Marwan Abdellah's
Page

Calligrapher, artist, biomedical engineer,
scientific visualization expert and passionate with in silico neuroscience.

Scroll Down

Research & Development

Mesh Reconstruction

sample-image

 
Generation of high fidelity, two-manifold and watertight polygonal surface meshes of neuroscientific models including spiny neurons, glial cells and blood vasculature from high resolution segmented electron microscopy stacks. These polygonal meshes are used to create homogeneous tetrahedral or volumetric meshes for reaction-diffusion simulations, for example using the STEPs simulator, to understand the functional mechanisms of neuro-glio-vascular ensemble.

Neuronal Visualization

sample-image

 
It is all about NeuroMorphoVis; an integrated, interactive, extensible and cross-platform framework for building, visualizing and analyzing digital reconstructions of neuronal morphology skeletons extracted from microscopy stacks. The framework is capable of detecting and repairing several tracing artifacts, allowing the generation of high fidelity surface meshes and high resolution volumetric models for simulation and in silico studies. NeuroMorphoVis is based on Blender 2.79 and freely available on Github.

In Silico Imaging

sample-image

 
Research and development of Monte Carlo-based optical models for rendering realistic visualizations of digitally-reconstrucred neocortical tissue models, allowing to simulate optical imaging experiments on a physically-plausible basis.

Fluorescence Rendering

sample-image

 
Development of efficient and unbiased physically-plausible optical models for rendering fluorescent structures in low- and highly-scattering turbid media. These models can be further employed to simulate the optical pipelines of several fluorescence-based optical microscopes, such as the epi-widefield or the light-sheet fluorescence microscopes, to digitally reconstruct in silico fluorescence imaging experiments. The models can also be used to simulate other types of experiments such as voltage sensitive dyes imaging and Calcium imaging.

Parallel Rendering

sample-image

 
High performance, distributed and parallel rendering (sort last and sort first) of large scale volumetric models of biological and medical imaging datasets on multi-CPU, multi-GPU and multi-node computing clusters using CUDA and OpenCL.

Biomedical Imaging

sample-image

 
Interactive GPU-based (using graphics or compute shaders) visualization and processing of biomedical datasets acquired with various imaging modalities such as computed tomography, magnetic resonance imaging and also four-dimensional ultrasound scanners.

Marwan Abdellah's Page