Publications by Marwan Muhammad Ahmed Abdellah

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

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

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

Structural and molecular characterization of astrocyte and vasculature connectivity in the mouse hippocampus and cortex

Henry Markram, Giovanna Ambrosini, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Romain Guiet, Nicolas René Chiaruttini, Elvis Boci

The relation of astrocytic endfeet to the vasculature plays a key functional role in the neuro‐glia‐vasculature unit. We characterize the spatial organization of astrocytes and the structural aspects that facilitate their involvement in molecular exchanges ...

Wiley2024

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

Henry Markram, Felix Schürmann, James Gonzalo King, Srikanth Ramaswamy, Juan Bautista Hernando Vieites, Alexis Arnaudon, Eilif Benjamin Muller, Michael Reimann, Huanxiang Lu, Ying Shi, Marwan Muhammad Ahmed Abdellah, Vishal Sood, Jean-Denis Georges Emile Courcol, Werner Alfons Hilda Van Geit, Lida Kanari, Juan Luis Riquelme Roman, Michael Emiel Gevaert, Pramod Shivaji Kumbhar, Liesbeth Maria L Vanherpe, Armando Romani, Cyrille Pierre Henri Favreau, Michele Migliore, Mohameth François Sy, Szabolcs Kali, Judit Planas Carbonell, Genrich Ivaska, Sàra Sàray, Carmen Alina Lupascu, Rosanna Migliore, Audrey Mercer, András Ecker, Alberto Antonietti, Cristina Colangelo, Anna-Kristin Kaufmann, Julian Martin Budd, Elisabetta Giacalone, Thomas Brice Delemontex, Davide Bella, Fabien Petitjean, , , , ,

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 ...

2024

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

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

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

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, Eleftherios Zisis, Jay Coggan, Juan José García Cantero, Alessandro Enrico Foni, Nadir Roman Guerrero

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

Thalamic control of sensory processing and spindles in a biophysical somatosensory thalamoreticular circuit model of wakefulness and sleep

Henry Markram, Rodrigo de Campos Perin, James Gonzalo King, Rajnish Ranjan, Grigori Chevtchenko, Sean Lewis Hill, Jayakrishnan Harikrishnavilas Raveendran Nair, Michael Reimann, Ying Shi, Marwan Muhammad Ahmed Abdellah, Jean-Denis Georges Emile Courcol, Werner Alfons Hilda Van Geit, Adrien Christian Fleury, Michael Emiel Gevaert, Pramod Shivaji Kumbhar, Oren Amsalem, Cyrille Pierre Henri Favreau, Mohameth François Sy, Samuel Claude Kerrien, Elisabetta Iavarone, Christian O'Reilly, Genrich Ivaska, András Ecker, Anna-Kristin Kaufmann, Benoît Jean-Albert Coste, Ioannis Magkanaris, Matthias Wolf, Marine Laure Bertschy, Patrycja Lurie, Mustafa Anil Tuncel, Fabien Petitjean, Nadir Roman Guerrero, Liviu Soltuzu, Alexander Désiré Ulbrich, Polina Litvak, Vignayanandam Ravindernath Muddapu, Joni Henrikki Herttuainen

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

Meshing of Spiny Neuronal Morphologies using Union Operators

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

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

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

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

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

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, Eleftherios Zisis, Jay Coggan, Samuel Lieven D. Lapere, Alessandro Enrico Foni, Nadir Roman Guerrero

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 UNIV PRESS2021

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

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

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

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

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

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

Objective Morphological Classification of Neocortical Pyramidal Cells

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

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

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

Pierre Magistretti, Renaud Jolivet, Henry Markram, Felix Schürmann, Corrado Cali, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Stefan Eilemann, Jay Coggan, Daniya Boges, Kalpana Kare, Markus Hadwiger, Marco Agus

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

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, Ahmet Bilgili, Stefan Eilemann

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

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