Publications by Stefan Eilemann

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

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

Henry Markram, Felix Schürmann, Juan Bautista Hernando Vieites, Marwan Muhammad Ahmed Abdellah, 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

Key/Value-enabled Flash Memory for Complex Scientific Workflows with On-line Analysis and Visualization

Felix Schürmann, Alessandro Curioni, Stefan Eilemann, Peter Morjan, Blake Fitch, Ralph Bellofatto, Bernard Metzler, Peter Kaltstein, Lars Schneidenbach

Scientific workflows are often composed of compute-intensive simulations and data-intensive analysis and visualization, both equally important for productivity. High-performance computers run the compute-intensive phases efficiently, but data-intensive pro ...

Ieee2016

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

Selim Arsever, Henry Markram, Raphael Dumusc, Felix Schürmann, James Gonzalo King, Rajnish Ranjan, Srikanth Ramaswamy, Sean Lewis Hill, Juan Bautista Hernando Vieites, Eilif Benjamin Muller, Daniel Keller, Idan Segev, Michael Reimann, John Richard Walker, Martin Telefont, Yun Wang, Ying Shi, Joseph William Graham, Marwan Muhammad Ahmed Abdellah, Julian Charles Shillcock, Jean-Denis Georges Emile Courcol, Ahmet Bilgili, Werner Alfons Hilda Van Geit, Athanassia Chalimourda, Stefan Eilemann, Guy Antoine Atenekeng Kahou, Jeffrey Christopher Muller, Lida Kanari, Stefano Zaninetta, Giuseppe Chindemi, Jafet Villafranca Diaz, Yury Brukau, Michael Emiel Gevaert, Stanislaw Ryszard Adaszewski, Nicolas Antille

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 ...

2015

Reconstruction and Simulation of Neocortical Microcircuitry

Nenad Buncic, Jean-Vincent Le Bé, Selim Arsever, Henry Markram, Gilad Silberberg, Sébastien Lasserre, Vincent Delattre, Raphael Dumusc, Rodrigo de Campos Perin, Imad Riachi, Thomas Berger, Felix Schürmann, James Gonzalo King, Rajnish Ranjan, Srikanth Ramaswamy, Michael Lee Hines, Sean Lewis Hill, Juan Bautista Hernando Vieites, Georges Khazen, Shruti Muralidhar, Anastasia Ailamaki, Eilif Benjamin Muller, Farhan Tauheed, Jean Pierre Ghobril, Julie Meystre, Daniel Keller, Idan Segev, Michael Reimann, Thomas Heinis, John Richard Walker, Martin Telefont, Yun Wang, Ying Shi, Joseph William Graham, Marwan Muhammad Ahmed Abdellah, Julian Charles Shillcock, Jean-Denis Georges Emile Courcol, Ahmet Bilgili, Werner Alfons Hilda Van Geit, Athanassia Chalimourda, , , , , , , , , , , , , , , , , , , , , , , , , , , ,

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

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

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 ...

BioMed Central2015