Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience
Marwan Abdellah, Juan José García Cantero, Nadir Román Guerrero, Alessandro Foni, Jay S. Coggan, Corrado Calì, Marco Agus, Eleftherios Zisis, Daniel Keller, Markus Hadwiger, Pierre J. Magistretti, Henry Markram, Felix Schürmann

Briefings in Bioinformatics 2023 - Oxford Academic, January 2023
Article    Article on Oxford Academic    BibTex
Ultraliser Code on GitHub    Data is available on Zenodo   

Thalamic control of sensory processing and spindles in a biophysical somatosensory thalamoreticular circuit model of wakefulness and sleep
Elisabetta Iavarone, Jane Simko, Ying Shi, Marine Bertschy, María García-Amado, Polina Litvak, Anna-Kristin Kaufmann, Christian O’Reilly, Oren Amsalem, Marwan Abdellah, Grigori Chevtchenko, Benoît Coste, Jean-Denis Courcol, András Ecker, Cyrille Favreau, Adrien Christian Fleury, Werner Van Geit, Michael Gevaert, Nadir Román Guerrero, Joni Herttuainen, Genrich Ivaska, Samuel Kerrien, James G King, Pramod Kumbhar, Patrycja Lurie, Ioannis Magkanaris, Vignayanandam Ravindernath Muddapu, Jayakrishnan Nair, Fernando L Pereira, Rodrigo Perin, Fabien Petitjean, Rajnish Ranjan, Michael Reimann, Liviu Soltuzu, Mohameth François Sy, M Anıl Tuncel, Alexander Ulbrich, Matthias Wolf, Francisco Clascá, Henry Markram, Sean L Hill

Cell Reports 2023 - Volume 42, Issue 3, 28 March 2023, 112200
Article    Article on ScienceDirect    BibTex

A calcium-based plasticity model for predicting long-term potentiation and depression in the neocortex
Giuseppe Chindemi, Marwan Abdellah, Oren Amsalem, Ruth Benavides-Piccione, Vincent Delattre, Michael Doron, Andras Ecker, Aurélien T Jaquier, James King, Pramod Kumbhar, Caitlin Monney, Rodrigo Perin, Christian Rössert, Anil M Tuncel, Werner Van Geit, Javier DeFelipe, Michael Graupner, Idan Segev, Henry Markram, Eilif B Muller

Nature Communications 2022, Nat Commun 13, 3038 (2022)
Article    Article on Nature Communications    BibTex
Supplementary Data   

In silico voltage-sensitive dye imaging reveals the emergent dynamics of cortical populations
Taylor H. Newton, Michael W. Reimann, Marwan Abdellah, Grigori Chevtchenko, Eilif B. Muller and Henry Markram.

Nature Communications 2021
Article    Article on Nature Communications    BibTex
Data is available on Zenodo   

Metaball skinning of synthetic astroglial morphologies into realistic mesh models for visual analytics and in silico simulations
Marwan Abdellah, Alessandro Foni, Eleftherios Zisis, Nadir Román Guerrero, Samuel Lapere, Jay S. Coggan, Daniel Keller, Henry Markram and Felix Schürmann

Oxford Bioinformatics, 2021
Article    Article on Oxford Academic    BibTex
Code on GitHub (The plugin is integrated into NeuroMorphoVis)    Data is available on Zenodo

Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis
Marwan Abdellah, Nadir Román Guerrero, Samuel Lapere, Jay S. Coggan, Daniel Keller, Benoit Coste, Snigdha Dagaer, Jean-Denis Courcol, Henry Markram and Felix Schürmann

Oxford Bioinformatics, 2020, Volume 36, Issue Supplement 1, July 2020
Article    Article on Oxford Academic    BibTex
VessMorphoVis on GitHub   

Objective morphological classification of neocortical pyramidal cells
Lida Kanari, Srikanth Ramaswamy, Ying Shi, Sebastien Morand, Julie Meystre, Rodrigo Perin, Marwan Abdellah, Yun Wang, Kathryn Hess and Henry Markram

Oxford Cerebral Cortex 2019, Volume 29, Issue 4, April 2019, Pages 1719–1735
Article    Article on Oxford Academic    Supplementary Data    BibTex

A process for digitizing and simulating biologically realistic oligocellular networks demonstrated for the Neuro-Glio-Vascular ensemble
Jay S. Coggan, Corrado Cali, Daniel Keller, Marco Agus, Daniya Boges, Marwan Abdellah, Kalpana Kare, Heikki O. Lehvaslaiho, Stefan Eilemann, Renaud B. Jolivet, Markus Hadwiger, Henry Markram, Felix Schürmann, Pierre J. Magistretti

Frontiers in Neuroscience
Energy Efficient Neural Code in Individual Neurons and Brain Circuits
Article    Article on Frontiers    BibTex

NeuroMorphoVis: a collaborative framework for visualization and analysis of neuronal morphology skeletons reconstructed from microscopy stacks
Marwan Abdellah, Juan Hernando, Stefan Eilemann, Samuel Lapere, Nicolas Antille, Henry Markram, and Felix Schürmann

Oxford Bioinformatics, Volume 34, Issue 13, 01 July 2018, Pages i574–i582, Published: 27 June 2018
Article    Article on Oxford Academic    BibTex
NeuroMorphoVis on GitHub   

Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies
Marwan Abdellah, Juan Hernando, Nicolas Antille, Stefan Eilemann, Henry Markram, and Felix Schürmann

BMC Bioinformatics 2017, Volume 18, Article 402 (2017), Published: 13 September 2017
Article    Article on BMC Bioinformatics    BibTex

Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation
Marwan Abdellah, Ahmet Bilgili, Stefan Eilemann, Julian Shillcock, Henry Markram, and Felix Schürmann

BMC Bioinformatics 2017, Volume 18, Supplement 2:62, Published: 15 February 2017
Article    Article on BMC Bioinformatics    BibTex

Reconstruction and simulation of neocortical microcircuitry
Henry Markram, Eilif Muller, Srikanth Ramaswamy, Michael W. Reimann, Marwan Abdellah, Carlos Aguado Sanchez, Anastasia Ailamaki, Lidia Alonso-Nanclares, Nicolas Antille, Selim Arsever, Guy Antoine Atenekeng Kahou, Thomas K. Berger, Ahmet Bilgili, Nenad Buncic, Athanassia Chalimourda, Giuseppe Chindemi, Jean-Denis Courcol, Fabien Delalondre, Vincent Delattre, Shaul Druckmann, Raphael Dumusc, James Dynes, Stefan Eilemann, Eyal Gal, Michael Emiel Gevaert, Jean-Pierre Ghobril, Albert Gidon, Joe W. Graham, Anirudh Gupta, Valentin Haenel, Etay Hay, Thomas Heinis, Juan B. Hernando, Michael Hines, Lida Kanari, Daniel Keller, John Kenyon, Georges Khazen, Yihwa Kim, James G. King, Zoltan Kisvarday, Pramod Kumbhar, Sébastien Lasserre, Jean-Vincent Le Bé, Bruno R.C. Magalhães, Angel Merchán-Pérez, Julie Meystre, Benjamin Roy Morrice, Jeffrey Muller, Alberto Muñoz-Céspedes, Shruti Muralidhar, Keerthan Muthurasa, Daniel Nachbaur, Taylor H. Newton, Max Nolte, Aleksandr Ovcharenko, Juan Palacios, Luis Pastor, Rodrigo Perin, Rajnish Ranjan, Imad Riachi, José-Rodrigo Rodríguez, Juan Luis Riquelme, Christian Rössert, Konstantinos Sfyrakis, Ying Shi, Julian C. Shillcock, Gilad Silberberg, Ricardo Silva, Farhan Tauheed, Martin Telefont, Maria Toledo-Rodriguez, Thomas Tränkler, Werner Van Geit, Jafet Villafranca Díaz, Richard Walker, Yun Wang, Stefano M. Zaninetta, Javier DeFelipe, Sean L. Hill, Idan Segev, Felix Schürmann

Cell, Volume 163, Issue 2, p456–492, 8 October 2015
Article    Article on Cell.com    BibTex

The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex
Srikanth Ramaswamy, Jean-Denis Courcol, Marwan Abdellah, Stanislaw Adaszewski, Nicolas Antille, Selim Arsever, Atenekeng Kahou Guy Antoine, Ahmet Bilgili, Yury Brukau, Giuseppe Chindemi, Raphael Dumusc, Stefan Eilemann, Lida Kanari, Daniel Keller, James G. King, Rajnish Ranjan, Michael Wolfgang Reimann, Christian Roessert, Martin Telefont, Werner Van Geit, Jafet Villafranca_Diaz, Richard Walker, Yun Wang, Stefano Zaninetta, Javier DeFelipe, Sean L Hill, Jeffrey Muller, Idan Segev, Felix Schürmann, Eilif Benjamin Muller and Henry Markram

Frontiers in Neural Circuits, ISSN 1662-5110
Data Report Article
Article    Article on Frontiers.com    BibTex

Physically-based in Silico light sheet microscopy for visualizing fluorescent brain models
Marwan Abdellah, Ahmet Bilgili, Stefan Eilemann, Henry Markram, and Felix Schürmann

BMC Bioinformatics 2015, ISSN 1662-5110
Article    Article on BMC Bioinformatics    BibTex
Code is available on GitHub   

High Performance GPU-based Fourier Volume Rendering
Marwan Abdellah, Ayman Eldeib, and Amr Sharawi

International Journal of Biomedical Imaging, 2015: 590727
Published online 2015 Feb 19. doi: 10.1155/2015/590727
Article    Article on PMC    BibTex

Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling
Marwan Abdellah, Alessandro Foni, Juan José García Cantero, Nadir Román Guerrero, Elvis Boci, Adrien Fleury, Jay S. Coggan, Daniel Keller, Judit Planas, Jean-Denis Courcol, Georges Khazen

bioRxiv, March 2024
Paper    Article on bioRxiv    BibTex
Data is available on Zenodo   

Long-term plasticity induces sparse and specific synaptic changes in a biophysically detailed cortical model
Andras Ecker, Daniela Egas Santander, Marwan Abdellah, Jorge Blanco Alonso, Sirio Bolanos-Puchet, Giuseppe Chindemi, James B. Isbister, James Gonzalo King, Pramod Kumbhar, Ioannis Magkanaris, Eilif B. Muller, Michael W. Reimann

bioRxiv, August 2023
Paper    Article on bioRxiv    BibTex
Data is available on Zenodo   

Community-based Reconstruction and Simulation of a Full-scale Model of Region CA1 of Rat Hippocampus
Armando Romani, Alberto Antonietti, Davide Bella, Julian Budd, Elisabetta Giacalone, Kerem Kurban, Sara Saray, Marwan Abdellah, Alexis Arnaudon, Elvis Boci, Cristina Colangelo, Jean-Denis Courcol, Thomas Delemontex, Andras Ecker, Joanne Falck, Cyrille Favreau, Michael Gevaert, Juan B Hernando, Joni Herttuainen, Genrich Ivaska, Lida Kanari, Anna-Kristin Kaufmann, James Gonzalo King, Pramod Kumbhar, Sigrun Lange, Huanxiang Lu, Carmen Alina Lupascu, Rosanna Migliore, Fabien Petitjean, Judit Planas, Pranav Rai, Srikanth Ramaswamy, Michael W Reimann, Juan Luis Riquelme, Nadir Roman Guerrero, Ying Shi, Vishal Sood, Mohameth Francois Sy, Werner Van Geit, Liesbeth Vanherpe, Tamas Freund, Audrey Mercer, Eilif Muller, Felix Schurmann, Alex M Thomson, Michele Migliore, Szabolcs Káli, Henry Markram

bioRxiv, May 2023
Paper    Article on bioRxiv    BibTex

Architecture of the Neuro-Glia-Vascular System
Eleftherios Zisis, Daniel Keller, Lida Kanari, Alexis Arnaudon, Michael Gevaert, Thomas Delemontex, Benoît Coste, Alessandro Foni, Marwan Abdellah, Corrado Calì, Kathryn Hess, Pierre Julius Magistretti, Felix Schürmann, Henry Markram

bioRxiv, January 2021
Paper    Article on bioRxiv    BibTex

Voltage-sensitive dye imaging reveals inhibitory modulation of ongoing cortical activity
Taylor H Newton, Marwan Abdellah, Grigori Chevtchenko, Eilif B. Muller and Henry Markram

bioRxiv, January 2018
Paper    Article on bioRxiv    BibTex

Objective Classification of Neocortical Pyramidal Cells
Lida Kanari, Srikanth Ramaswamy, Ying Shi, Sebastien Morand, Julie Meystre, Rodrigo Perin, Marwan Abdellah, Yun Wang, Kathryn Hess, Henry Markram

bioRxiv, January 2018
Paper    Article on bioRxiv    Supplementary Data    BibTex

A physically plausible model for rendering highly scattering fluorescent participating media
Marwan Abdellah, Ahmet Bilgili, Stefan Eilemann, Henry Markram, Felix Schürmann

arXiv.org, June 2017
Paper    Article on arXiv    BibTex

Meshing of spiny neuronal morphologies using union operators
Marwan Abdellah, Juan José García Cantero, Alessandro Foni, Nadir Román Guerrero, Elvis Boci, and Felix Schürmann

EG Computer Graphics & Visual Computing (CGVC) 2022, Leeds, UK, September 2022
Paper on Eurographics Digital Library    Data is available on Zenodo    BibTex
The implementation is integrated into NeuroMorphoVis and is freely available on GitHub   

High fidelity visualization of large scale digitally reconstructed brain circuitry with signed distance functions
Jonas Karlsson, Marwan Abdellah, Sebastien Speierer, Alessandro Foni, Samuel Lapere, and Felix Schürmann

IEEE Visualization Conference (IEEE Vis 2019), Vancouver, Canada, October 2019
Paper on IEEEXplore Digital Library    Conference Website   
Code is available on GitHub as a Brayns plugin   

Generating high fidelity surface meshes of neocortical neurons using skin modifiers
Marwan Abdellah, Cyrille Favreau, Juan Hernando, Samuel Lapere, and Felix Schürmann

EG Computer Graphics & Visual Computing (CGVC) 2019, Bangor, Wales, UK, September 2019
Paper on Eurographics Digital Library    Data is available on Zenodo    BibTex
The implementation is integrated into NeuroMorphoVis and is freely available on GitHub   

NeuroMorphoVis: a collaborative framework for visualization and analysis of neuronal morphology skeletons reconstructed from microscopy stacks
Marwan Abdellah, Juan Hernando, Stefan Eilemann, Samuel Lapere, Nicolas Antille, Henry Markram, and Felix Schürmann

Workshop on Biological Data Visualization (BioVis 2018) at ISMB 2018, Chicago, IL, USA, July 2018
PDF    Paper on Oxford Academic    BibTex
NeuroMorphoVis on GitHub   

From big data to big displays: high-performance visualization at Blue Brain
Stefan Eilemann, Marwan Abdellah, Nicolas Antille, Ahmet Bilgili, Grigory Chevtchenko, Raphael Dumusc, Cyrille Favreau, Juan Hernando, Daniel Nachbaur, Pawel Podhajski, Jafet Villafranca, and Felix Schürmann

International Conference on High Performance Computing, 2017, Frankfurt, Germany
Paper on arXiv    ISC Conference    BibTex

Parallel generation of digitally reconstructed radiographs on heterogeneous multi-GPU workstations
Marwan Abdellah, Asem Abdelaziz, Eslam Ali, Sherief Abdelaziz, Abdelrahman Sayed, Mohamed I. Owis and Ayman Eldeib

38^th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2016), Florida, USA, August 2016
Paper on IEEEXplore    BibTex

Efficient rendering of digitally reconstructed radiographs on heterogeneous computing architectures using central slice theorem
Marwan Abdellah, Mohamed Abdallah, Mohamed Alzanati and Ayman Eldeib

38^th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2016), Florida, USA, August 2016
Paper on IEEEXplore    BibTex

Physically-based rendering of highly scattering fluorescent solutions using path tracing
Marwan Abdellah, Ahmet Bilgili, Stefan Eilemann, Henry Markram, and Felix Schürmann

Eurographics 2016, May 2016 in Lisbon, Portugal
Paper on Eurographics Digital Library    BibTex

Interactive high resolution reconstruction of 3D ultrasound volumes on the GPU
Marwan Abdellah, Asem Abdelaziz and Ayman Eldeib

2016 IEEE International Symposium on Biomedical Imaging: From Nano to Macro
April 2016 in Prague, Czech Republic
Paper on IEEEXplore Digital Library    BibTex

Optimized GPU-accelerated Framework for X-ray Rendering using k-space Volume Reconstruction
Marwan Abdellah, Yassin Amer and Ayman Eldeib

XIV Mediterranean Conference on Medical & Biological Engineering & Computing (MEDICON 2016)
April 2016 in Paphos, Cyprus
Paper on Springer    BibTex

Accelerating DRR Generation Using Fourier Slice Theorem on the GPU
Marwan Abdellah, Ayman M. Eldeib, Mohamed Owis

37^th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2015)
August 2015 in Milan, Italy
Paper on IEEEXplore Digital Library    BibTex

GPU Acceleration for Digitally Reconstructed Radiographs Using Bindless Texture Objects and CUDA/OpenGL Interoperability
Marwan Abdellah, Ayman M. Eldeib, Mohamed Owis

37^th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2015)
August 2015 in Milan, Italy
Paper on IEEEXplore Digital Library    BibTex

Physically-based In Silico Light Sheet Microscopy for Visualizing Fluorescent Brain Models
Marwan Abdellah, Ahmet Bilgili, Stefan Eilemann, Henry Markram, and Felix Schürmann

5^th Symposium on Biological Data Visualization (BioVis 2015)
July 2015 in Dublin, Ireland
Paper    Paper on BMC Bioinformatics    BibTex
Code on GitHub   

A Computational Model of Light-Sheet Fluorescence Microscopy using Physically-based Rendering
Marwan Abdellah, Ahmet Bilgili, Stefan Eilemann, Henry Markram, and Felix Schürmann

Eurographics 2015, May 2015 in Zürich, Switzerland
Paper on Eurographics Digital Library    BibTex

Offline Large Scale Fourier Volume Rendering on Low-end Hardware
Marwan Abdellah, Ayman Eldeib, and Amr Sharawi

IEEE, Proceedings of 7^th Cairo International Biomedical Engineering Conference (CIBEC 2014)
December 2014 in Cairo, Egypt
Paper on IEEEXplore Digital Library    BibTex

MATLAB-based Fourier Volume Rendering Framework
Marwan Abdellah, Ayman Eldeib, and Amr Sharawi

IEEE, Proceedings of 7^th Cairo International Biomedical Engineering Conference (CIBEC 2014)
December 2014 in Cairo, Egypt
Paper on IEEEXplore Digital Library    BibTex

cufftShift: High Performance CUDA-accelerated FFT-shift Library
Marwan Abdellah

Proceedings of the 22^nd High Performance Computing Symposium (HPC '14), Article No. 5
April 2014 in Tampa, FL, USA
Paper on ACM Digital Library    BibTex

Constructing a Functional Fourier Volume Rendering Pipeline on Heterogeneous Platforms
Marwan Abdellah, Ayman Eldeib, and Amr Shaarawi

Proceedings of the 6^th Cairo International Biomedical Engineering Conference (CIBEC 2012)
December 2012 in Cairo, Egypt
Paper on IEEEXplore Digital Library    BibTex

High Performance Multi-dimensional (2D/3D) FFT-Shift Implementation on Graphics Processing Units (GPUs)
Marwan Abdellah, Ayman Eldeib, and Amr Shaarawi

Proceedings of the 6^th Cairo International Biomedical Engineering Conference (CIBEC 2012)
December 2012 in Cairo, Egypt
Paper on IEEEXplore Digital Library    BibTex

High Performance CUDA-based Implementation for the 2D Version of the Maximum Subarray Problem (MSP)
Salah Saleh, Marwan Abdellah, Ahmed A. Abdel Raouf, and Yasser M. Kadah

Proceedings of the 6^th Cairo International Biomedical Engineering Conference (CIBEC 2012)
December 2012 in Cairo, Egypt
Paper on IEEEXplore Digital Library    BibTex

Parallel Rendering on Hybrid Multi-GPU Clusters
Stefan Eilemann, Ahmet Bilgili, Marwan Abdellah, Juan Hernando, Maxim Makhinya, and Renato Pajarola

Eurographics Symposium on Parallel Graphics and Visualization (EGPGV '12), May 2012 in Cagliari, Italy
Paper on Eurographics Digital Library    BibTex

GPU-Based Reconstruction and Display for 4D Ultrasound Data
Ahmed Elnokrashy, Ahmed Elmalky, Tamer Hosny, Marwan Abdellah, Alaa Megawer, Abubakr Alsebai, Abou-Bakr Youssef and Yasser Kadah

2009 IEEE International Ultrasonics Symposium, September 2009 in Rome, Italy
Paper on IEEEXplore Digital Library    BibTex

Software Development for Low Cost, High quality, Real-time, 4D Ultrasound on Personal Computers
Marwan Abdellah, Alaa Megawer and Yasser M. Kadah

26^th National Radio Science Conference (NRSC), Union Radio Scientifique Internationale (URSI)
March 2009 in Cairo, Egypt
Paper on IEEEXplore Digital Library    BibTex

Advances in neuronal morphology analysis, meshing and visualization with NeuroMorphoVis
Marwan Abdellah, Samuel Lapere, Felix Schürmann, Henry Markram

Biological Data Visualization at International Society of Molecular Biology (ISMB) 2019
Basel, Switzerland, July 2019
Poster   

Characterization of detection iso-contours in a single fiber photometry system
M. Mansy, M. Abdellah, H. Kim, F. Schürmann and K. Oweiss

Society for Neuroscience (SfN) 2017
USA, 2017
Poster   

Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies
Marwan Abdellah, Juan Hernando, Nicolas Antille, Stefan Eilemann, Henry Markram, and Felix Schürmann

Biological Data Visualization (BioVis) at International Society of Molecular Biology (ISMB) 2017
Prague, Czech Republic, July 2017
Poster   

In silico voltage sensitive dye imaging in a digital reconstruction of somatosensory cortex
Taylor H. Newton, Marwan Abdellah, Eilif Muller, Felix Schürmann, Henry Markram

Society for Neuroscience (SfN) 2016
USA, 2016

A unifying model of the neocortical column 15: high performance computing and software development challenges
F. Delalondre, M. Abdellah, C. Aguado Sanchez, A. Bilgili, N. Buncic, J. Courcol, S. Eilemann, V. Haenel, S.L. Hill, T. Heinis, J.B. Hernando, M. Hines, J.G. King, E. Muller, B.R.C. Magalhaes, G. Mateescu, J. Muller, K. Muthurasa, D. Nachbaur, L. Pastor, J.M. Pena, R. Ranjan, M.W. Reimann , F. Tauheed, W. Van Geit, A. Ailamaki. H. Markram, and F. Schürmann

Society for Neuroscience (SfN) 2012
USA, 2012

In silico brain imaging: physically-plausible methods for visualizing neocortical microcircuitry
Marwan Abdellah

Ph.D. Thesis, Neuroscience, September 2017
Blue Brain Project (BBP), Neuroscience Doctoral School (EDNE)
École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
Thesis Page    BibTex

High performance Fourier volume rendering on graphics processing units (GPUs)
Marwan Abdellah

M.Sc. Thesis, Biomedical Engineering, February 2012
Systems & Biomedical Engineering Department (SBME)
Faculty of Engineering, Cairo University, Cairo, Egypt
Thesis Page    BibTex