Saturday, December 14, 2024

EPFL: Breakdown and repair of the aging brain metabolic system



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.

Publication: https://www.biorxiv.org/content/10.1101/2023.08.30.555341v2 

Scientific Collaborator: Polina Shichkova, Ph. D

Data visualization tool: Blue Brain BioExplorer

EPFL: Neuromodulation of neocortical microcircuitry: a multi-scale framework to model the effects of cholinergic release


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.

Publication: https://infoscience.epfl.ch/entities/publication/0a69c342-ac83-4fa3-bc08-44b886969d60

Scientific Collaborator: Cristina Colangelo, Ph.D

Data visualization tool: Blue Brain BioExplorer 

Saturday, November 30, 2024

NVIDIA: Wanted! Business Card on a Mission

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.

Wednesday, November 27, 2024

NVIDIA: Bringing Brain Simulations to Life with NVIDIA Omniverse

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. 

Data sources:

- BluePyOpt: https://github.com/BlueBrain/BluePyOpt

- Neuromorpho.org: https://neuromorpho.org/

Thursday, November 21, 2024

NVIDIA: Blood flow visualization with Omniverse

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.


- AstroVascPy: https://github.com/BlueBrain/AstroVascPy

Tuesday, November 19, 2024

NVIDIA: Playing with Omniverse and Exploring Brain Digital Twins in High-Quality 3D

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.



This is just the beginning, but the potential is huge.

Data sources:
- EPFL Blue Brain Project: https://lnkd.in/gH3cgPAs
- Tractome Dataset: https://lnkd.in/dGwgsv5z
- Flywire: https://flywire.ai

Saturday, November 16, 2024

EPFL: Modeling of blood flow dynamics in the rat somatosensory cortex

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 to Stéphanie Battini for her outstanding work and for being such a fantastic collaborator—it’s been an absolute pleasure to work alongside you!

Publication: https://www.biorxiv.org/content/10.1101/2024.11.14.623572v1

Model: https://github.com/BlueBrain/AstroVascPy

Tuesday, November 12, 2024

Gource: A Tool for Validating Project Quality



Gource
is 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

Gource visualizes refactoring by 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

Gource illustrates the evolution of project structure as 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

Gource highlights 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 for validating 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.

Links

Gource: https://github.com/acaudwell/Gource

Demo Project: https://github.com/BlueBrain/BioExplorer/

AI: The Fourth Industrial Revolution explained simply

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.

Looking forward to 2030! 😀

Monday, November 11, 2024

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


Huge congrats to Sebastien 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.

So proud of that movie!

Link to the publication: https://www.biorxiv.org/content/10.1101/2024.11.06.622212v1

Wednesday, November 6, 2024

Neuroscience: VR Tractome Dataset Diffusion Tensor Imaging as a point cloud

Hey tech enthusiasts,

I'm thrilled to announce that I've just deployed a virtual reality experience that takes Diffusion Tensor Imaging (DTI) to the next level. Imagine walking through the intricate neural pathways of the human brain, visualized as a mesmerizing network of point clouds—now possible in full VR.

Try it here: https://diffusion-tensor-imaging.netlify.app

The experience is based on DTI data from the Tractome project, which you can explore right here:

- Tractome Dataset: https://github.com/FBK-NILab/tractome

Grab your favorite VR headset—like the Meta Quest—and get ready for an immersive adventure that lets you journey through the brain in a completely new way. Whether you’re a neuroscientist, a VR enthusiast, or just someone curious about the inner workings of the mind, this is your chance to dive deep into brain connectivity, like never before.


For those who want to dive under the hood, I've shared the source code to create the point cloud LAS dataset, which you can find here:

- MetaBrain DTI Point Cloud: https://github.com/favreau/MetaBrain/tree/main/DTI

This repository provides everything you need to generate these beautiful visualizations and bring them into VR.


So, put on that headset, fire up the point cloud, and get ready to be amazed by the beauty of the brain.

Happy exploring!

Tuesday, October 8, 2024

Science: Rendering the Beautiful FlyWire Dataset In Just 2 Hours

When tasked with rendering a dataset as intricate and breathtaking as the one I recently worked on, the tools at my disposal had to be cutting-edge. Fortunately, I had the privilege of developing and utilizing the open-source Blue Brain BioExplorer. With this powerful software, I was able to render a stunning, complex dataset in just two hours, starting from scratch.

The dataset in question showcased neural circuits and synaptic connections, which demanded precise visualization. Standard off-the-shelf tools wouldn’t have been up to the task, but the BioExplorer—specifically designed for handling massive neural data—allowed me to create high-quality images quickly and efficiently.

What might have taken days using generic software took only two hours with the BioExplorer, demonstrating the importance of having the right tools for the job. This custom solution, optimized for large-scale data and high-performance environments, allowed me to bring the dataset to life, offering a detailed, clear, and beautiful view of neural structures.

The ability to achieve such results in record time speaks volumes about the power of specialized software. The Blue Brain BioExplorer not only makes working with complex data manageable, but it transforms the data into something visually inspiring, informing, educating, and sparking curiosity along the way.

We thank the Princeton FlyWire team and members of the Murthy and Seung labs, as well as members of the Allen Institute for Brain Science, for development and maintenance of FlyWire (supported by BRAIN Initiative grants MH117815 and NS126935 to Murthy and Seung). We also acknowledge members of the Princeton FlyWire team and the FlyWire consortium for neuron proofreading and annotation.

Flywire: https://flywire.ai

Blue Brain BioExplorer: https://github.com/BlueBrain/BioExplorer

Dataset: https://codex.flywire.ai/api/download

Monday, October 7, 2024

Just for fun: Online open-source online SWC neuron visualizer

With SfN coming up, I’ve put together a small neuron visualizer for SWC files. It's nothing too fancy, just a fun, simple base for anyone who wants to interactively visualize neurons. Best part? It’s open source and super easy to tweak

You can also hook it up to http://www.neuromorpho.org if you need access to a broader neuron database. Feel free to play around, modify the code, and let me know what you think. It’s all about making things simpler and more accessible.

Try it live: https://single-neuron.scientific-visualization.org

Visualize a morphology from neuromorpho using the swc url parameter:

https://single-neuron.scientific-visualization.org/?swc=https://neuromorpho.org/dableFiles/tarusawa/CNG%20version/WT-iPS-derived-cell-14L.CNG.swc

Source code: https://github.com/favreau/MetaBrain

Wednesday, September 25, 2024

AI: Minds in Motion - A Simple and Fun Visual Exploration of Human Influence

As I was driving to visit a friend, I started chatting with ChatGPT about a project that I've been thinking about for some time: How humans influence each other over time. What began as a simple idea soon turned into a full-fledged visual simulation—Minds in Motion.


Thanks to the power of AI, I was able to bring this concept to life in just 3 hours—from brainstorming the idea to coding, deploying, and even writing this post.

In Minds in Motion, each particle represents an individual, defined by its color and influence—either positive or negative.

- Positive influence: When a particle interacts with another, it blends its color with the other particle, representing a dynamic visual exchange.
- Negative influence: The particle darkens when interacting with a negatively charged particle, reflecting a less constructive influence.

Each particle moves randomly, creating real-time interactions that reflect the complexity of human relationships. It’s fascinating to watch these particles evolve, influence one another, and change as they "meet" in the digital space.

It’s more than just a visual—it's an exploration of how we, as humans, shape and are shaped by the connections we make. Watching these particles evolve is both mesmerizing and insightful, as it mirrors the subtle, but powerful, influence we experience in our own lives.

The best part? The entire project—from naming it, coding it, deploying it on GitHub Pages, and writing this post—was made possible with the help of AI, all in just a few hours!

🚀 Live project: https://minds-in-motion.scientific-visualization.org

🚀 Source code: https://github.com/favreau/MindsInMotion

Big thanks to AI for turning a passing thought on a car ride into a fully deployed project. The future is here, and it’s fast!

Sunday, September 22, 2024

A Philosophy Rooted in Pragmatism, Simplicity, Art and Performance

As a new chapter of my career is about to begin, it is time to reflect on a life-long passion for high-performance computing, pragmatism, and a constant wonder for innovation, beauty, and simplicity.

From a Child’s Dream to the Exploration of Advanced Scientific Fields

The journey into the world of technology began with a child's dream and an old ZX81. Back then, I might have been fascinated by the idea of making computers do amazing things, even with severely limited power. Those early machines—like the Amstrad CPC 6128—were pushed to their limits, with 3D animations developed using every last byte of 128K of memory. Writing code that split the screen into different memory blocks to animate simple sinusoidal curves was just the beginning of a lifelong obsession with performance and efficiency.

Discovering DirectX Before the World Knew It

In 1995, an opportunity arose to intern at Microsoft, where I had access to DirectX before it was officially released. At that time, OpenGL was still emerging, and this early exposure to DirectX opened new possibilities for real-time visualization. It was no longer just about coding; it became about making things happen fast, with as little overhead as possible. That experience shaped an approach to 3D rendering, which would influence much of the work that followed.

Telecom Simplicity: Crafting Simple Yet Robust Systems

In the world of telecoms at Sopra Steria, I encountered systems that were designed to be simple yet incredibly robust. Telecom systems can often become complex, but the ones built during that time were stripped down to their essentials—no fluff, no unnecessary features, just clean, effective code. This reaffirmed the belief that simplicity is key to both performance and longevity. The notion that code should be easy to replace, rather than just easy to evolve, became a guiding principle.

Banking Frameworks: A Lesson in Complexity

After telecoms, I transitioned into banking, facing entirely new challenges. Large frameworks that, while powerful, often came with a cost: a significant loss of performance. This experience highlighted the importance of balancing compute power and data storage without sacrificing the need for speed.

Speed of Light Raytracing: Sol-R and NVIDIA Quadro K6000

The development of Sol-R, a real-time ray tracer, represented a new frontier in scientific visualization. Dubbed the Speed-Of-Light Raytracer, it used a quantum number generator to enhance image quality. This project caught the attention of NVIDIA, who sent me a Quadro K6000 to push the boundaries even further. This opened doors to high-fidelity, real-time scientific visualization, transforming the way ray tracing was applied in high-performance computing.

High-Performance Visualization at EPFL: Computational Neuroscience

Arriving at EPFL to work on the Blue Brain Project felt like everything learned up to that point was coming together. Creating Brayns, a modular rendering platform, allowed researchers to focus on their work without being overwhelmed by overly complex software. The system was designed to be flexible and replaceable—if something worked, it stayed; if not, it could be removed without disruption.

Later, Brayns evolved into BioExplorer, a tool that delves deeper into computational neuroscience. During the COVID-19 pandemic, BioExplorer was used to produce an educational film on how glucose affects the SARS-CoV-2 infection process. This tool demonstrated its adaptability, pushing the boundaries of scientific visualization into other fields like neurons, astrocytes, blood vessels, high-energy physics, and more.

Demonstrating the Brain’s Complexity: ISC 2016

In 2016, a first-of-its-kind demonstration of interactive in-silico brain tissue visualization took place at ISC in Frankfurt. This showcased the power of high-fidelity graphics and real-time brain visualization. Sharing the booth with the Stephen Hawking Center for Theoretical Cosmology, who were presenting their black hole collision simulation, made the experience even more memorable. It was a symbolic moment where brain science and cosmology—two highly complex systems—came together, each requiring immense computational power.

A Childhood Dream: Visiting the K Computer

One of the highlights of my career was visiting the K Computer in Kobe, Japan. Standing before such a machine was like seeing a childhood dream come to life. From the days of tinkering with a ZX81 to one of the world’s most powerful supercomputers, this was a moment of reflection on how far technology had come—and how much further there was to go.

CERN Legend Collaboration: Unveiling the Invisible

Collaborating with René Brun, creator of ROOT, to visualize magnetic fields and high-energy particle collisions was another significant milestone. Handling enormous datasets and creating visualizations that made these invisible phenomena understandable was a challenge that relied on an intimate balance of compute and storage, ensuring the performance remained high enough to deliver meaningful insights.

Outreach and Exhibitions: Bringing Science to the Public

Science should not be confined to laboratories; it needs to be shared with the world. That's why one has been involved in several outreach initiatives, showcasing advanced scientific work at public exhibitions. The work has been featured at the Centre Pompidou in Paris, the CCCB in Barcelona and Madrid, and the Rosey Institute in Switzerland (Featuring in the Harvard Brain Magazine). These exhibitions made computational neuroscience more accessible to the public, engaging them in the beauty and complexity of these fields.

Music, Swimming, and Simplicity in Life

Beyond technology, one finds balance through music and swimming. Playing the drums, guitar, banjo, and now learning the cello, there has always been a love for creative expression. Performing at the Montreux Jazz Festival was a highlight, showcasing that creativity and precision apply to more than just coding.

Swimming is another form of connecting to simplicity. Regularly participating in 15-kilometer marathons and monofin swimming, it’s about stripping away complications—just like in coding—and focusing on the essentials. Free diving without equipment echoes the same principle: keep it simple, keep it efficient.

Recent Work: Virtual Reality and AI

Recently, one has been working on virtual reality experiences using point clouds to allow users to navigate through a Google Earth-like version of the virtual brain. This project pushes the boundaries of immersion and visualization, offering a new way to explore complex brain structures.

Furthermore, AI has been integrated at every step of the process—from understanding the subject matter to software design and implementation, to using generative AI and style transfer for improving image quality, AI has become an indispensable tool for refining the experience and creating more visually compelling representations of brain data.

A Philosophy Rooted in Pragmatism, Simplicity, Beauty and Performance

Over the years, pragmatism has emerged as a key principle. There’s no one-size-fits-all solution—whether it’s Object-Oriented Programming versus Procedural Programming, or balancing compute and storage—every project is unique and requires the right tools for the job.

Strong support for open source has always been a part of this philosophy. Sharing code openly for over a decade has reinforced the belief that progress is achieved through collaboration rather than isolation.

Looking Forward: The Next Chapter

As the Blue Brain Project concludes, I look forward to what lies ahead. From the early days of exploring cutting edge technologies to pushing the boundaries of super-computing, AI, and science, the same principles—simplicity, performance, and adaptability—will continue to drive the journey forward.

Wednesday, August 28, 2024

Expanding the Horizons of Interactive Scientific Visualization: A New Approach with Point Clouds

In my relentless pursuit to make scientific visualization not only more accessible but also far more comprehensive, I've decided to take a bold leap by employing a rather unconventional technology for molecular systems: point clouds. Borrowing a page from the world of photogrammetry, this technique offers a unique and powerful way to immerse ourselves in the intricate complexities of molecular structures.

 https://sars-cov-2.scientific-visualization.org

 

The beauty of point clouds lies in their simplicity and adaptability. By leveraging existing technical solutions, I've managed to adapt this technology to create an immersive exploration environment for complex molecular systems. Imagine diving into the microscopic world, not just observing but truly experiencing it in a way that's never been done before.

 


For a groundbreaking example, follow this link on your Meta Quest browser. Click on the VR button in the top left corner, and prepare to be amazed as you explore the SARS-CoV-2 virus in a manner that will redefine your understanding of molecular visualization.

This model (generated with the Blue Brain BioExplorer) was a pivotal part of a project I had the privilege to contribute to at EPFL during the early days of the COVID-19 pandemic.

A machine reveals how glucose helps the SARS-CoV-2 virus

The point cloud engine is Potree: https://github.com/potree/potree