Blue Brain Portal


Multi-scale models of the rat and mouse brain integrate models of ion channels, single cells, microcircuits, brain regions, and brain systems at different levels of granularity (molecular models, morphologically detailed cellular models, and abstracted point neuron models).

Ion Channels

Channelpedia is a knowledge base system centered on genetically expressed ion channel experimental data and models. The platform encourages researchers of the field to contribute, build and refine the information through an interactive wiki-like interface. It is web-based, freely accessible and currently contains 187 annotated ion channels with 45 Hodgkin-Huxley models and very soon it will also contain whole cell electrophysiology data from more than 15,000 cells.


A neuronal microcircuit is the smallest functional ecosystem in any brain region that encompasses a diverse morphological and electrical assortment of neurons, and their synaptic interactions. Blue Brain has pioneered data-driven digital reconstructions and simulations of microcircuits to investigate how local neuronal structure gives rise to global network dynamics. These methods could be extended to digitally reconstruct microcircuits in any brain region.

Blue Brain Cell Atlas

The Blue Brain Cell Atlas is the first digital 3D cell atlas of the whole mouse brain. It provides neuroscientists with a unique insight into the cellular composition of the mouse brain. Users can view and download the number, major types and 3D positions of all neurons and glia in all 737 areas of the mouse brain.


Neurons are electrically excitable cells, which are the primary building blocks of the central nervous system. There is an astounding diversity in their anatomical and physiological features. Neurons receive, process, and transmit information through electrochemical signals that are exchanged at specialized contact points called synapses. Blue Brain has developed cutting-edge methods to model and simulate the structure and function of the wide variety of neurons to understand how they govern information processing in the brain.

Brain Regions

A goal of the Blue Brain is to make available to Neuroscientists and the wider community, brain regions as our work progresses. As part of the community modeling work with the Human Brain Project consortium, we have released a first version of the dense reconstruction of the full rat hippocampus CA1 to the HBP Brain Simulation Platform. As other brain region models become publicly available, Blue Brain will add them in this section.