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.

Contents

• Programming
• Python
• Matlab
• C++
• JavaScript
• R
• Resources
• Ebooks
• Blogs
• MOOCs
• Communities
• Newsletters
• Miscellaneous

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.
• NuPic - Numenta Platform for Intelligent Computing is an implementation of Hierarchical Temporal Memory (HTM), a theory of intelligence based strictly on the neuroscience of the neocortex.
• 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.
• 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.