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

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! 😀

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

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!