Web Databases


Several efforts have been made to provide web-based databases to the neuroscience community. Some provide tools for input of morphometric and time series data, links to compartmental modeling, and scientific visualization.

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Allen Cell Types Database

A database of neuronal cell types based on multimodal characterization of single cells. Featuring: electrophysiological characterization of intrinsic firing properties based on whole cell current clamp, image data and morphological reconstruction, abstract point models and detailed compartmental models.

Brain Architecture Management System

Database of Rat brain regions, cells, molecules and connectivity (Mihail Bota).

Mouse and primate brain atlases, and mouse connectivity data. Integrated database and tools for image analysis and visualization of brain connectivity.


Chinese effort to map the human connectome.

Cell Centered Database (CCDB)

This database houses structural and protein distribution information derived from confocal, multiphoton, and electron microscopy, including correlated microscopy. Volume reconstructions are stored along with pointers to all of the raw images and the processing details required to reconstruct the volume from the raw data.

Cerebellar Development Transcriptome Database (CDT-DB)

The CDT-DB provides spatio-temporal gene expression profile data on the postnatal development of the mouse cerebellum.

Cerebellum Database

Experimental and modeling literature related to information transfer and computation in the cerebellar cortex.


Channelpedia is a knowledge base system centered on genetically expressed ion channel models. It is web-based, freely accessible and currently contains 187 annotated ion channels with 50 Hodgkin-Huxley models.

CoCoMac - Cortical Connectivity in Macaque

The main database contains details of hundreds (400+) of tracing studies in their original descriptions. Further data are continuously added. There are associated tools, and hooks to CARET and Catacomb software (begun by Rolf Kötter).

CONNECT - Consortium Of Neuroimagers for the Non-invasive Exploration of Brain Connectivity and Tracts

Mapping of human brain microstructure and connectivity with diffusion MRI. is a website describing current efforts to comprehensively map out mammalian whole-brain connectivity and structure at the synaptic-level using high-throughput volume electron microscopy.

Cortical Neurophysiology Database

An Internet-accessible database of electrophysiological and other information describing cortical neurons and their characteristic responses to somatosensory and other stimuli.

CRCNS - Collaborative Research in Computational Neuroscience - Data sharing - Neurodata Without Borders (NWB)

The data include physiological recordings from sensory and memory systems, eg: single electrode recordings from macaque visual cortex, locust auditory receptor cells, multi-unit recordings from the rat hippocampusa, calcium imaging of rat somatosensory cortex. More to be added. This project is also developing a common data format across these sample data sets which serve as primary use cases.

Cricket Cercal System Database

Contains over 100 anatomical reconstructions of sensory neurons and interneurons from the cricket cercal sensory system. Each neuron has been aligned to a common coordinate system, preserving anatomical relationships.

DOQCS - Database of Quantitative Cellular Signaling

A repository of models of signaling pathways that includes GENESIS Kinetikit files. Doqcs provides a navigation utility for exploring connections at the level of molecules, between molecules and pathways, and between pathways.

Duke Southampton Archive of Neuronal Morphology


EEGbase is a system for storage, management, sharing and retrieval of EEG/ERP data, metadata, tools and documents related to electrophysiology.


An online atlas and database of the Drosophila nervous system.


A public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain.

Glomerular Response Archive

Images depicting the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli.

A comprehensive knowledge base of neuron types in the rodent hippocampal formation (dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex). Literature mining and data reconciliation identified 122 neuron types based on neurotransmitter, axonal and dendritic patterns, synaptic specificity, electrophysiology, and molecular biomarkers.

Hippocampus RNA-seq atlas

Here, you can interactively analyze and visualize RNA-seq data for all excitatory cell populations in the hippocampus at multiple levels of granularity. Analysis can be hypothesis driven by supplying predetermined lists of genes, or the dataset can be explored in a gene discovery-based fashion using enrichment and/or differential expression queries.

Histology World: Nervous System Histology

ICG - IonChannelGenealogy

Provides a comprehensive and quantitative assay of ion channel models currently available in the neuroscientific modeling community, all browsable in interactive visualizations. Currently, the database contains 3487 models with 2378 quantitatively evaluated ion channels for the NEURON simulator.

IUPHAR Database of Receptors and Ion Channels

Incorporating detailed pharmacological, functional and pathophysiological information on G Protein-Coupled Receptors, Voltage-Gated Ion Channels, Ligand-Gated Ion Channels and Nuclear Hormone Receptors.

L-Neuron Database

Virtual Neuromorphology Electronic Database

Ligand Gated Ion Channel Database

Mouse Brain Proteome

High-resolution mass spectrometry-based proteomics for in-depth analysis of the mouse brain and its major brain regions and cell types.

Mouse Connectome Project

The Mouse Connectome Project aims to create a three-dimensional digital connectome atlas of the C57Black/6J mouse brain. The site will offer a catalog of neural tracer injection cases, which will be updated continuously to eventually cover the entire brain.

Neural Signal Archive

This site provides a public archive of neural signals recorded from various types of cells and sites in neural systems. BrainML Data Server

This site hosts a public neurophysiology database at Weill Medical College, Cornell. Initial data is predominately from cortical areas.


The goal of the NeuroElectro Project is to extract information about the electrophysiological properties (e.g. resting membrane potentials and membrane time constants) of diverse neuron types from the existing literature and place it into a centralized database.


NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. It contains over 37,000 3D neuronal reconstructions reflecting more than 280 cell types from over 200 labs and is being continuously updated. Reconstructions can be saved in GENESIS, NEURON and NeuroML formats.


NeuronBank will organize information about identified neuron location, physiology, morphology, and connectivity in nudibranch molluscs.

Open Connectome Project

Data sharing across conectome methodologies from EM to MRI.

SenseLab Project

A set of interoperable databases and database tools for collecting and analyzing information initially on the olfactory pathway.

3D Model Database

3DModelDB is a collection of 3D printable versions of published neuron morphologies, both traced and artificial. Each printable model is associated with a morphology suitable for running simulations.

Cellular Properties Database

archives synaptic receptors, ion channels, and neurotransmitters by neuron type, now across 18 brain regions.

MicroCurcuit Database

models of circuits within different brain regions.

Model Database

ModelDB now contains over 700 models of neurons and circuits, that can be searched by model type, and that can be run as published or modified by the user.

Neuron Database

NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors and neurotransmitter substances.

Odor Database

now contains over 250 odor molecules known to interact with odorant receptors.

Odor Map Database

archives 2DG and fMRI spatial activity patterns elicited by odorants in the glomerular layer of rats and mice.

Olfactory Receptor Database

now contains over 14,000 genes and proteins.


Morphologies of individual tangential cells from the blowfly lobula plate are converted into a 3D mesh of cylinders of variable length and diameter. Each of the, typically 2000, cylinders can then be treated as an isopotential compartment in a compartmental modeling package. Images only.

USC Brain Project

Brain Operation Database (BODB)

NeuroScholar 1.00

A web-based connectivity database that is multi-user and textual.

Virtual Atlas of the Honeybee Brain

Virtual Fly Brain

A hub for Drosophila melanogaster neural anatomy and imaging data.


A database of behavioral and structural anatomy of Caenorhabditis elegans. Includes images, 3-D reconstructions, viewers, search tools, literature summaries and links to primary sources.

Zebrafish Database


Models of chanels, neurons, networks and synapses.

BioModels Database

Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies. Models are available in SBML. All data is shared between BioModels Database and DOQCS so that either set of interfaces and tools may be used on the merged collection.

Channel Database

ChannelDB is an implementation of a database of ionic conductance models stored in simulator-independent NeuroML format.


Channelpedia is a knowledge base system centered on genetically expressed ion channel models. It is web-based, freely accessible and currently contains 187 annotated ion channels with 50 Hodgkin-Huxley models.

GENESIS Database and Modeler's Workspace


An implementation of a database of ionic conductance models stored in simulator-independent NeuroML format.

Reciprocal Development Agreements

Collaborations among several of the projects listed on this page are ongoing. They grew out of a workshop presented at CNS*97, organized by Rogene Eichler-West.

Half-Center Oscillator model database (HCO-db)

A half-center oscillator (HCO) is a common circuit building block of central pattern generator (CPG) networks that produce rhytmic motor patterns in animals. The target of this project is to understand how intrinsic membrane and synaptic parameters affect the electrical activity of a half-center oscillator model (HCO) and how different parameter regimes influence stabilitygand modulatability of the HCO model’s output.

iModel - Interactive Models for Visual & Neural Computation

This site allows you to explore computer models of neural computation at levels ranging from simple linear filters to large-scale networks of spiking units. The initial focus is on models of the visual system, from retina to visual cortex.


Part of the SenseLab project (see above), ModelDB is a curated database of published models in the broad domain of computational neuroscience. It addresses the need for access to such models in order to evaluate their validity and extend their use. It can handle computational models expressed in any textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.

NeuroML Model Database

The NeuroML Model Database is a relational database that provides a means for exchanging multiscale NeuroML model descriptions and their components.

Open Source Brain

The core set of models currently under development in the OSB are conductance based models of (often multicompartmental) neurons. This class of neuronal model is particularly suited to collaborative development, as models of channels and synapses, or whole cell models, are often reused between studies. NeuroML is the preferred model description format for OSB. Models described using NeuroML 2.0 can be automatically included in NeuroML-db (see above).

Physiome Model Repository - Neurobiology

Once the CellML Model Repository, a curation / translation of published mathematical models into CellML code.

This page is maintained by Jim Perlewitz ( )
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Last updated May 31, 2016.

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