EPFL Blue Brain Project - A Swiss Brain Initiative

This December, Blue Brain celebrates the completion of its 20-year mission to establish simulation neuroscience as a vital complement to experimental, theoretical, and clinical approaches to understanding the brain. Thank you for being part of this journey! 🎉 Our models, data, algorithms, and simulation platform remain accessible via https://lnkd.in/d4BgCqms #Openscience #OpenSource

📢 We are happy to share our latest connectomics work published in iScience. We explore the effect of the higher order structure on neuronal function in our biologically detailed model as well as the MICrONS EM data set from Allen Institute. Simplified models of neural networks revealed the need of a tradeoff in brain coding: more redundancy in neuronal activity enhances fault tolerance but reduces memory capacity. The severity of the tradeoff is mediated by the level of neuronal variability. The diverse architecture of biological neural networks helps regulate the tradeoff, letting subpopulations optimize for different goals. We developed a metric, based on simplicial complexes, that captures connectivity complexity allowing us to distinguish between subpopulations.   Subpopulations with low simplicial complexity drive efficient activity, while those with high complexity support network reliability, easing the robustness-efficiency tradeoff. This approach may help reconcile seemingly paradoxical findings that assume uniform connectivity. Full paper: https://lnkd.in/evwCSUpt With Daniela Egas Santander, Christoph Pokorny, András Ecker, Jānis Lazovskis, Matteo Santoro, Jason P. Smith, Kathryn Hess, Ran Levi, Michael Reimann

As the Blue Brain Project reaches its conclusion, it’s the perfect moment to reflect on the incredible journey of scientific discovery and advancement over the past two decades. From groundbreaking milestones to influential publications, the project has significantly contributed to the field of #Simulation #Neuroscience. Explore a comprehensive digest of our key achievements and the research that has shaped this project. 🔗 https://lnkd.in/e8AM_Mri And if you want to try simulation neuroscience for yourselves, check out our platform and its future developments at openbluebrain.com

📢 We are happy to announce that our latest connectomics work has been published in The MIT Press' Network Neuroscience. In this methods paper, we present a novel Python framework for rapid connectome manipulations of detailed, biologically realistic network models in SONATA format. Important use cases include • wiring a network model from scratch in a biologically realistic way • rewiring an existing connectome while preserving certain aspects of connectivity • and transplanting connectivity characteristics from one connectome to another. The resulting network models can be readily simulated using any simulator supporting SONATA, allowing systematic and reproducible characterization of causal effects of manipulations on network activity. We employed the framework to manipulate the connectome of a detailed model of the rat somatosensory cortex in two particular ways: first, we increased specific VIP+ interneuron connectivity based on trends found in Allen Institute's MICrONS data; second, we progressively removed higher-order features of E-to-E connectivity. We ran a series of network simulations and found specific changes in activity causally linked to these manipulations. Publication 👉 https://lnkd.in/egp7saZ3 Interested in our framework? Check out our code repositories here: https://lnkd.in/e8vqSqzS and advanced use case examples here: https://lnkd.in/ef4XgaAY Find out more about SONATA https://lnkd.in/eCZsPJCZ Application to the physiology of the somatosensory cortex - physiology: https://lnkd.in/eh3mnugg MICrONS: https://lnkd.in/giU__qkQ With Christoph Pokorny, Omar Awile, James Isbister, Kerem Kurban, Matthias W., Michael Reimann. With thanks to Allen Institute.

📣 Preprint alert 📣 Discover the 1st comprehensive mouse brain atlas based on Allen Institute's Common Coordinate Framework version 3 ! Our new 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 and extended the olfactory bulb. 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. You can find all the details related to this work here: https://lnkd.in/ej28p-mA With Sebastien Piluso, Csaba Verasztó, Harry Carey, Emilie Delattre, Thibaud Henri L'Yvonnet, Eloïse Colnot, Armando Romani, Jan Bjaalie, Henry Markram, Daniel Keller

📣 Publication Alert! Our latest connectomics work is out in Cerebral Cortex. We have analyzed one of our favorite open datasets: Allen Institute's MICrONS cortical mm^3. In this EM dataset we found new rules for neuronal connectivity & describe them: • We found the higher-order structure of excitation contains specific motifs that form a backbone of connectivity in a fan-out structure. • Inhibitory connectivity is structured by this, providing specific competition between the motifs. • Disinhibition in turn targets these neurons. Our SSCx model (linktr.ee/BlueBrainPjt) provided a valuable null model to compare findings against: it has the excitatory “fan-out tracks”, but not the specific inhibition. 📌 Clearly, inhibition is computationally powerful and should be studied more! Let us know your feedback! Full paper 👉 https://lnkd.in/egS7URKi

Did you see that our Somatosensory cortex and Hippocampus models are out? Why does it matter? Check out this brief article.

Studying the hippocampus? Our latest model is now hosted on www.hippocampushub.eu It offers scientists a versatile platform, complete with extensive analysis tools and an interface that facilitates further research on the hippocampus. All the newly released articles and downloadable assets relating to our hippocampus model -including the model itself- can also be found here 👉 https://lnkd.in/eQ6jaRjZ Let us know your feedback!

All the articles and downloadable goodies of our just released somatosensory cortex model -including the model itself!- can be found here 👉 https://lnkd.in/eQ6jaRjZ What will you use the model for? Check it out and give us your feedback.

We’re delighted to share that our general atlas-based open model of the Somatosensory Cortex is out in three eLife Sciences Publications, Ltd. papers! Comprising eight somatosensory cortex subregions with 4.2 million morphological and electrically-detailed neurons, and 14.2 billion synapses, it also includes local, mid-range, and extrinsic connectivity. We used it to study emergent network-level plasticity, spike sorting, intra- and inter-area coding, EEG/LFP and as well as structure-function relationships. Its atlas-based geometry, and anatomical and physiological detail set the stage for community-driven refinement and validation with any new atlas-based data! Any prediction the model makes also has a precise correspondence in real animals where it can be tested in real life. Using calcium-based plasticity rules (see Giuseppe Chindemi’s work), we explored how dendrites, synapse clustering and realistic connectivity combine under in vivo-like conditions. Learning was stable and successfully predicted more changes for synapses embedded in high-dimensional connectivity motifs. The finding about motifs extends previous work by predicting an additional non-local effect: Plasticity of one connection is determined by all other connections between surrounding neurons! We describe how and prove its presence in electron microscopy data. Interested in cortical anatomy? Go to https://lnkd.in/eCpZG2Xv to discover 6 mm of rat cortex, combining both local and long-range connectivity, improved by electron microscopy data, exploring how brain shape affects connectivity. Curious how anatomy & physiology interact? https://lnkd.in/eh3mnugg shows calibration and validation of multi-scale physiology, interareal communication, implications of inhibitory targeting rules as well as optogenetic/lesion studies of rate/synchrony/contrast tuning and inter-laminar processing. We’d love for you to use the model too. The complete 4.2 million neuron model and all the necessary tools to deal with such a large model are openly available. As is a smaller 210K-neuron model with improved connectivity based on EM-derived inhibitory targeting. Want to know what the model is useful for? Check out the plasticity paper or any other publication using the model: LFP, EEG, assembly formation, structure-function and the video showing the impact of connectome complexity on activity. Everything is available here 👉 https://lnkd.in/eQ6jaRjZ Let us know your feedback!