Blue Brain Portal

Welcome to the Blue Brain Portal – a knowledge space for simulation neuroscience


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).

The Real Neuron Challenge

Built by Blue Brain’s Neuroscientific Software Engineering team, this challenge enables everyone from scientists, to STEM students, to visualize reconstructed and synthesized neurons and decide if they can spot the differences between them. This game shows that it is hard to distinguish which cells are digitally generated and it demonstrates that synthesized neurons are similar to biological in terms of morphological properties.


Data is of vital importance to the study of the Brain. For neuroscientists in this section, there are ion channel recordings, morphological reconstructions, electrical recordings from neocorticol neurons and molecular properties of neurons. These are available on Blue Brain platforms, the EBRAINS Cellular Level Simulation Platform and the Hippocampus Hub.


Blue Brain has published 237 papers and pre-prints in scientific journals.

Software Suites

Blue Brain’s reconstruction and related simulations are made possible by a comprehensive software ecosystem for each step in the reconstruction and simulation process. Blue Brain systematically releases open source software.

Online Tools

A collection of platforms and atlases from the Blue Brain and our collaborators to assist users with simulation neuroscience.

Online Learning

Take a massive open online courses taught by a multi-disciplinary team of world-renowned scientists in Simulation Neuroscience.  Simulation Neuroscience is an emerging approach to integrate the knowledge dispersed throughout the field of neuroscience.

News and Announcements

The Blue Brain Project News

Creating 3D surface models of spiny neurons

— 08.12.22 — Understanding the functional aspects of our brain implies understanding the structure-function relationship of billions of individual interconnected neurons; a particularly convoluted problem as the structure of each neuron affects the whole network and its dynamics. Neurons have visually complex structures, multiple classes of shapes (morphologies) and electrophysiological classifications, making them complicated computational objects to study. Accurate visualization of simulation results depend on highly accurate “3D surface” (mesh) models, where each component can be mapped; however the generation of such models is challenging. Here, the EPFL Blue Brain Project presents a simple and effective method to create mesh models of spiny neurons (neurons with small spikes along their surface) from their corresponding morphologies. Authors: Marwan Abdellah Prof. Felix Schürmann | Source: Blue Brain Project

Pioneering Algebraic Topology in the Blue Brain Project

— In the Spring of 2022, the EPFL Blue Brain Project announced in a paper published in Cell Reports that it had found a way to mathematically build the 3D tree-like geometries of neurons using algebraic topology. One of the main branches of pure mathematics, algebraic topology allowed Blue Brain to describe the geometrical shapes of neurons in a way that could be used to build their digital twins. This breakthrough opens the path to using computers to automatically build digital copies of any of the thousands of different types of neurons found in the brain. The study, led by Blue Brain’s Neuromathematics Leader Lida Kanari and EPFL Professor Kathryn Hess of the Laboratory for Topology and Neuroscience, was the latest in a series of Blue Brain studies where algebraic topology helped tackle and solve a wide range of previously intractable neuroscience problems.

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