Marwan Muhammad Ahmed Abdellah

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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) ...

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 ...

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 ...

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 ...

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 ...

We present a physically-based computational model of the light sheet fluorescence microscope (LSFM). Based on Monte Carlo ray tracing and geometric optics, our method simulates the operational aspects and image formation process of the LSFM. This simulated ...

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 ...

Marwan Muhammad Ahmed Abdellah

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

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

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

Meshing of Spiny Neuronal Morphologies using Union Operators

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

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

Digital Reconstruction of the Neuro-Glia-Vascular Architecture

Objective Morphological Classification of Neocortical Pyramidal Cells

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

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

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

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

Reconstruction and Simulation of Neocortical Microcircuitry

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

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

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

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

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

Physically-based in silico light sheet microscopy for visualizing fluorescent brain models

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