🐭 Researchers simulate entire mouse brain with nine million neurons

• The supercomputer Fugaku has created one of the world's largest and most detailed simulations of a brain, with nine million neurons and 26 billion synapses from the entire mouse cortex.
• The simulation can be used to study diseases like Alzheimer's and epilepsy in a virtual environment, and test new treatments digitally before they are tried on living tissue.
• Fugaku can perform over 400 quadrillion calculations per second, which enables simulation of the brain's structure and function down to the cellular level.

Virtual mouse cortex with 86 interconnected regions

Researchers at the Allen Institute and Tadashi Yamazaki from the University of Electro-Communications in Japan, together with colleagues from the Research Organization for Information Science and Technology, Yamaguchi University, and RIKEN Center for Computational Science, have created a complete simulation of the mouse cortex. The model contains almost ten million neurons, 26 billion synapses, and 86 interconnected brain regions.

The simulation shows both form and function. It captures ion flows and voltage changes in membranes within many compartments of the neurons' tree-like structures. Synapses activate and electrical signals move through the membranes just like in living brain cells.

The project will be presented at SC25, the leading supercomputing conference, in mid-November. A paper about the work will be published in conjunction with the conference.

Testing treatments in a digital environment

Researchers can now use the model to ask detailed questions about what happens in diseases, how brain waves shape focus, or how seizures spread in the brain. Previously, these questions could only be answered through experiments on real brain tissue, one at a time. Now hypotheses can be tested virtually.

Simulations can show how problems begin before symptoms appear. New treatments or therapies can be tested safely in the digital environment.

Anton Arkhipov at the Allen Institute, who worked on the project, says this shows the door is open to running these types of brain simulations effectively with sufficient computing power. He describes it as a technical milestone that gives confidence that much larger models are achievable with precision and scale.

Supercomputer with 158,976 nodes

Fugaku, jointly developed by RIKEN and Fujitsu, is one of the world's fastest supercomputers. It can perform over 400 quadrillion operations per second. If someone started counting right now, one number per second, it would take over 12.7 billion years to reach that number.

The supercomputer consists of thousands of small parts called nodes, which are grouped in layers like boards, shelves, and racks. Together, the components total 158,976 nodes, which allows Fugaku to handle enormous amounts of data and calculations.

The name Fugaku comes from Mount Fuji. Just like the mountain's high peak and broad base, the name was chosen to symbolize computing power and reach.

Yamazaki explains that Fugaku is used for research in many areas of computational science, such as astronomy, meteorology, and drug discovery, contributing to solving many societal problems. In this project, the supercomputer was used for a simulation of neural circuits.

Data from real brains

The Allen Institute provided the virtual brain's blueprint and biophysical properties through real data from the Allen Cell Types Database and the Allen Connectivity Atlas. Fugaku then brought the data to life.

Using the Allen Institute's Brain Modeling ToolKit, the team translated data into the working digital simulation of the cortex. A neuron simulator called Neulite transformed equations into neurons that fire signals just like their living counterparts.

Yamazaki emphasizes that it is a technical achievement, but only the first step. He believes that God is in the details and therefore believes in biophysically detailed models.

Arkhipov describes that the long-term goal is to build models of the entire brain, eventually even human models, with all the biological details that the institute is uncovering. The team is now moving from modeling individual brain areas to simulating the entire mouse brain.

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