awesome-awesomeness/html/neuroscience.md2.html

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