Computational Neuroscience at Coursera
Computational Neuroscience: Neuronal Dynamics of Cognition at edX
Neuronal Dynamics at edX
The open book for this course is available here
Neuroscience course material from OpenCourseWare (OCW) at MIT Department of Brain and Cognitive Sciences - HUGE list!
Simulation Neuroscience at edX
Interactive webpage illustrating spiking neural models
A series of notebooks that serves as an introduction to theoretical/computational neuroscience (for beginners)
Introduction To Modern Brain-Computer Interface Design
-----------------
Open Data
-----------------
This only lists neuroscience-specific open data repositories. For general science data repositories that may contain neuroscience data like
re3data
,
see this Open Science Resources page
3D Brain Atlas Reconstructor
Allen Brain Atlas Data Portal
More detail here
Associated software here
BODB - Brain Operation Database System
BossDB.org — hundreds of terabytes of microscopy
Brain Slices- Repository of brain tissue images
C-BIG - Biological Imaging and Genetic repository
Channelpedia - Wiki of neuron ion channels, hosted by the Blue Brain Project
CRCNS - Collaborative Research in Computational Neuroscience
GIN - Modern Research Data Management for Neuroscience
IDA LONI - Image and Data Archive for neuroscience by Laboratory of Neuro Imaging
INDI - International Neuroimaging Data-Sharing Initiative
iEEG.org - National Institutes of Neurological Disorders and Stroke EEG data repository for epilepsy research
NCBI databases - National Center for Biotechnology Information database list, VERY comprehensive!
NDA - National Institute of Mental Health Data Archive
NeuroVault - Public repository of MRI and PET statistical maps, parcellations, and atlases
NIF - Neuroscience Information Framework, massive search engine for neuroscience data, tools, etc.
NITRC - NeuroImaging Tools and Resources Collaboratory
NMC - Neocortical Microcircuit Collaboration, part of Blue Brain
NWB - Neurodata Without Borders - A standardized format for electrophysiological, and in the future other, neuroscience data. Some data sets available on the site in this format.
OpenNeuro - Free and open platform for neuroimaging data (succeeds OpenfMRI)
Whole Brain Catalog - Virtual catalog of a mouse brain
WormBase - Database of nematode information
ZFIN - Zebrafish Model Organism Database
Neo - Python library for enabling interoperability of electrophysiological data, including conversion from proprietary file formats
Neurodata Without Borders: Neurophysiology (NWB:N) data standard for neurophysiology, including intracellular, extracellular, optical physiology, tracking, and stimulus data
ndx-simulation-output Large-scale simulation data scheme extenstion to NWB:N
NSDF - Neuroscience Simulation Data Format, built on top of HDF5
SONATA format for large-scale, efficient model specification and output data schema of neural simulations, co-developed by Allen Institute for Brain Sciences and Blue Brain Project
BioModels - Not neuroscience-specific
ModelDB - Repository of computational neuroscience models for simulation
, built by
Senselab
Senselab
hosts several other databases, but ModelDB is the most popular:
CellPropDB - Cellular Properties Database provides a simple repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells.
NeuronDB - Provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances.
MicrocircuitDB - Provides an accessible location for storing and efficiently retrieving realistic computational models of brain microcircuits and networks.
3DModelDB - A collection of 3D printable versions of published neuron morphologies, both traced and artificial.
ORModelDB - A resource that is a repository of the results of the efforts of the community is computationally elucidating the structure of the olfactory receptor with a view to establishing a mechanistic basis for OR-odorant binding.
OdorMapDB - Olfactory Bulb Odor Map DataBase
OdorDB - Odor Molecules DataBase
ORDB - Olfactory Receptor DataBase
NeuroElectro - Repository of data-mined and human-curated neuron celltype electrophysiological data
NeuroMorpho - Curated repository of digitally reconstructed neuron geometries
OSB - Open Source Brain
OpenWorm - Popular platform for simulation and analysis of nematode neuroscience models!
"Integrated Models" RRID on SciCrunch - Compilation of model sources
-------------------
Open Code
-------------------
Based on Imaging Analysis
Allen SDK - Allen (Institute) Software Development Kit for Allen Brain Atlas
CaImAn - Calcium Imaging Analysis
CATMAID - The Collaborative Annotation Toolkit for Massive Amounts of Image Data
FreeSurfer - Popular open-source MRI processing and analysis software
NiBabel - Python library for enabling interoperability of neuroimaging data, including conversion from and between many file formats
TrakEM2 - Morphological data mining and analysis tool
TREES - MATLAB toolbox for analyzing neuron microscopy
V-NeuroStack - 3D time stacks for finding patterns in spontaneous activity of neurons in mouse brain slices
---------------------------------------------------
Organizations and Communities
---------------------------------------------------
CodeNeuro - Bringing neuroscience and data science together
CNS - Organization for Computational Neuroscience
G-NODE - German Informatics Node
INCF - International Neuroinformatics Coordinating Facility
NeuralEnsemble, focused on software development in neuroscience
Neuroinformatics Research Group at Harvard
Neurostars - Neuroscience Q and A website
NIMH - National Institute of Mental Health
An Open Computational Neuroscience list I've made on Twitter
Organization for Human Brain Mapping
Reddit /r/Neuroscience resources
SFN - Society for Neuroscience
计算神经科学在线课程
1.
计算神经科学系列课程
苏黎世大学与苏黎世联邦理工大学共建的转化神经模型单元（Translational Neuromodeling Unit，简称TNU）的系列教学视频，包括
计算精神病学
（含视频、幻灯片、代码等）
，
计算神经影像诊断
，以及
fMRI数据分析方法与模型
等。
2.
计算神经科学（Rajesh P. N. Rao & Adrienne Fairhall）
英文名Computational Neuroscience，是Coursera上的华盛顿大学的计算神经科学基本参考《理论神经科学》来上，比较全面。
3.
纽约大学 - 神经与认知科学的数学工具（Mike Landy & Eero Simoncelli）
Mathematical Tools for Neural and Cognitive Science，这是纽约大学的研究生课程，让学生学习神经和认知数据和系统的可视化、分析和建模的基本数学方法。本课程涵盖数学和统计工具的基本集合，提供假设、动机、逻辑和几何直觉，以及每个工具的简单推导。概念通过大量的计算练习得到加强。目标是让学生能够理解、使用和解释这些工具。有视频（zoom中国区看不到），课件和作业。
4.
计算神经科学导论（麻省理工学院，Sebastian Seung，2004）
5.
计算神经科学：认知的神经动力学（洛桑联邦理工学院，edX）
6.
神经信息学（伦敦大学学院，Kenneth Harris & Matteo Carandini）
ADNI dataset
