EPFL: An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain

Glad to share Dr. Sebastien Piluso's work on the new atlas version paper, emerging from a long-standing research effort at the Blue Brain Project, is officially out in Imaging Neuroscience!

https://lnkd.in/dGdYhWyC

This work not only presents the first atlas covering the mouse central nervous system, but also provides anatomical reference data that unlock precise atlas segmentation of experimental brain images.

We even aim to shift the conceptualization of brain atlases from a single-volume reference model to a more versatile, next-generation framework.
This paves the way for large-scale brain image segmentation and the automated analysis of massive datasets using efficient, automated, and reproducible tools.

To showcase the capabilities of this dataset, we generated the first cellular atlas of the entire mouse brain, automatically identifying the coordinates, anatomical regions, and cell types of all its ~70 million constituent neurons. Additionally, we created an isotropic 10 μm-resolution average Nissl template from over 80,000 histological sections, revealing unprecedented anatomical contrasts without using interpolation.

Finally, these data serve as the foundational basis for constructing a precise and generic model of a digital mouse brain, now maintained by the Open Brain Institute. We have succeeded in bridging both ends by converting post-mortem anatomical images directly into realistic in silico data, which represents a significant step forward in the field of brain simulation.

Do not hesitate to explore, use, and share widely with colleagues!

I would like to thank all those who contributed to this work, and give a special thank you to Cyrille Favreau for the wonderful image visualization and Karin Holm for invaluable editorial support!

EPFL: A multiscale electro-metabolic model of a rat neocortical circuit reveals the impact of ageing on central cortical layers

🧠 Why does the brain demand so much energy? What happens when that supply falters with age?

In this study, we present a multiscale model of electro-metabolic coupling in a digitally reconstructed rat neocortex. By combining detailed electrophysiological modeling with neuro-glial-vascular (NGV) metabolic dynamics, we explore how energy demand varies across neurons and circuits, and how ageing disrupts this balance.

Key insights: 

🔹 Energy use varies by neuron type and circuit location

 🔹 Middle cortical layers are especially vulnerable to age-related metabolic decline

 🔹 Our model bridges single-cell metabolism and whole-circuit function 

We’re excited that this work brings us closer to understanding how energy dynamics influence brain ageing. 🙏

A big thank you to everyone in the EPFL Blue Brain Project - A Swiss Brain Initiative who contributed over the years to advancing neuroscience. In particular, I’d like to recognize the amazing contributors to this article: Alessandro Cattabiani, Darshan Mandge, Polina Shichkova, James Isbister, Jean Jacquemier, James Gonzalo King, Henry Markram, and Daniel Keller.

💫 Special thanks to Cyrille Favreau and Elvis Boci for their beautiful work on Figure 1 (below👇), Karin Holm for editorial support, and everyone else who helped shape this research.

📖 Read more: https://lnkd.in/dg-A-rVQ

EPFL: Discover the Beauty of the Brain

I'm beyond excited to share something truly special from my work with the Blue Brain Project!

Over the past decade (2014–2024), I’ve crafted a breathtaking collection of computational neuroscience visuals using Blue Brain Brayns 1.1.0 (up to 2019) and Blue Brain BioExplorer (from 2020 onward). 

All these mesmerizing images and videos are now publicly available under the EPFL/Blue Brain Project CC BY 4.0 License.

You can download the entire collection from my online gallery.

Let’s make the wonders of computational neuroscience accessible to everyone, one incredible visual at a time.

 Dive in and explore!

EPFL: Modeling of Blood Flow Dynamics in Rat Somatosensory Cortex

Background: 

The cerebral microvasculature forms a dense network of interconnected blood vessels where flow is modulated partly by astrocytes. Increased neuronal activity stimulates astrocytes to release vasoactive substances at the endfeet, altering the diameters of connected vessels.

Methods:

 Our study simulated the coupling between blood flow variations and vessel diameter changes driven by astrocytic activity in the rat somatosensory cortex. We developed a framework with three key components: coupling between the vasculature and synthesized astrocytic morphologies, a fluid dynamics model to compute flow in each vascular segment, and a stochastic process replicating the effect of astrocytic endfeet on vessel radii.

Visualization with NVIDIA Omniverse

Results: 

The model was validated against experimental flow values from the literature across cortical depths. We found that local vasodilation from astrocyte activity increased blood flow, especially in capillaries, exhibiting a layer-specific response in deeper cortical layers. Additionally, the highest blood flow variability occurred in capillaries, emphasizing their role in cerebral perfusion regulation. We discovered that astrocytic activity impacted blood flow dynamics in a localized, clustered manner, with most vascular segments influenced by two to three neighboring endfeet.

Conclusions: 

These insights enhance our understanding of neurovascular coupling and guide future research on blood flow-related diseases.

Link to the publication: https://www.mdpi.com/2227-9059/13/1/72