Web Databases

Page Contents


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.

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.

Blue Brain Cell Atlas

The Blue Brain Cell Atlas is a comprehensive online resource that describes the number, types, and positions of cells in all areas of the mouse brain. The user can download cell numbers for statistical analysis, download cell positions and types for modeling and visualize brain areas. Uses imaging data from the Allen Institute for Brain Science to generate cell positions and assign their type.

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.


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). 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.

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.

Eyewire Museum

An interactive archive of over 1000 mouse retinal cells with dense 3D anatomy, connectivity and associated physiology.


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

Fruit Fly Brain Observatory

FFBO stores and processes data related to the neural circuits of the fly brain: including location, morphology, connectivity and biophysical properties of every neuron, integrates the structural and genetic data, automatically generates models of the fly brain simulatable on multiple GPUs.

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 3D Model

Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files.

Histology World: Nervous System Histology

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.

Multiscale Atlas of the Larval Zebrafish Brain

The overall goal is to create a realistic multiscale circuit model of the larval zebrafish brain – from the nanoscale at the synaptic level, to the microscale describing local circuits, to the macroscale brain-wide activity patterns distributed across many regions.

Neural Signal Archive

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


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.


This application aims to make it easier to visualize gene expression in mouse brain cell types. The data here is compiled for a project aiming to select cell type specific genes in brain.


NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. It contains over 245,000 3D neuronal and glial reconstructions reflecting more than 1000 cell types from over 900 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.

Primate Cell Type Database

Intracellular recordings of non-human primates (NHP) cells sampled from the lateral prefrontal cortex. To includa:e electrophysiological, morphological, molecular data.

Rodent Brain Workbench (rbwb)

The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented resources.

SenseLab Project

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

3D Model Database

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 1600 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.

Olfactory Receptors Model Database

contains computationally determined OR structures, and downloadable figure and movie files representing the interactions of ORs and odorants.


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.


A full adult fly brain (FAFB), imaged at synaptic resolution.

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

Data Formats

Facilitating transfer of data between laboratories and applications.

BIDS (Brain Imaging Data Structure)

A simple and intuitive way to organize and describe neuroimaging and behavioral data.


The SONATA Data Format is a Scalable Open Data Format for multiscale neuronal network models and simulation output, jointly developed by the Allen Institute for Brain Science (AIBS) and the Blue Brain Project (BBP) of the École polytechnique fédérale de Lausanne (EPFL).


Models of chanels, neurons, synapses and circuits.

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.

Fruit Fly Brain Observatory

The Fruit Fly Brain Observatory integrates within a single database, genetic, anatomical, neurophysiological data with computational models. It can generate models of the fly brain that can be simulated on multiple GPUs.

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.

ICGenealogy - Ion Channel Genealogy

Quantifies the similarity in kinetics between ion channel models using a series of standardized voltage clamp simulation protocols and subsequent cluster analysis. Currently, the database contains 4815 models with 3706 quantitatively evaluated ion channels for the NEURON simulator.

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.

Neocortical Microcircuit Collaboration Portal

This portal provides an online public resource of the Blue Brain Project's first release of a digital reconstruction of the microcircuitry of juvenile Rat somatosensory cortex, access to experimental data sets used in the reconstruction, and the resulting models.

NeuroML Model Database

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

Olfactory Receptors Model Database

Part of the SenseLab project (see above), contains computationally predicted olfactory receptor structures.

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.


General data repositories and related search engines.


Store, share, discover research.

Google Dataset Search

Similar to how Google Scholar works, Dataset Search lets you find datasets wherever they’re hosted, whether it’s a publisher's site, a digital library,i or an author's personal web page.


A place where researchers can publicly store and share unthresholded statistical maps, parcellations, and atlases produced by MRI and PET studies.

Scalable Brain Atlas

This site provides interactive access to more than twenty publicly accessible brain atlases. It displays brain regions and reference images in 2d and 3d multi-slice views, with easy search and navigation.

This page is maintained by Jim Perlewitz ( )
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Last updated Apr. 21, 2023.

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