Programming

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.

JavaScript

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

Matlab

• FieldTrip - Toolbox for MEG and EEG analysis.
• Psychtoolbox-3 - Free set of Matlab and GNU Octave functions for vision and neuroscience research.

Python

• 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.
• 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.

R

• brainGraph - Package for performing graph theory analyses of brain MRI data.
• nat: NeuroAnatomy Toolbox - Package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

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.
• Action Potential - Forum operated by neuroscience editors at the journal, Nature.
• 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, this blog typically covers one research paper in a single entry.

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.

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

Miscellaneous

• Awesome Public Datasets - Neuroscience - High-quality open neuroscience datasets.
• NeuronDB - Searchable database for of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances.
• 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.
• ModelDB - Searchable database for computational neuroscience models.
• neuroSummerSchools - List of summer (and seasonnal) summer schools in neuroscience and related fields.
• McCulloch & Pitts Neural Net Simulator - Simulator for a historical computational model based on neurons.

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

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.