Publications by Juan Bautista Hernando Vieites

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy

Henry Markram, Kathryn Hess Bellwald, Eilif Benjamin Muller, Srikanth Ramaswamy, Michael Reimann, James Gonzalo King, Lida Kanari, Ying Shi, Armando Romani, Adrien Michel Achille Devresse

The function of the neocortex is fundamentally determined by its repeating microcircuit motif, but also by its rich, hierarchical, interregional structure with a highly specific laminar architecture. The last decade has seen the emergence of extensive new ...

2024

Enhancement of brain atlases with region-specific coordinate systems: flatmaps and barrel column annotations

Michael Reimann, Armando Romani, Aleksandra Zuzanna Teska, Felix Schürmann, Juan Bautista Hernando Vieites, Huanxiang Lu, Sirio Bolaños Puchet

Digital brain atlases define a hierarchy of brain regions and their locations in three-dimensional space. They provide a standard coordinate system in which diverse datasets can be integrated for visualization and analysis. They also enable building of dat ...

2024

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

Henry Markram, Eilif Benjamin Muller, Srikanth Ramaswamy, Michael Reimann, James Gonzalo King, Lida Kanari, Ying Shi, Armando Romani, Davide Bella, Felix Schürmann

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 ...

2024

The SONATA data format for efficient description of large-scale network models

Eilif Benjamin Muller, James Gonzalo King, Adrien Michel Achille Devresse, Werner Alfons Hilda Van Geit, Jean-Denis Georges Emile Courcol, Juan Bautista Hernando Vieites, Michael Emiel Gevaert, Judit Planas Carbonell

Increasing availability of comprehensive experimental datasets and of high-performance computing resources are driving rapid growth in scale, complexity, and biological realism of computational models in neuroscience. To support construction and simulation ...

2020

Generating High Fidelity Surface Meshes of Neocortical Neurons using Skin Modifiers

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

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

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

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

Henry Markram, Sean Lewis Hill, Lida Kanari, Eilif Benjamin Muller, Srikanth Ramaswamy, Ying Shi, Rajnish Ranjan, Michael Reimann, Felix Schürmann, James Gonzalo King

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 ...

Frontiers Research Foundation2015

Reconstruction and Simulation of Neocortical Microcircuitry

Anastasia Ailamaki, Henry Markram, Sean Lewis Hill, Eilif Benjamin Muller, Rodrigo de Campos Perin, Lida Kanari, Srikanth Ramaswamy, Vincent Delattre, Michael Reimann, Ying Shi

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 ...

Elsevier2015

A neuron membrane mesh representation for visualization of electrophysiological simulations

Henry Markram, Sean Lewis Hill, Felix Schürmann, Juan Bautista Hernando Vieites, Sébastien Lasserre

We present a process to automatically generate three-dimensional mesh representations of the complex, arborized cell membrane surface of cortical neurons (the principal information processing cells of the brain) from nonuniform morphological measurements. ...

Institute of Electrical and Electronics Engineers2012

Towards real-time visualization of detailed neural tissue models: View frustum culling for parallel rendering

Felix Schürmann, Juan Bautista Hernando Vieites

Recent efforts to model neural tissue in great anatomical detail play an important role in the shift towards simulation-based brain research. Visualization of those detailed models is an important part of the scientific workflow, allowing domain scientists ...

IEEE2012