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Felix Schürmann

Cette personne n’est plus à l’EPFL

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Publications associées (82)

Toward Biophysical Mechanisms of Neocortical Computation after 50 Years of Barrel Cortex Research

Carl Petersen, Graham Knott, Felix Schürmann

2021

Supervised Learning With Perceptual Similarity for Multimodal Gene Expression Registration of a Mouse Brain Atlas

Henry Markram, Felix Schürmann, Csaba Erö, Daniel Keller, Huanxiang Lu, Francesco Casalegno, Dimitri Bruno Marie Rodarie

The acquisition of high quality maps of gene expression in the rodent brain is of fundamental importance to the neuroscience community. The generation of such datasets relies on registering individual gene expression images to a reference volume, a task en ...

FRONTIERS MEDIA SA2021

Digital Reconstruction of the Neuro-Glia-Vascular Architecture

Kathryn Hess Bellwald, Henry Markram, Felix Schürmann, Corrado Cali, Alexis Arnaudon, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Lida Kanari, Eleftherios Zisis, Michael Emiel Gevaert, Benoît Jean-Albert Coste, Thomas Brice Delemontex, Alessandro Enrico Foni

Astrocytes connect the vasculature to neurons mediating the supply of nutrients and biochemicals. They are involved in a growing number of physiological and pathophysiological processes that result from biophysical, physiological, and molecular interaction ...

OXFORD UNIV PRESS INC2021

Fully-Asynchronous Fully-Implicit Variable-Order Variable-Timestep Simulation of Neural Networks

Felix Schürmann, Michael Lee Hines, Bruno Ricardo Da Cunha Magalhães

State-of-the-art simulations of detailed neurons follow the Bulk Synchronous Parallel execution model. Execution is divided in equidistant communication intervals, with parallel neurons interpolation and collective communication guiding synchronization. Su ...

2020

Polynomial Evaluation on Superscalar Architecture, Applied to the Elementary Function e(x)

Felix Schürmann, Timothée Ewart, Fabien Jonathan Delalondre, Francesco Cremonesi

The evaluation of small degree polynomials is critical for the computation of elementary functions. It has been extensively studied and is well documented. In this article, we evaluate existing methods for polynomial evaluation on superscalar architecture. ...

2020

An Optimizing Multi-platform Source-to-source Compiler Framework for the NEURON MODeling Language

Felix Schürmann, James Gonzalo King, Michael Lee Hines, Pramod Shivaji Kumbhar, Omar Awile, Jorge Blanco Alonso, Liam Roger George Keegan

Domain-specific languages (DSLs) play an increasingly important role in the generation of high performing software. They allow the user to exploit domain knowledge for the generation of more efficient code on target architectures. Here, we describe a new c ...

Springer2020

Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis

Henry Markram, Felix Schürmann, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Jean-Denis Georges Emile Courcol, Jay Coggan, Benoît Jean-Albert Coste, Samuel Lieven D. Lapere, Nadir Roman Guerrero

Motivation: Accurate morphological models of brain vasculature are key to modeling and simulating cerebral blood flow in realistic vascular networks. This in silico approach is fundamental to revealing the principles of neurovascular coupling. Validating t ...

OXFORD UNIV PRESS2020

Excitation states of metabolic networks predict dose-response fingerprinting and ligand pulse phase signalling

Pierre Magistretti, Henry Markram, Felix Schürmann, Daniel Keller, Jay Coggan

With a computational model of energy metabolism in an astrocyte, we show how a system of enzymes in a cascade can act as a functional unit of interdependent reactions, rather than merely a series of independent reactions. These systems may exist in multipl ...

2020

Understanding Computational Costs of Cellular-Level Brain Tissue Simulations Through Analytical Performance Models

Felix Schürmann, Francesco Cremonesi

Computational modeling and simulation have become essential tools in the quest to better understand the brain's makeup and to decipher the causal interrelations of its components. The breadth of biochemical and biophysical processes and structures in the b ...

HUMANA PRESS INC2020

An efficient analytical reduction of detailed nonlinear neuron models

Felix Schürmann, Idan Segev, Guy Eyal, Michael Emiel Gevaert, Pramod Shivaji Kumbhar, Oren Amsalem

Detailed conductance-based nonlinear neuron models consisting of thousands of synapses are key for understanding of the computational properties of single neurons and large neuronal networks, and for interpreting experimental results. Simulations of these ...

Nature Research2020

Analytic performance modeling and analysis of detailed neuron simulations

Felix Schürmann, Francesco Cremonesi, Gerhard Wellein

Big science initiatives are trying to reconstruct and model the brain by attempting to simulate brain tissue at larger scales and with increasingly more biological detail than previously thought possible. The exponential growth of parallel computer perform ...

2020

Caries Detection with Near-Infrared Transillumination Using Deep Learning

Henry Markram, Felix Schürmann, Francesco Casalegno, Taylor Howard Newton

Dental caries is the most prevalent chronic condition worldwide. Early detection can significantly improve treatment outcomes and reduce the need for invasive procedures. Recently, near-infrared transillumination (TI) imaging has been shown to be effective ...

2019

Generating High Fidelity Surface Meshes of Neocortical Neurons using Skin Modifiers

Felix Schürmann, Juan Bautista Hernando Vieites, Marwan Muhammad Ahmed Abdellah, Cyrille Pierre Henri Favreau, Samuel Lieven D. Lapere

We present the results of exploring the capabilities of skinning modifiers to generate high fidelity polygonal surface meshes of neurons from their morphological skeletons that are segmented from optical microscopy slides. Our algorithm is implemented in B ...

2019

CoreNEURON : An Optimized Compute Engine for the NEURON Simulator

Felix Schürmann, James Gonzalo King, Michael Lee Hines, Fabien Jonathan Delalondre, Aleksandr Ovcharenko, Pramod Shivaji Kumbhar, Jérémy Pierre Benoit Fouriaux

The NEURON simulator has been developed over the past three decades and is widely used by neuroscientists to model the electrical activity of neuronal networks. Large network simulation projects using NEURON have supercomputer allocations that individually ...

2019

Fully-Asynchronous Cache-Efficient Simulation of Detailed Neural Networks

Felix Schürmann, Michael Lee Hines

Modern asynchronous runtime systems allow the re-thinking of large-scale scientific applications. With the example of a simulator of morphologically detailed neural networks, we show how detaching from the commonly used bulk-synchronous parallel (BSP) exec ...

SPRINGER INTERNATIONAL PUBLISHING AG2019

The Scientific Case for Brain Simulations

Alain Destexhe, Felix Schürmann, Michele Migliore

A key element of the European Union's Human Brain Project (HBP) and other large-scale brain research projects is the simulation of large-scale model networks of neurons. Here, we argue why such simulations will likely be indispensable for bridging the scal ...

CELL PRESS2019

Asynchronous Branch-Paralle Simulation of Detailed Neuron Models

Felix Schürmann, Michael Lee Hines

Simulations of electrical activity of networks of morphologically detailed neuron models allow for a better understanding of the brain. State-of-the-art simulations describe the dynamics of ionic currents and biochemical processes within branching topologi ...

2019

High Fidelity Visualization of Large Scale Digitally Reconstructed Brain Circuitry with Signed Distance Functions

Felix Schürmann, Marwan Muhammad Ahmed Abdellah, Sébastien Nicolas Speierer, Samuel Lieven D. Lapere, Jonas Kristofer Karlsson, Alessandro Enrico Foni

We explore a first proof-of-concept application for visualizing large scale digitally reconstructed brain circuitry using signed distance functions. The significance of our method is demonstrated in comparison with using implicit geometry that is limited t ...

IEEE2019

A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex

Henry Markram, Olivier Burri, Felix Schürmann, Julie Meystre, Daniel Keller, Romain Guiet, Rahul Valiya Veettil

Obtaining a catalog of cell types is a fundamental building block for understanding the brain. The ideal classification of cell-types is based on the profile of molecules expressed by a cell, in particular, the profile of genes expressed. One strategy is, ...

2019

Exploiting Flow Graph of System of ODEs to Accelerate the Simulation of Biologically-Detailed Neural Networks

Felix Schürmann, Michael Lee Hines, Bruno Ricardo Da Cunha Magalhães

Exposing parallelism in scientific applications has become a core requirement for efficiently running on modern distributed multicore SIMD compute architectures. The granularity of parallelism that can be attained is a key determinant for the achievable ac ...

IEEE2019

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