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.
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.
The theoretical construct of the Santhalamus Claustex postulates its
role as a speculative brain region crucial in the synthesis of emotions
and the consolidation of memories. Envisioned as an intricate network of
neural clusters, this hypothetical region purportedly orchestrates an
interplay between emotional processing and memory formation within the
human brain.
Recent suppositions
suggest a potential link between the activation of the Santhalamus
Claustex and exposure to specific sensory stimuli during festive
occasions.
It is hypothesized that the repetitive exposure to traditional auditory
cues, such as festive carols, and the olfactory experience induced by
the inhalation of mulled wine’s aromatic compounds, may elicit activity
within this speculative neural territory.
Brain simulation refers to the
process of creating a computer-based model or simulation that mimics
the functions and behaviors of the brain. This ambitious field of
research aims to understand, replicate, and potentially emulate the
complex workings of the brain in a digital environment.
Simulating the brain requires understanding and
replicating the intricate connections between neurons, known as
synapses. Modeling how information is transmitted and processed through
these connections is a crucial aspect of brain simulation.
The study presented explores the complex relationship between the aging
brain, energy metabolism, blood flow and neuronal activity by
introducing a comprehensive, data-driven molecular model of the
neuro-glial vascular system, including all key enzymes, transporters,
metabolites, and blood flow vital for neuronal electrical activity with
16’800 interaction pathways. We find significant alterations in
metabolite concentrations and differential effects on ATP supply in
neurons and astrocytes and within subcellular compartments within aged
brains, and identify reduced Na+/K+-ATPase as the
leading cause of impaired neuronal action potentials. The model predicts
that the metabolic pathways cluster more closely in the aged brain,
suggesting a loss of robustness and adaptability. Additionally, the aged
metabolic system displays reduced flexibility, undermining its capacity
to efficiently respond to stimuli and recover from damage. Through
transcription factor analysis, the estrogen-related receptor alpha
(ESRRA) emerged as a central target connected to these aging-related
changes. An unguided optimization search pinpointed potential
interventions capable of restoring the brain’s metabolic flexibility and
restoring action potential generation. These strategies include
increasing the NADH cytosol-mitochondria shuttle, NAD+ pool, ketone
β-hydroxybutyrate, lactate and Na+/K+-ATPase and reducing blood glucose levels. The model is open-sourced to help guide further research in brain metabolism.
Neuromodulation of neocortical microcircuits is one of the most fascinating and mysterious aspects of brain physiology. Despite over a century of research, the neuroscientific community has yet to uncover the fundamental biological organizing principles underlying neuromodulatory release.
Phylogenetically, Acetylcholine (ACh) is perhaps the oldest neuromodulator, and one of the most well-studied. ACh regulates the physiology of neurons and synapses, and modulates neural microcircuits to bring about a reconfiguration of global network states. ACh is known to support cognitive processes such as learning and memory, and is involved in the regulation of arousal, attention and sensory processing. While the effects of ACh in the neocortex have been characterized extensively, integrated knowledge of its mechanisms of action is lacking.
Furthermore, the ways in which ACh is released from en-passant axons originating in subcortical nuclei are still debatable. Simulation-based paradigms play an important role in testing scientific hypotheses, and provide a useful framework to integrate what is already known and systematically explore previously uncharted territory.
Importantly, data-driven computational approaches highlight gaps in current knowledge and guide experimental research. To this end, I developed a multi-scale model of cholinergic innervation of rodent somatosensory cortex comprising two distinct sets of ascending projections implementing either synaptic (ST) or volumetric transmission (VT). The model enables the projection types to be combined in arbitrary proportions, thus permitting investigations of the relative contributions of these two transmission modalities.
Using our ACh model, we find that the two modes of cholinergic release act in concert and have powerful desynchronizing effects on microcircuit activity. Furthermore we show that this modeling framework can be extended to other neuromodulators, such as dopamine and serotonin, with minimal constraining data. In summary, our results suggest a more nuanced view of neuromodulation in which multiple modes of transmitter release - ST vs VT - are required to produce synergistic functional effects.
Wanted: one ambitious business card, last seen in 2012, lounging on a bench in front of NVIDIA’s former US offices.
Picture it: 2012, bright-eyed me, full of dreams, standing at the gates of NVIDIA, the tech giant of my fantasies. Armed with nothing but a neatly printed business card and an overabundance of optimism, I did what any sensible person would do: I left my card on a bench. The strategy? Genius. The logic? Questionable. But hey, in my head, it was the ultimate mic drop. Someone would find it? get intrigued?
Instead, life had other plans, steering me toward EPFL's Blue Brain Project, where I spent a decade on the wildest, most rewarding ride of my career. From unraveling neural mysteries to building tools that merged science and creativity.
Still, every now and then, I wonder—what happened to that card? Is it still there, weathered and waiting? If you find it, congratulations! And guess what? It’s still valid, and I’d love to hear from you.
In computational neuroscience, visualizing the brain is crucial to understanding its complex behavior. NVIDIA Omniverse is revolutionizing this process by turning neuron simulations into vibrant, dynamic visualizations—bridging the gap between data and discovery.
Using Omniverse, we can map electrical currents in neurons to vivid colors, creating real-time, interactive displays of brain activity. Researchers can zoom into individual neurons, explore neural networks, and observe dynamic changes in activity—all in stunning 3D.
Omniverse empowers researchers to build digital twins of brain regions. These twins enable the simulation of diseases, testing of interventions, and real-time collaboration. Its USD-based scalability and Python integration make it an unparalleled tool for neuroscience visualization.
From advancing research on neurological disorders to immersive education tools, Omniverse empowers neuroscientists to transform raw data into actionable insights.
Today, I explored the
incredible flexibility of NVIDIA's fully scriptable Omniverse platform
by developing an interactive blood flow visualization. The dataset,
originally generated using AstroVascPy (https://lnkd.in/d3dxN6yJ),
was initially in SONATA format and later converted into OpenUSD for
compatibility. The simulation data was integrated as custom attributes
directly tied to the streamline geometry, allowing for a dynamic,
frame-based rendering.
With each
simulation frame, the radius and color of the streamlines update
automatically, reflecting changes in the dataset in real time. This
approach combines the power of Python scripting with the robust
visualization capabilities of Omniverse, making it effortless to bring
complex, multi-dimensional simulation data to life.
Omniverse's
fully scriptable architecture played a critical role in streamlining
this process, enabling custom workflows tailored to specific datasets
and visualization requirements. This project highlights how the platform
can bridge scientific simulation and interactive visualization,
offering researchers powerful tools to analyze and present intricate
biological processes with unprecedented clarity.
I’ve
been having a blast experimenting with NVIDIA Omniverse, using
neuroscience data to delve into the concept of brain digital twins.
While it’s not a finished solution (yet), it’s an incredible sandbox for
interactive visualization and testing the limits of what’s possible in
rendering complex neural structures.
Bringing
brain models to life in immersive, high-quality 3D is both captivating
and full of promise. Omniverse provides a glimpse into a future where
neuroscience can be explored in entirely new ways, making it an exciting
platform to experiment with.
I'm very proud of this
publication, where I contributed to the visualization of a comprehensive
simulation framework to study neurovascular coupling in the rat
somatosensory cortex. This study sheds light on the fascinating
interplay between astrocytic activity and cerebral microvasculature,
revealing how astrocytic endfeet drive localized vessel diameter
changes, particularly in capillaries, to regulate blood flow. A huge
congratulations toStéphanie Battinifor her outstanding work and for being such a fantastic collaborator—it’s been an absolute pleasure to work alongside you!
Gourceis an
open-source visualization tool that animates your project's history,
making it invaluable for assessing development quality, refactoring
efforts, and overall contributions.
Validating Code Quality Through Visualizations
Gourcevisualizes refactoringby
animating file changes, showing how files move, split, or consolidate
over time. This helps developers and stakeholders quickly understand
improvements in code quality, reduction of technical debt, and the
effectiveness of refactoring efforts.
Assessing Project Structure and Stability
Gourceillustrates the evolution of project structureas
a dynamic tree, with commits visually highlighted. This allows teams to
track development focus, identify potential problem areas, and validate
the stability of critical components, ensuring the quality of the
evolving codebase.
Recognizing Contributor Impact
Gourcehighlights individual contributions,
bringing visibility to crucial but often-overlooked work like testing,
infrastructure, and maintenance. By summarizing contributions, Gource
helps validate each team member’s impact on the project's quality.
Demonstrating Project Health and Progress
Gource’s animations transform complex commit histories into clear,
engaging visuals, allowing stakeholders to easily understand project
health, growth, and quality improvements over time.
Conclusion
Gource is a powerful tool forvalidating and communicating project quality.
It provides an engaging way to understand development progress,
refactoring outcomes, and individual contributions, turning commit
history into a meaningful story of continuous improvement.
The
21st century's tech revolution evolved by decade: the 2000s brought
massive data through the internet, the 2010s saw GPU-powered computing
take off, and the 2020s combined data and compute into transformative
AI. Each decade set the stage, driving us into an AI-centric Fourth
Industrial Revolution.
Huge congrats toSebastien Piluso! It
was a pleasure and a real learning experience working for the inspiring science of finaly completing the truncated version of the mouse brain atlas. The
Blue Brain Project presents the first comprehensive mouse brain atlas
based on the Allen Institute’s Common Coordinate Framework version 3.
This atlas includes anatomical Nissl reference data that has been
precisely aligned within this reference space, providing the scientific
community with a crucial tool for automated and accurate mapping of a
wide range of histological slices or volumes of the mouse brain. We have
also integrated additional layers, such as the spinal cord, barrel
columns, as well as the granular and molecular layers in the cerebellum.
This allowed us to create an enhanced version of our cell atlas,
mapping every cell in the mouse brain by location, region, and type.
From this data, properties such as neuron soma and morphology can be
derived, paving the way for increasingly accurate simulation models.
