{"slug": "analyticalmonk--awesome-neuroscience", "title": "Neuroscience", "description": "A curated list of awesome neuroscience libraries, software and any content related to the domain.", "github_url": "https://github.com/analyticalmonk/awesome-neuroscience", "stars": "1.3K", "tag": "Health and Social Science", "entry_count": 58, "subcategory_count": 12, "subcategories": [{"name": "General", "parent": "", "entries": [{"name": "Programming", "url": "#programming", "description": ""}, {"name": "Resources", "url": "#resources", "description": ""}]}, {"name": "Python", "parent": "Programming", "entries": [{"name": "Nengo", "url": "https://github.com/nengo/nengo", "description": "Library for creating and simulating large-scale brain models.", "stars": "822"}, {"name": "Nitime", "url": "https://github.com/nipy/nitime", "description": "Timeseries analysis for neuroscience data.", "stars": "244"}, {"name": "Nilearn", "url": "https://github.com/nilearn/nilearn", "description": "Module for performing statistical learning/machine learning on NeuroImaging data.", "stars": "1.2k"}, {"name": "DIPY", "url": "https://github.com/nipy/dipy", "description": "Toolbox for analysis of MR diffusion imaging.", "stars": "712"}, {"name": "MNE-Python", "url": "https://github.com/mne-tools/mne-python", "description": "Community-driven software for processing time-resolved neural signals including electroencephalography (EEG) and magnetoencephalography (MEG).", "stars": "2.7k"}, {"name": "NiBabel", "url": "https://github.com/nipy/nibabel", "description": "Provides read and write access to some common medical and neuroimaging file formats.", "stars": "652"}, {"name": "PsychoPy", "url": "https://github.com/psychopy/psychopy", "description": "Package for running psychology and neuroscience experiments. It allows for creating psychology stimuli in Python.", "stars": "1.7k"}, {"name": "NuPic", "url": "https://github.com/numenta/nupic", "description": "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.", "stars": "6.3k"}, {"name": "Brian2", "url": "https://github.com/brian-team/brian2", "description": "Free, open source simulator for spiking neural networks.", "stars": "933"}, {"name": "expyriment", "url": "https://github.com/expyriment/expyriment", "description": "Platform-independent lightweight Python library for designing and conducting timing-critical behavioural and neuroimaging experiments.", "stars": "113"}, {"name": "BindsNET", "url": "https://github.com/Hananel-Hazan/bindsnet", "description": "Package for simulating spiking neural networks for reinforcement & machine learning.", "stars": "1.5k"}, {"name": "SpikeInterface", "url": "https://github.com/SpikeInterface/spikeinterface", "description": "Framework designed to unify spike-sorting technologies", "stars": "517"}, {"name": "NiMARE", "url": "https://nimare.readthedocs.io/en/latest/", "description": "NiMARE is a Python package for neuroimaging meta-analyses"}]}, {"name": "Matlab", "parent": "Programming", "entries": [{"name": "Brain Dynamics Toolbox", "url": "https://bdtoolbox.org/", "description": "Open software for simulating dynamical systems in neuroscience."}, {"name": "BrainStorm", "url": "https://neuroimage.usc.edu/brainstorm/", "description": "Open-source application dedicated to the analysis of brain recordings (MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology)."}, {"name": "EEGLAB", "url": "https://sccn.ucsd.edu/eeglab/", "description": "Interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data."}, {"name": "FieldTrip", "url": "https://github.com/fieldtrip/fieldtrip", "description": "Toolbox for MEG and EEG analysis.", "stars": "840"}, {"name": "Psychtoolbox-3", "url": "http://psychtoolbox.org/", "description": "Free set of Matlab and GNU Octave functions for vision and neuroscience research."}, {"name": "SPM", "url": "https://www.fil.ion.ucl.ac.uk/spm/", "description": "Free and open source software for the  analysis of brain imaging data sequences (fMRI, PET, SPECT, EEG, MEG)."}]}, {"name": "C++", "parent": "Programming", "entries": [{"name": "Brayns", "url": "https://github.com/BlueBrain/Brayns", "description": "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.", "stars": "289"}]}, {"name": "JavaScript", "parent": "Programming", "entries": [{"name": "Brainbrowser", "url": "https://github.com/aces/brainbrowser", "description": "Library exposing set of web-based 3D visualization tools primarily targetting neuroimaging.", "stars": "352"}, {"name": "jsPsych", "url": "https://www.jspsych.org/", "description": "Library for creating and running behavioural experiments in a web browser."}]}, {"name": "R", "parent": "Programming", "entries": [{"name": "nat: NeuroAnatomy Toolbox", "url": "https://github.com/jefferis/nat", "description": "Package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.", "stars": "64"}, {"name": "brainGraph", "url": "https://github.com/cwatson/brainGraph", "description": "Package for performing graph theory analyses of brain MRI data.", "stars": "175"}]}, {"name": "Ebooks", "parent": "Resources", "entries": [{"name": "Neuroscience Online", "url": "http://nba.uth.tmc.edu/neuroscience/m/index.htm", "description": "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."}, {"name": "Computational Cognitive Neuroscience", "url": "https://grey.colorado.edu/CompCogNeuro/index.php/CCNBook/Main", "description": "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."}, {"name": "Neuronal Dynamics", "url": "https://neuronaldynamics.epfl.ch", "description": "Open-access electronic textbook that covers computational and theoretical neuroscience. Provided by \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL)."}, {"name": "Andy's Brain Book", "url": "https://andysbrainbook.readthedocs.io/en/latest/", "description": "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."}, {"name": "NiPraxis", "url": "https://textbook.nipraxis.org/intro.html", "description": "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."}]}, {"name": "Blogs", "parent": "Resources", "entries": [{"name": "Neuroskeptic", "url": "https://www.discovermagazine.com/author/neuroskeptic", "description": "[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."}, {"name": "The Neurocritic", "url": "http://neurocritic.blogspot.in/", "description": "Often critical takes on the most sensationalistic recent findings in Human Brain Imaging, Cognitive Neuroscience, and Psychopharmacology."}, {"name": "The scicurious brain", "url": "https://blogs.scientificamerican.com/scicurious-brain/", "description": "Maintained by [Scientific American](https://blogs.scientificamerican.com/), this blog typically covers one research paper in a single entry."}, {"name": "Action Potential", "url": "http://blogs.nature.com/actionpotential", "description": "Forum operated by neuroscience editors at the journal, Nature."}, {"name": "Andy's Brain Blog", "url": "https://www.andysbrainblog.com/", "description": "A large collection of articles, tutorials, and videos, covering many of the popular neuroimaging tools and methods."}]}, {"name": "MOOCs", "parent": "Resources", "entries": [{"name": "The Fundamentals of Neuroscience | Harvard & edX", "url": "https://www.mcb80x.org/", "description": "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."}, {"name": "Introduction to Neuroscience | MIT OCW", "url": "https://ocw.mit.edu/courses/brain-and-cognitive-sciences/9-01-introduction-to-neuroscience-fall-2007/", "description": "Introduction to the mammalian nervous system, with emphasis on the structure and function of the human brain."}, {"name": "Computational Neuroscience | Coursera", "url": "https://www.coursera.org/learn/computational-neuroscience", "description": "Provides an introduction to basic computational methods for understanding what nervous systems do and for determining how they function."}, {"name": "Medical Neuroscience", "url": "https://www.coursera.org/learn/medical-neuroscience", "description": "Explores the functional organization and neurophysiology of the human central nervous system, while providing a neurobiological framework for understanding human behavior."}, {"name": "Neuromatch Academy", "url": "https://github.com/NeuromatchAcademy/course-content", "description": "Jupyter notebooks for the three-week intensive summer school in computational neuroscience.", "stars": "2.7k"}]}, {"name": "Communities", "parent": "Resources", "entries": [{"name": "Quora", "url": "https://www.quora.com/topic/Neuroscience-1", "description": "Neuroscience topic on Quora contains answers, often by experts, to questions ranging from basic to advanced."}, {"name": "Reddit", "url": "https://www.reddit.com/r/ScienceNetwork/comments/ptye0/link_tables/", "description": "List of neuroscience, psychology and cognitive science subreddits."}, {"name": "StackExchange", "url": "https://psychology.stackexchange.com", "description": "Psychology and neuroscience StackExchange site."}, {"name": "neuroimaging@python.org", "url": "https://mail.python.org/mailman/listinfo/neuroimaging", "description": "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)."}]}, {"name": "Newsletters", "parent": "Resources", "entries": [{"name": "On The Brain", "url": "http://neuro.hms.harvard.edu/harvard-mahoney-neuroscience-institute/hmni-newsletter", "description": "Harvard Mahoney Neuroscience Institute's quarterly e-newsletter."}, {"name": "Comp-neuro", "url": "http://www.tnb.ua.ac.be/mailman/listinfo/comp-neuro", "description": "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."}, {"name": "BrainPost", "url": "https://www.brainpost.co/", "description": "A mailing list that delivers weekly easy-to-read summaries of the latest neuroscience publications."}]}, {"name": "Miscellaneous", "parent": "Resources", "entries": [{"name": "Awesome Public Datasets - Neuroscience", "url": "https://github.com/awesomedata/awesome-public-datasets#neuroscience", "description": "High-quality open neuroscience datasets.", "stars": "60k"}, {"name": "McCulloch & Pitts Neural Net Simulator", "url": "https://justinmeiners.github.io/neural-nets-sim/", "description": "Simulator for a historical computational model based on neurons."}, {"name": "ModelDB", "url": "https://senselab.med.yale.edu/ModelDB/default.cshtml", "description": "Searchable database for computational neuroscience models."}, {"name": "NeuronDB", "url": "https://senselab.med.yale.edu/NeuronDB", "description": "Searchable database for  of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances."}, {"name": "NeuroElectro", "url": "https://neuroelectro.org/", "description": "Searchable database of neurons and their electrophysiological properties (extracted from literature)"}, {"name": "Neuroscience Mindmap", "url": "https://learn-anything.xyz/neuroscience", "description": "Interactive mindmap containing curated resources for anyone interested in learning neuroscience."}, {"name": "neuroSummerSchools", "url": "https://github.com/PhABC/neuroSummerSchools", "description": "List of summer (and seasonal) summer schools in neuroscience and related fields.", "stars": "215"}, {"name": "Brain Matters", "url": "https://brainpodcast.com/", "description": "Neuroscience podcast where real neuroscientists sit down and talk about the brain."}, {"name": "NeuroHackademy", "url": "https://neurohackademy.org/course_type/lectures/", "description": "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)."}, {"name": "SORTED", "url": "https://github.com/PTDZ/SORTED", "description": "SORTED: a list of interesting science ideas and links (cognitive/neuro & data science)", "stars": "13"}]}], "name": ""}