Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

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: 1 day 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.
  - 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.
  - 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
  - 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.
- 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.
  - EEGLAB - Interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data.
- 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.
  - 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 10 R 1 JavaScript 1 C++ 1 MATLAB 1

Ecosyste.ms: Awesome

awesome-neuroscience

Programming

Python

Matlab

JavaScript

R

C++

Resources

Ebooks

Blogs

MOOCs

Communities

Newsletters

Miscellaneous