297 lines
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HTML
297 lines
14 KiB
HTML
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<p><img src="./AWESOME2.png" width="50%"></p>
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<blockquote>
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<p>Curated list of awesome neuroscience libraries, software and any
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content related to the domain.</p>
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</blockquote>
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<p><a href="https://en.wikipedia.org/wiki/Neuroscience">Neuroscience</a>
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is the study of how the nervous system develops, its structure, and what
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it does. Neuroscientists focus on the brain and its impact on behavior
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and cognitive functions. Traditionally, neuroscience has been seen as a
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branch of biology, but it has grown to encompass a wide range of
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interdisciplinary fields that work together toward elucidating brain
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function at multiple levels of investigation.</p>
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<p><a href="https://github.com/sindresorhus/awesome"><img
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src="https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg"
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alt="Awesome" /></a></p>
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<h2 id="contents">Contents</h2>
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<ul>
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<li><a href="#programming">Programming</a>
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<ul>
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<li><a href="#python">Python</a></li>
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<li><a href="#matlab">Matlab</a></li>
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<li><a href="#c">C++</a></li>
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<li><a href="#javascript">JavaScript</a></li>
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<li><a href="#r">R</a></li>
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</ul></li>
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<li><a href="#resources">Resources</a>
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<ul>
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<li><a href="#ebooks">Ebooks</a></li>
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<li><a href="#blogs">Blogs</a></li>
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<li><a href="#moocs">MOOCs</a></li>
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<li><a href="#communities">Communities</a></li>
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<li><a href="#newsletters">Newsletters</a></li>
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<li><a href="#miscellaneous">Miscellaneous</a></li>
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</ul></li>
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</ul>
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<h2 id="programming">Programming</h2>
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<p>Software, libraries and frameworks for development purposes.</p>
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<h3 id="python">Python</h3>
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<ul>
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<li><a href="https://github.com/nengo/nengo">Nengo</a> - Library for
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creating and simulating large-scale brain models.</li>
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<li><a href="https://github.com/nipy/nitime">Nitime</a> - Timeseries
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analysis for neuroscience data.</li>
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<li><a href="https://github.com/nilearn/nilearn">Nilearn</a> - Module
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for performing statistical learning/machine learning on NeuroImaging
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data.</li>
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<li><a href="https://github.com/nipy/dipy">DIPY</a> - Toolbox for
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analysis of MR diffusion imaging.</li>
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<li><a href="https://github.com/mne-tools/mne-python">MNE-Python</a> -
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Community-driven software for processing time-resolved neural signals
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including electroencephalography (EEG) and magnetoencephalography
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(MEG).</li>
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<li><a href="https://github.com/nipy/nibabel">NiBabel</a> - Provides
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read and write access to some common medical and neuroimaging file
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formats.</li>
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<li><a href="https://github.com/psychopy/psychopy">PsychoPy</a> -
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Package for running psychology and neuroscience experiments. It allows
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for creating psychology stimuli in Python.</li>
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<li><a href="https://github.com/numenta/nupic">NuPic</a> - Numenta
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Platform for Intelligent Computing is an implementation of Hierarchical
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Temporal Memory (HTM), a theory of intelligence based strictly on the
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neuroscience of the neocortex.</li>
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<li><a href="https://github.com/brian-team/brian2">Brian2</a> - Free,
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open source simulator for spiking neural networks.</li>
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<li><a href="https://github.com/expyriment/expyriment">expyriment</a> -
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Platform-independent lightweight Python library for designing and
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conducting timing-critical behavioural and neuroimaging
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experiments.</li>
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<li><a href="https://github.com/Hananel-Hazan/bindsnet">BindsNET</a> -
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Package for simulating spiking neural networks for reinforcement &
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machine learning.</li>
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<li><a
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href="https://github.com/SpikeInterface/spikeinterface">SpikeInterface</a>
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- Framework designed to unify spike-sorting technologies</li>
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<li><a href="https://nimare.readthedocs.io/en/latest/">NiMARE</a> -
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NiMARE is a Python package for neuroimaging meta-analyses</li>
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</ul>
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<h3 id="matlab">Matlab</h3>
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<ul>
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<li><a href="https://bdtoolbox.org/">Brain Dynamics Toolbox</a> - Open
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software for simulating dynamical systems in neuroscience.</li>
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<li><a href="https://neuroimage.usc.edu/brainstorm/">BrainStorm</a> -
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Open-source application dedicated to the analysis of brain recordings
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(MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit
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electrophysiology).</li>
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<li><a href="https://sccn.ucsd.edu/eeglab/">EEGLAB</a> - Interactive
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Matlab toolbox for processing continuous and event-related EEG, MEG and
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other electrophysiological data.</li>
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<li><a href="https://github.com/fieldtrip/fieldtrip">FieldTrip</a> -
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Toolbox for MEG and EEG analysis.</li>
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<li><a href="http://psychtoolbox.org/">Psychtoolbox-3</a> - Free set of
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Matlab and GNU Octave functions for vision and neuroscience
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research.</li>
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<li><a href="https://www.fil.ion.ucl.ac.uk/spm/">SPM</a> - Free and open
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source software for the analysis of brain imaging data sequences (fMRI,
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PET, SPECT, EEG, MEG).</li>
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</ul>
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<h3 id="c">C++</h3>
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<ul>
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<li><a href="https://github.com/BlueBrain/Brayns">Brayns</a> -
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Minimalistic visualiser that can perform ray-traced rendering of
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neurons. Ray-tracing can help to highlight areas of neural circuits
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where cells touch each other and where synapses are being created
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leading to a better understanding of how individual cells and
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subsequently the brain functions.</li>
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</ul>
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<h3 id="javascript">JavaScript</h3>
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<ul>
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<li><a href="https://github.com/aces/brainbrowser">Brainbrowser</a> -
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Library exposing set of web-based 3D visualization tools primarily
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targetting neuroimaging.</li>
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<li><a href="https://www.jspsych.org/">jsPsych</a> - Library for
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creating and running behavioural experiments in a web browser.</li>
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</ul>
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<h3 id="r">R</h3>
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<ul>
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<li><a href="https://github.com/jefferis/nat">nat: NeuroAnatomy
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Toolbox</a> - Package for the (3D) visualisation and analysis of
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biological image data, especially tracings of single neurons.</li>
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<li><a href="https://github.com/cwatson/brainGraph">brainGraph</a> -
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Package for performing graph theory analyses of brain MRI data.</li>
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</ul>
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<h2 id="resources">Resources</h2>
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<p>Interesting resources related to neuroscience.</p>
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<h3 id="ebooks">Ebooks</h3>
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<ul>
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<li><a
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href="http://nba.uth.tmc.edu/neuroscience/m/index.htm">Neuroscience
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Online</a> - Open-access electronic textbook and interactive courseware
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covering neuroscience in depth. Provided by the Department of
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Neurobiology and Anantomy at the University of Texas Medical School at
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Houston.</li>
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<li><a
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href="https://grey.colorado.edu/CompCogNeuro/index.php/CCNBook/Main">Computational
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Cognitive Neuroscience</a> - Text which provides an in-depth
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introduction to the main ideas in the computational cognitive
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neuroscience, a field which aims to understand the brain by using
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biologically based computational models.</li>
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<li><a href="https://neuronaldynamics.epfl.ch">Neuronal Dynamics</a> -
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Open-access electronic textbook that covers computational and
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theoretical neuroscience. Provided by École Polytechnique Fédérale de
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Lausanne (EPFL).</li>
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<li><a href="https://andysbrainbook.readthedocs.io/en/latest/">Andy’s
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Brain Book</a> - Book companion to <a
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href="https://www.andysbrainblog.com/">Andy’s Brain Blog</a>. Provides
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an introduction to working in a Unix environment, fMRI analysis, and
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commonplace neuroimaging tools and topics.</li>
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<li><a href="https://textbook.nipraxis.org/intro.html">NiPraxis</a> -
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Textbook for the <a href="https://nipraxis.org/">NiPraxis course</a>,
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covers fundamental concepts in neuroimaging analysis and how they relate
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to the wider world of statistics, engineering and computer science.
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Learn how to work with data and code to get a deeper understanding of
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how fMRI methods work, how they can fail, how to fix them, and how to
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develop new methods.</li>
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</ul>
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<h3 id="blogs">Blogs</h3>
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<ul>
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<li><a
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href="https://www.discovermagazine.com/author/neuroskeptic">Neuroskeptic</a>
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- <a href="http://discovermagazine.com/">Discover magazine</a>’s
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neuroscience blog which offers a look at the latest developments in
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neuroscience, psychiatry and psychology through a critical lens.</li>
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<li><a href="http://neurocritic.blogspot.in/">The Neurocritic</a> -
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Often critical takes on the most sensationalistic recent findings in
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Human Brain Imaging, Cognitive Neuroscience, and
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Psychopharmacology.</li>
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<li><a href="https://blogs.scientificamerican.com/scicurious-brain/">The
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scicurious brain</a> - Maintained by <a
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href="https://blogs.scientificamerican.com/">Scientific American</a>,
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this blog typically covers one research paper in a single entry.</li>
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<li><a href="http://blogs.nature.com/actionpotential">Action
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Potential</a> - Forum operated by neuroscience editors at the journal,
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Nature.</li>
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<li><a href="https://www.andysbrainblog.com/">Andy’s Brain Blog</a> - A
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large collection of articles, tutorials, and videos, covering many of
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the popular neuroimaging tools and methods.</li>
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</ul>
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<h3 id="moocs">MOOCs</h3>
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<p><a
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href="https://en.wikipedia.org/wiki/Massive_open_online_course">Massive
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Open Online Courses (MOOCs)</a> are free Web-based distance learning
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programs that are designed for the participation of large numbers of
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geographically dispersed students. MOOCs may be patterned on a college
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or university course or may be less structured.</p>
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<ul>
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<li><a href="https://www.mcb80x.org/">The Fundamentals of Neuroscience |
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Harvard & edX</a> - Serves an introductory survery of topics in
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neuroscience and has no specific prerequisites, though some prior
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exposure to biology and/or chemistry can be helpful.</li>
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<li><a
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href="https://ocw.mit.edu/courses/brain-and-cognitive-sciences/9-01-introduction-to-neuroscience-fall-2007/">Introduction
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to Neuroscience | MIT OCW</a> - Introduction to the mammalian nervous
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system, with emphasis on the structure and function of the human
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brain.</li>
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<li><a
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href="https://www.coursera.org/learn/computational-neuroscience">Computational
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Neuroscience | Coursera</a> - Provides an introduction to basic
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computational methods for understanding what nervous systems do and for
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determining how they function.</li>
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<li><a
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href="https://www.coursera.org/learn/medical-neuroscience">Medical
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Neuroscience</a> - Explores the functional organization and
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neurophysiology of the human central nervous system, while providing a
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neurobiological framework for understanding human behavior.</li>
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<li><a
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href="https://github.com/NeuromatchAcademy/course-content">Neuromatch
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Academy</a> - Jupyter notebooks for the three-week intensive summer
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school in computational neuroscience.</li>
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</ul>
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<h3 id="communities">Communities</h3>
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<ul>
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<li><a href="https://www.quora.com/topic/Neuroscience-1">Quora</a> -
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Neuroscience topic on Quora contains answers, often by experts, to
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questions ranging from basic to advanced.</li>
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<li><a
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href="https://www.reddit.com/r/ScienceNetwork/comments/ptye0/link_tables/">Reddit</a>
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- List of neuroscience, psychology and cognitive science
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subreddits.</li>
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<li><a href="https://psychology.stackexchange.com">StackExchange</a> -
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Psychology and neuroscience StackExchange site.</li>
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<li><a
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href="https://mail.python.org/mailman/listinfo/neuroimaging">neuroimaging@python.org</a>
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- A list for discussion of neuroimaging analysis in Python. Among other
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things, this list is home to discussions concerning <a
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href="https://nipy.org/">NiPy</a> projects (including NiBabel, Nilearn,
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dipy, MNE-Python, and more).</li>
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</ul>
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<h3 id="newsletters">Newsletters</h3>
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<ul>
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<li><a
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href="http://neuro.hms.harvard.edu/harvard-mahoney-neuroscience-institute/hmni-newsletter">On
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The Brain</a> - Harvard Mahoney Neuroscience Institute’s quarterly
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e-newsletter.</li>
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<li><a
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href="http://www.tnb.ua.ac.be/mailman/listinfo/comp-neuro">Comp-neuro</a>
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- A mailing list that is is intended to address the broad range of
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research approaches and issues involved in the general field of
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computational neuroscience.</li>
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<li><a href="https://www.brainpost.co/">BrainPost</a> - A mailing list
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that delivers weekly easy-to-read summaries of the latest neuroscience
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publications.</li>
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</ul>
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<h3 id="miscellaneous">Miscellaneous</h3>
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<ul>
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<li><a
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href="https://github.com/awesomedata/awesome-public-datasets#neuroscience">Awesome
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Public Datasets - Neuroscience</a> - High-quality open neuroscience
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datasets.</li>
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<li><a href="https://justinmeiners.github.io/neural-nets-sim/">McCulloch
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& Pitts Neural Net Simulator</a> - Simulator for a historical
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computational model based on neurons.</li>
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<li><a
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href="https://senselab.med.yale.edu/ModelDB/default.cshtml">ModelDB</a>
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- Searchable database for computational neuroscience models.</li>
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<li><a href="https://senselab.med.yale.edu/NeuronDB">NeuronDB</a> -
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Searchable database for of three types of neuronal properties: voltage
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gated conductances, neurotransmitter receptors, and neurotransmitter
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substances.</li>
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<li><a href="https://neuroelectro.org/">NeuroElectro</a> - Searchable
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database of neurons and their electrophysiological properties (extracted
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from literature)</li>
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<li><a href="https://learn-anything.xyz/neuroscience">Neuroscience
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Mindmap</a> - Interactive mindmap containing curated resources for
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anyone interested in learning neuroscience.</li>
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<li><a
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href="https://github.com/PhABC/neuroSummerSchools">neuroSummerSchools</a>
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- List of summer (and seasonal) summer schools in neuroscience and
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related fields.</li>
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<li><a href="https://brainpodcast.com/">Brain Matters</a> - Neuroscience
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podcast where real neuroscientists sit down and talk about the
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brain.</li>
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<li><a
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href="https://neurohackademy.org/course_type/lectures/">NeuroHackademy</a>
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- Summer school in neuroimaging and data science, held at the University
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of Washington eScience Institute. Lectures are available through the
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institute’s <a
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href="https://www.youtube.com/@UWeScienceInstitute">YouTube
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channel</a>.</li>
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<li><a href="https://github.com/PTDZ/SORTED">SORTED</a> - SORTED: a list
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of interesting science ideas and links (cognitive/neuro & data
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science)</li>
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</ul>
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<h2 id="contribute">Contribute</h2>
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<p>Contributions welcome! Read the <a
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href="contributing.md">contribution guidelines</a> first.</p>
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<h2 id="license">License</h2>
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<p><a href="http://creativecommons.org/publicdomain/zero/1.0"><img
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src="http://mirrors.creativecommons.org/presskit/buttons/88x31/svg/cc-zero.svg"
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alt="CC0" /></a></p>
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<p>To the extent possible under law, <a
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href="https://github.com/analyticalmonk">Akash Tandon</a> has waived all
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copyright and related or neighboring rights to this work.</p>
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<p><a
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href="https://github.com/analyticalmonk/awesome-neuroscience">neuroscience.md
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Github</a></p>
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