutorials, and videos, covering many of the popular neuroimaging tools and methods.

MOOCs

Introduction to Neuroscience | MIT OCW

Introduction to the mammalian nervous system, with emphasis on the structure and function of the human brain.

Computational Neuroscience | Coursera

Provides an introduction to basic computational methods for understanding what nervous systems do and for determining how they function.

Medical Neuroscience

Explores the functional organization and neurophysiology of the human central nervous system, while providing a neurobiological framework for understanding human behavior.

Neuromatch Academy

Jupyter notebooks for the three-week intensive summer school in computational neuroscience.

Massive Open Online Courses (MOOCs) are free Web-based distance learning programs that are designed for the participation of large numbers of geographically dispersed students.
MOOCs may be patterned on a college or university course or may be less structured.

Communities

Quora

Neuroscience topic on Quora contains answers, often by experts, to questions ranging from basic to advanced.

r/neuroscience

Subreddit for discussion of neuroscience news, research, and questions.

StackExchange

Psychology and neuroscience StackExchange site.

neuroimaging@python.org

A list for discussion of neuroimaging analysis in Python. Among other things, this list is home to discussions concerning [NiPy](https://nipy.org/) projects (including NiBabel, Nilearn, dipy, MNE-Python, and more).

Newsletters

On The Brain

Harvard Mahoney Neuroscience Institute's quarterly e-newsletter.

BrainPost

A mailing list that delivers weekly easy-to-read summaries of the latest neuroscience publications.

Miscellaneous

Awesome Public Datasets - Neuroscience

High-quality open neuroscience datasets.

McCulloch & Pitts Neural Net Simulator

Simulator for a historical computational model based on neurons.

ModelDB

Searchable database for computational neuroscience models.

NeuroElectro

Searchable database of neurons and their electrophysiological properties (extracted from literature)

Neuroscience Mindmap

Interactive mindmap containing curated resources for anyone interested in learning neuroscience.

neuroSummerSchools

List of summer (and seasonal) summer schools in neuroscience and related fields.

Brain Matters

Neuroscience podcast where real neuroscientists sit down and talk about the brain.

NeuroHackademy

Summer school in neuroimaging and data science, held at the University of Washington eScience Institute. Lectures are available through the institute's [YouTube channel](https://www.youtube.com/@UWeScienceInstitute).

SORTED

SORTED: a list of interesting science ideas and links (cognitive/neuro & data science)

BIDS

Brain Imaging Data Structure: community standard for organizing neuroimaging and behavioral data, supported by most modern neuroimaging tools.

OpenNeuro

Free and open platform for sharing and analyzing neuroimaging data (MRI, MEG, EEG, iEEG, ECoG, ASL, PET).