Programming / Python

• NiMARE - NiMARE is a Python package for neuroimaging meta-analyses

Resources / Ebooks

• Andy's Brain Book - Book companion to Andy's Brain Blog. Provides an introduction to working in a Unix environment, fMRI analysis, and commonplace neuroimaging tools and topics.

• NiPraxis - Textbook for the NiPraxis course, 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.

Resources / Blogs

• Andy's Brain Blog - A large collection of articles, tutorials, and videos, covering many of the popular neuroimaging tools and methods.

Resources / Communities

• neuroimaging@python.org - A list for discussion of neuroimaging analysis in Python. Among other things, this list is home to discussions concerning NiPy projects (including NiBabel, Nilearn, dipy, MNE-Python, and more).

Resources / Miscellaneous

• 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.

• SORTED (⭐13) - SORTED: a list of interesting science ideas and links (cognitive/neuro & data science)

Programming / Python

• SpikeInterface (⭐517) - Framework designed to unify spike-sorting technologies

Resources / Miscellaneous

• NeuroElectro - Searchable database of neurons and their electrophysiological properties (extracted from literature)

Programming / 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.

• SPM - Free and open source software for the analysis of brain imaging data sequences (fMRI, PET, SPECT, EEG, MEG).

Resources / MOOCs

• Neuromatch Academy (⭐2.7k) - Jupyter notebooks for the three-week intensive summer school in computational neuroscience.

Programming / JavaScript

• jsPsych - Library for creating and running behavioural experiments in a web browser.

Resources / Newsletters

• BrainPost - A mailing list that delivers weekly easy-to-read summaries of the latest neuroscience publications.

Resources / Blogs

• Neuroskeptic - Discover magazine's neuroscience blog which offers a look at the latest developments in neuroscience, psychiatry and psychology through a critical lens.

Resources / Miscellaneous

• neuroSummerSchools (⭐215) - List of summer (and seasonal) summer schools in neuroscience and related fields.

Programming / Python

• BindsNET (⭐1.5k) - Package for simulating spiking neural networks for reinforcement & machine learning.

Resources / Miscellaneous

• Brain Matters - Neuroscience podcast where real neuroscientists sit down and talk about the brain.

Resources / Miscellaneous

• McCulloch & Pitts Neural Net Simulator - Simulator for a historical computational model based on neurons.

Programming / R

• nat: NeuroAnatomy Toolbox (⭐64) - Package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

• brainGraph (⭐175) - Package for performing graph theory analyses of brain MRI data.

Resources / Ebooks

• Neuronal Dynamics - Open-access electronic textbook that covers computational and theoretical neuroscience. Provided by École Polytechnique Fédérale de Lausanne (EPFL).

Resources / Communities

• StackExchange - Psychology and neuroscience StackExchange site.

Resources / Newsletters

• 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.

Resources / Miscellaneous

• Awesome Public Datasets - Neuroscience (⭐60k) - High-quality open neuroscience datasets.

Resources / Miscellaneous

• NeuronDB - Searchable database for of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances.

Resources / 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.

Resources / Ebooks

• 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.

Resources / Miscellaneous

• ModelDB - Searchable database for computational neuroscience models.

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.

Resources / Miscellaneous

• Neuroscience Mindmap - Interactive mindmap containing curated resources for anyone interested in learning neuroscience.

Programming / C++

• Brayns (⭐289) - 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.

Programming / JavaScript

• Brainbrowser (⭐352) - Library exposing set of web-based 3D visualization tools primarily targetting neuroimaging.

Programming / Python

• Brian2 (⭐933) - Free, open source simulator for spiking neural networks.

Resources / Blogs

• The scicurious brain - Maintained by Scientific American, this blog typically covers one research paper in a single entry.

• Action Potential - Forum operated by neuroscience editors at the journal, Nature.

Resources / MOOCs

• 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.

• 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.

Programming / Python

• Nilearn (⭐1.2k) - Module for performing statistical learning/machine learning on NeuroImaging data.

• DIPY (⭐712) - Toolbox for analysis of MR diffusion imaging.

Resources / Blogs

• The Neurocritic - Often critical takes on the most sensationalistic recent findings in Human Brain Imaging, Cognitive Neuroscience, and Psychopharmacology.

Programming / Python

• expyriment (⭐113) - Platform-independent lightweight Python library for designing and conducting timing-critical behavioural and neuroimaging experiments.

Programming / Matlab

• Psychtoolbox-3 - Free set of Matlab and GNU Octave functions for vision and neuroscience research.

Programming / Python

• Nengo (⭐822) - Library for creating and simulating large-scale brain models.

• PsychoPy (⭐1.7k) - Package for running psychology and neuroscience experiments. It allows for creating psychology stimuli in Python.

• NuPic (⭐6.3k) - 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.

Programming / Matlab

• FieldTrip (⭐840) - Toolbox for MEG and EEG analysis.

Programming / Python

• Nitime (⭐244) - Timeseries analysis for neuroscience data.

• MNE-Python (⭐2.7k) - Community-driven software for processing time-resolved neural signals including electroencephalography (EEG) and magnetoencephalography (MEG).

• NiBabel (⭐652) - Provides read and write access to some common medical and neuroimaging file formats.

Resources / MOOCs

• Introduction to Neuroscience | MIT OCW - Introduction to the mammalian nervous system, with emphasis on the structure and function of the human brain.

Resources / Newsletters

• On The Brain - Harvard Mahoney Neuroscience Institute's quarterly e-newsletter.