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).

Blue Brain Mouse whole-neocortex connectome model

The Mouse whole-neocortex connectome model integrates data from two recent datasets – the Allen Mouse Brain Connectivity Atlas and Janelia MouseLight – to identify and parameterize principles of neocortical connectivity. Statistical connectome instances compatible with the principles and at sub-cellular resolution are then generated. They will serve as a null model to compare future measurements against and to enable whole-neocortex simulations of brain activity.

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 180 annotated ion channels with 50 Hodgkin-Huxley models and very soon it will also contain whole cell electrophysiology data from more than 15,000 cells.


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.


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.

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 EBRAINS Cellular Level Simulation Platform. As other brain region models become publicly available, Blue Brain will add them in this section.

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.

Brain Molecular Atlas

The Brain Molecular Atlas is a simulation-ready database to accelerate molecular and systems biology.

Blue Brain scientists performed an extensive meta-analysis to integrate protein and metabolite quantitative data from publicly available resources and created this simulation-ready database to support more standardized and comparable molecular and systems biology studies.


The first digital reconstruction of the Neuro-Glia-Vascular (NGV) Architecture providing a new framework to study brain function in health and disease.

Topological Neuron Synthesis

The topological synthesis can be used to study the differences between healthy and diseased states of different brain regions and specifically, what structural alterations of neurons are causing important problems to the networks they form.