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Marwan Muhammad Ahmed Abdellah

Cette personne a quitté l’EPFL

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Publications associées (24)

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In Silico Brain Imaging Physically-plausible Methods for Visualizing Neocortical Microcircuitry

Marwan Muhammad Ahmed Abdellah

The recent years have witnessed growing interest in the power of scientific visualization for simulation-based neuroscience. The research presented in this thesis develops methods to generate physically-realistic visualizations of neocortical models recons ...

EPFL2017

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

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

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

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 University Press2020

Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D

Marwan Muhammad Ahmed Abdellah

To understand the dynamic nature of the genome, the localization and rearrangement of DNA and DNA-binding proteins must be analyzed across the entire nucleus of single living cells. Recently, we developed a computational light microscopy technique, called ...

Nature Publishing Group2024

Meshing of Spiny Neuronal Morphologies using Union Operators

Felix Schürmann, Marwan Muhammad Ahmed Abdellah, Nadir Roman Guerrero, Alessandro Enrico Foni, Elvis Boci, Juan José García Cantero

Neurons are characterized by thin and long interleaving arborizations in which creating accurate mesh models of their cellular membranes is challenging. While union operators are central for CAD/CAM modeling and computer graphics applications, their applic ...

2022

Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation

Henry Markram, Felix Schürmann, Marwan Muhammad Ahmed Abdellah, Julian Charles Shillcock, Stefan Eilemann, Ahmet Bilgili

Background: We present a visualization pipeline capable of accurate rendering of highly scattering fluorescent neocortical neuronal models. The pipeline is mainly developed to serve the computational neurobiology community. It allows the scientists to visu ...

2017

A Process for Digitizing and Simulating Biologically Realistic Oligocellular Networks Demonstrated for the Neuro-Glio-Vascular Ensemble

Pierre Magistretti, Henry Markram, Felix Schürmann, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Renaud Jolivet, Stefan Eilemann, Jay Coggan, Corrado Cali

One will not understand the brain without an integrated exploration of structure and function, these attributes being two sides of the same coin: together they form the currency of biological computation. Accordingly, biologically realistic models require ...

2018

Metaball skinning of synthetic astroglial morphologies into realistic mesh models for visual analytics and in silico simulations

Henry Markram, Felix Schürmann, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Jay Coggan, Nadir Roman Guerrero, Alessandro Enrico Foni, Samuel Lieven D. Lapere, Eleftherios Zisis

Motivation: Astrocytes, the most abundant glial cells in the mammalian brain, have an instrumental role in developing neuronal circuits. They contribute to the physical structuring of the brain, modulating synaptic activity and maintaining the blood-brain ...

Oxford University Press2021

Digital Reconstruction of the Neuro-Glia-Vascular Architecture

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

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

Objective Morphological Classification of Neocortical Pyramidal Cells

Henry Markram, Kathryn Hess Bellwald, Rodrigo de Campos Perin, Marwan Muhammad Ahmed Abdellah, Lida Kanari, Srikanth Ramaswamy, Ying Shi, Julie Meystre

A consensus on the number of morphologically different types of pyramidal cells (PCs) in the neocortex has not yet been reached, despite over a century of anatomical studies, due to the lack of agreement on the subjective classifications of neuron types, w ...

Oxford University Press (OUP)2019

Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies

Henry Markram, Felix Schürmann, Marwan Muhammad Ahmed Abdellah, Juan Bautista Hernando Vieites, Stefan Eilemann, Nicolas Antille

Background: We present a software workflow capable of building large scale, highly detailed and realistic volumetric models of neocortical circuits from the morphological skeletons of their digitally reconstructed neurons. The limitations of the existing a ...

2017

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

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

Reconstruction and Simulation of Neocortical Microcircuitry

Anastasia Ailamaki, Henry Markram, Felix Schürmann, Eilif Benjamin Muller, Sean Lewis Hill, Idan Segev, Srikanth Ramaswamy, Michael Reimann, Daniel Keller, Thomas Heinis, Werner Alfons Hilda Van Geit, Rodrigo de Campos Perin, Marwan Muhammad Ahmed Abdellah, James Gonzalo King, Lida Kanari, Farhan Tauheed, Julian Charles Shillcock, Pramod Shivaji Kumbhar, Gilad Silberberg, Ying Shi, Vincent Delattre, Jean-Denis Georges Emile Courcol, Rajnish Ranjan, Juan Bautista Hernando Vieites, Stefan Eilemann, Michael Emiel Gevaert, Giuseppe Chindemi, Jean-Vincent Le Bé, Julie Meystre, Taylor Howard Newton, Max Christian Nolte, Nicolas Antille, Georges Khazen, Sébastien Lasserre, Jean Pierre Ghobril, Jeffrey Christopher Muller, Aleksandr Ovcharenko, Shruti Muralidhar, Ahmet Bilgili, Daniel Nachbaur

We present a first-draft digital reconstruction of the microcircuitry of somatosensory cortex of juvenile rat. The reconstruction uses cellular and synaptic organizing principles to algorithmically reconstruct detailed anatomy and physiology from sparse ex ...

Elsevier2015

Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience

Pierre Magistretti, Henry Markram, Felix Schürmann, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Jay Coggan, Nadir Roman Guerrero, Alessandro Enrico Foni, Eleftherios Zisis, Juan José García Cantero

Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) ...

2023

Large-depth three-photon fluorescence microscopy imaging of cortical microvasculature on nonhuman primates with bright ATE probe In vivo

Marwan Muhammad Ahmed Abdellah

Multiphoton microscopy has been a powerful tool in brain research, three-photon fluorescence microscopy is increasingly becoming an emerging technique for neurological research of the cortex in depth. Nonhuman primates play important roles in the study of ...

ELSEVIER SCI LTD2022

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

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

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

Assemblies, synapse clustering and network topology interact with plasticity to explain structure-function relationships of the cortical connectome

Eilif Benjamin Muller, Michael Reimann, Marwan Muhammad Ahmed Abdellah, James Gonzalo King, András Ecker, Pramod Shivaji Kumbhar, Giuseppe Chindemi, Daniela Egas Santander, James Bryden Isbister, Ioannis Magkanaris, Sirio Bolaños Puchet, Jorge Blanco Alonso

Synaptic plasticity underlies the brain’s ability to learn and adapt. While experiments in brain slices have revealed mechanisms and protocols for the induction of plasticity between pairs of neurons, how these synaptic changes are coordinated in biologica ...

2024

Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling

Daniel Keller, Marwan Muhammad Ahmed Abdellah, Jean-Denis Georges Emile Courcol, Jay Coggan, Judit Planas Carbonell, Nadir Roman Guerrero, Alessandro Enrico Foni, Georges Khazen, Elvis Boci, Adrien Christian Fleury, Juan José García Cantero

Understanding the intracellular dynamics of brain cells entails performing three-dimensional molecular simulations incorporating ultrastructural models that can capture cellular membrane geometries at nanometer scales. While there is an abundance of neuron ...

Oxford University Press (OUP)2024