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awesome-neuroscience

A curated list of awesome neuroscience libraries, software and any content related to the domain.
https://github.com/analyticalmonk/awesome-neuroscience

Last synced: 4 days ago
JSON representation

  • Programming

    • 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.
      • BindsNET - Package for simulating spiking neural networks for reinforcement & machine learning.
      • NiMARE - NiMARE is a Python package for neuroimaging meta-analyses
      • 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

    • 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.
      • 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).
      • FieldTrip - Toolbox for MEG and EEG analysis.

    • JavaScript

      • jsPsych - Library for creating and running behavioural experiments in a web browser.
      • Brainbrowser - Library exposing set of web-based 3D visualization tools primarily targetting neuroimaging.

    • R

      • nat: NeuroAnatomy Toolbox - Package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
      • 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.

    • 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.

  • Resources

    • 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.
      • 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.
      • The Neurocritic - Often critical takes on the most sensationalistic recent findings in Human Brain Imaging, Cognitive Neuroscience, and Psychopharmacology.
      • The scicurious brain - Maintained by [Scientific American](https://blogs.scientificamerican.com/), this blog typically covers one research paper in a single entry.
      • Action Potential - Forum operated by neuroscience editors at the journal, Nature.
      • Andy's Brain Blog - A large collection of articles, tutorials, and videos, covering many of the popular neuroimaging tools and methods.
      • The scicurious brain - Maintained by [Scientific American](https://blogs.scientificamerican.com/), this blog typically covers one research paper in a single entry.

    • MOOCs

      • Massive Open Online Courses (MOOCs) - based distance learning programs that are designed for the participation of large numbers of geographically dispersed students.
      • The Fundamentals of Neuroscience | Harvard & edX - 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.
      • 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.

    • Communities

      • Quora - Neuroscience topic on Quora contains answers, often by experts, to questions ranging from basic to advanced.
      • Reddit - List of neuroscience, psychology and cognitive science subreddits.
      • StackExchange - Psychology and neuroscience StackExchange site.
      • [email protected] - 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.
      • Comp-neuro - 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.
      • 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.
      • NeuronDB - Searchable database for of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances.
      • 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.
      • 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).
      • ModelDB - Searchable database for computational neuroscience models.
Programming Languages
Python 11 R 2 JavaScript 1 C++ 1 MATLAB 1
Categories
Resources 31 Programming 27 License 4
Sub Categories
Python 15 Miscellaneous 13 Blogs 6 Matlab 6 MOOCs 5 Ebooks 4 Communities 4 R 3 Newsletters 3 JavaScript 2 C++ 1
Keywords
neuroscience 10 python 7 neuroimaging 5 science 3 statistics 3 machine-learning 3 brain-imaging 3 psychology 2 eeg 2 ecog 2 visualisation 2 fmri 2 connectomics 2 neurons 2 meg 2 brain-connectivity 2 r 2 experiment-control 2 brain 2 spiking-neural-networks 2 psychophysics 1 psychopy 1 psycholinguistics 1 linguistics 1 experimental-design 1 experiment 1 trk 1 tck 1 artificial-intelligence 1 hierarchical-temporal-memory 1 machine-intelligence 1 neocortex 1 biological-simulations 1 brian 1 brian2 1 code-generation 1 computational-neuroscience 1 aaron-swartz 1 awesome-public-datasets 1 datasets 1 opendata 1 nengo 1 neural-networks 1 brain-mri 1 decoding 1 mvpa 1 electrocorticography 1 electroencephalography 1 magnetoencephalography 1 visualization 1