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Eilif Benjamin Muller

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Related publications (36)

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NineML: the network interchange for neuroscience modeling language

Eilif Benjamin Muller, Sean Lewis Hill

The growing number of large-scale neuronal network models has created a need for standards and guidelines to ease model sharing and facilitate the replication of results across different simulators. To foster community efforts towards such standards, the I ...

2011

Modeling and simulation of neocortical micro- and mesocircuitry. Part II: Physiology and experimentation

Weina Ji, Henry Markram, Felix Schürmann, Daniel Keller, Eilif Benjamin Muller, Michael Reimann, Werner Alfons Hilda Van Geit, Srikanth Ramaswamy, Matthias Wolf, James Gonzalo King, Alexis Arnaudon, András Ecker, Rajnish Ranjan, Jean-Denis Georges Emile Courcol, Armando Romani, Pramod Shivaji Kumbhar, Judit Planas Carbonell, Giuseppe Chindemi, Michael Emiel Gevaert, Christian Andreas Rössert, Fernando Joaquim Leite Pereira, Omar Awile, Mustafa Anil Tuncel, Daniela Egas Santander, James Bryden Isbister, Natali Barros Zulaica, Samuel Lieven D. Lapere, Sirio Bolaños Puchet, Maria Reva, Genrich Ivaska, Tanguy Pierre Louis Damart, Darshan Mandge, Joni Henrikki Herttuainen, Christoph Pokorny, Elvis Boci, Vishal Sood, Thomas Brice Delemontex, Aleksandra Zuzanna Teska, Polina Litvak, Alexander Dietz, Jorge Blanco Alonso, Gianluca Ficarelli

Cortical dynamics underlie many cognitive processes and emerge from complex multi-scale interactions, which are challenging to study in vivo. Large-scale, biophysically detailed models offer a tool which can complement laboratory approaches. We present a m ...

2024

In silico voltage-sensitive dye imaging reveals the emergent dynamics of cortical populations

Henry Markram, Eilif Benjamin Muller, Michael Reimann, Marwan Muhammad Ahmed Abdellah, Grigori Chevtchenko, Taylor Howard Newton

Voltage-sensitive dye imaging (VSDI) is a powerful technique for interrogating membrane potential dynamics in assemblies of cortical neurons, but with effective resolution limits that confound interpretation. To address this limitation, we developed an in ...

Nature Research2021

Data-driven integration of hippocampal CA1 synaptic physiology in silico

Eilif Benjamin Muller, Michael Reimann, Srikanth Ramaswamy, András Ecker, Armando Romani

The anatomy and physiology of monosynaptic connections in rodent hippocampal CA1 have been extensively studied in recent decades. Yet, the resulting knowledge remains disparate and difficult to reconcile. Here, we present a data-driven approach to integrat ...

2020

BlueCelluLab: Biologically Detailed Neural Network Experimentation API

Henry Markram, Eilif Benjamin Muller, Werner Alfons Hilda Van Geit, Lida Kanari, Mustafa Anil Tuncel, Darshan Mandge, Aurélien Tristan Jaquier

The NEURON simulator, established in 1984 and continuously developed since, stands as the preeminent tool for neuron simulation within computational neuroscience. Its widespread adoption and compatibility with computational clusters and supercomputers unde ...

The Open Journal2024

Estimating the Readily-Releasable Vesicle Pool Size at Synaptic Connections in the Neocortex

Henry Markram, Eilif Benjamin Muller, Rodrigo de Campos Perin, Srikanth Ramaswamy, Giuseppe Chindemi, Natali Barros Zulaica

Previous studies based on the 'Quantal Model' for synaptic transmission suggest that neurotransmitter release is mediated by a single release site at individual synaptic contacts in the neocortex. However, recent studies seem to contradict this hypothesis ...

2019

PyNN: a common interface for neuronal network simulators

Eilif Benjamin Muller

Computational neuroscience has produced a diversity of software for simulations of networks of spiking neurons, with both negative and positive consequences. On the one hand, each simulator uses its own programming or configuration language, leading to con ...

Frontiers Research Foundation2008

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy

Henry Markram, Kathryn Hess Bellwald, Felix Schürmann, Daniel Keller, Eilif Benjamin Muller, Michael Reimann, Werner Alfons Hilda Van Geit, Lida Kanari, Srikanth Ramaswamy, Matthias Wolf, James Gonzalo King, Alexis Arnaudon, Ying Shi, András Ecker, Jean-Denis Georges Emile Courcol, Armando Romani, Pramod Shivaji Kumbhar, Judit Planas Carbonell, Michael Emiel Gevaert, Fernando Joaquim Leite Pereira, Liesbeth Maria L Vanherpe, Huanxiang Lu, Daniela Egas Santander, James Bryden Isbister, Ran Levi, Benoît Jean-Albert Coste, Samuel Lieven D. Lapere, Sirio Bolaños Puchet, Juan Bautista Hernando Vieites, Cyrille Pierre Henri Favreau, Joni Henrikki Herttuainen, Christoph Pokorny, Vishal Sood, Thomas Brice Delemontex, Adrien Michel Achille Devresse, Nicolas René Jean Ninin, Alexander Dietz, Hugo Thabo Dictus, Gianluca Ficarelli

The function of the neocortex is fundamentally determined by its repeating microcircuit motif, but also by its rich, hierarchical, interregional structure with a highly specific laminar architecture. The last decade has seen the emergence of extensive new ...

2024

A comprehensive workflow for general-purpose neural modeling with highly configurable neuromorphic hardware systems

Eilif Benjamin Muller

In this article, we present a methodological framework that meets novel requirements emerging from upcoming types of accelerated and highly configurable neuromorphic hardware systems. We describe in detail a device with 45 million programmable and dynamic ...

2011

The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex

Henry Markram, Felix Schürmann, Eilif Benjamin Muller, Sean Lewis Hill, Idan Segev, Srikanth Ramaswamy, Michael Reimann, Daniel Keller, Werner Alfons Hilda Van Geit, Marwan Muhammad Ahmed Abdellah, James Gonzalo King, Lida Kanari, Julian Charles Shillcock, Ying Shi, Jean-Denis Georges Emile Courcol, Rajnish Ranjan, Juan Bautista Hernando Vieites, Stefan Eilemann, Michael Emiel Gevaert, Giuseppe Chindemi, Nicolas Antille, Jeffrey Christopher Muller, Ahmet Bilgili

We have established a multi-constraint, data-driven process to digitally reconstruct, and simulate prototypical neocortical microcircuitry, using sparse experimental data. We applied this process to reconstruct the microcircuitry of the somatosensory corte ...

Frontiers Research Foundation2015

Morphological Diversity Strongly Constrains Synaptic Connectivity and Plasticity

Henry Markram, Eilif Benjamin Muller, Srikanth Ramaswamy, Michael Reimann

Synaptic connectivity between neurons is naturally constrained by the anatomical overlap of neuronal arbors, the space on the axon available for synapses, and by physiological mechanisms that form synapses at a subset of potential synapse locations. What i ...

Oxford University Press (OUP)2017

BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience

Henry Markram, Felix Schürmann, Eilif Benjamin Muller, Idan Segev, Werner Alfons Hilda Van Geit, Jean-Denis Georges Emile Courcol, Giuseppe Chindemi, Michael Emiel Gevaert

At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parametrising such models to conform to the multitude of available experimental constraints is a global nonlinear optimisation problem with a comple ...

Frontiers Research Foundation2016

Rich cell-type-specific network topology in neocortical microcircuitry

Henry Markram, Eilif Benjamin Muller, Idan Segev, Srikanth Ramaswamy, Michael Reimann

Uncovering structural regularities and architectural topologies of cortical circuitry is vital for understanding neural computations. Recently, an experimentally constrained algorithm generated a dense network reconstruction of a similar to 0.3-mm(3) volum ...

Nature Publishing Group2017

PyNEST: a convenient interface to the NEST simulator

Eilif Benjamin Muller, Marc-Oliver Gewaltig

The neural simulation tool NEST (http://www.nest-initiative.org) is a simulator for heterogeneous networks of point neurons or neurons with a small number of compartments. It aims at simulations of large neural systems with more than 10^4 neurons and 10^7 ...

Frontiers Research Foundation2008

Community-based reconstruction and simulation of a full-scale model of region CA1 of rat hippocampus

Alberto Antonietti, Davide Bella, Pranav Rai, Henry Markram, Felix Schürmann, Eilif Benjamin Muller, Michael Reimann, Marwan Muhammad Ahmed Abdellah, Werner Alfons Hilda Van Geit, Lida Kanari, Srikanth Ramaswamy, James Gonzalo King, Alexis Arnaudon, Ying Shi, András Ecker, Jean-Denis Georges Emile Courcol, Armando Romani, Pramod Shivaji Kumbhar, Judit Planas Carbonell, Michael Emiel Gevaert, Nadir Roman Guerrero, Liesbeth Maria L Vanherpe, Huanxiang Lu, Mohameth François Sy, Cristina Colangelo, Juan Bautista Hernando Vieites, Cyrille Pierre Henri Favreau, Genrich Ivaska, Anna-Kristin Kaufmann, Joni Henrikki Herttuainen, Elvis Boci, Vishal Sood, Thomas Brice Delemontex, Fabien Petitjean, Julian Martin Budd, Mustafa Kerem Kurban

The CA1 region of the hippocampus is one of the most studied regions of the rodent brain, thought to play an important role in cognitive functions such as memory and spatial navigation. Despite a wealth of experimental data on its structure and function, i ...

2024

A calcium-based plasticity model for predicting long-term potentiation and depression in the neocortex

Henry Markram, Eilif Benjamin Muller, Rodrigo de Campos Perin, Marwan Muhammad Ahmed Abdellah, Werner Alfons Hilda Van Geit, James Gonzalo King, András Ecker, Vincent Delattre, Pramod Shivaji Kumbhar, Giuseppe Chindemi, Christian Andreas Rössert, Mustafa Anil Tuncel, Aurélien Tristan Jaquier, Caitlin Claire Monney

Pyramidal cells (PCs) form the backbone of the layered structure of the neocortex, and plasticity of their synapses is thought to underlie learning in the brain. However, such long-term synaptic changes have been experimentally characterized between only a ...

Nature Portfolio2022

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data

Eilif Benjamin Muller, Werner Alfons Hilda Van Geit, Armando Romani

Anatomically and biophysically detailed data-driven neuronal models have become widely used tools for understanding and predicting the behavior and function of neurons. Due to the increasing availability of experimental data from anatomical and electrophys ...

2021

The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow

Stefano Maximiliano Antonel, Henry Markram, Felix Schürmann, Eilif Benjamin Muller, Werner Alfons Hilda Van Geit, Ying Shi, Jean-Denis Georges Emile Courcol, Armando Romani, Christian Andreas Rössert, Maurizio Ferdinando Pezzoli, Olivier Richard Hagens

Every neuron is part of a network, exerting its function by transforming multiple spatiotemporal synaptic input patterns into a single spiking output. This function is specified by the particular shape and passive electrical properties of the neuronal memb ...

2018

Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways

Eilif Benjamin Muller

Most neurons in peripheral sensory pathways initially respond vigorously when a preferred stimulus is presented, but adapt as stimulation continues. It is unclear how this phenomenon affects stimulus coding in the later stages of sensory processing. Here, ...

Public Library Science2013

Network-timing-dependent plasticity

Henry Markram, Eilif Benjamin Muller, Daniel Keller, Vincent Delattre

Bursts of activity in networks of neurons are thought to convey salient information and drive synaptic plasticity. Here we report that network bursts also exert a profound effect on Spike-Timing-Dependent Plasticity (STDP). In acute slices of juvenile rat ...

2015