Publications related to Scientific visualization

Orchestrating chromosome conformation capture analysis with Bioconductor

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Nature Research2024

Probing Catalytic Sites and Adsorbate Spillover on Ultrathin FeO2-x Film on Ir(111) during CO Oxidation

Harald Brune, Hao Yin, Wei Fang

The spatially resolved identification of active sites on the heterogeneous catalyst surface is an essential step toward directly visualizing a catalytic reaction with atomic scale. To date, ferrous centers on platinum group metals have shown promising pote ...

Amer Chemical Soc2024

Painting Taylor vortices with cellulose nanocrystals: Suspension flow supercritical spectral dynamics

Marianne Liebi

We study the flow stability and spatiotemporal spectral dynamics of cellulose nanocrystal (CNC) suspensions in a custom Taylor-Couette flow cell using the intrinsic shear induced birefringence and liquid crystalline properties of CNC suspensions for flow v ...

Aip Publishing2024

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Martin Weigert

Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and s ...

Nature Portfolio2024

From Automated Bootstrapping to Collaborative Editing: A Framework for 4D City Reconstruction

Rémi Guillaume Petitpierre, Paul Robert Guhennec, Beatrice Vaienti, Didier Louis Dupertuis

We propose a framework for the construction of 4D scientific models for cities of the past. It leverages both the use of computational methods for bootstrapping, and a collaborative interface for visualisation and edition. This permits to continuously enri ...

Zenodo2023

ROSMOSE: A Web-based Optimization Tool to Aid Decision-making for the Design and Operation of Industrial and Urban Energy Systems

François Maréchal, Daniel Alexander Florez Orrego, Meire Ellen Gorete Ribeiro Domingos, Cédric Terrier, Michel Lopez

Energy efficiency is crucial for the sustainable operation of all industrial and urban sectors. However, practicing engineers have seldom access to open-source tools that can readily evaluate and compare scenarios in terms of energy consumption, cost, and ...

2023

Vortex shedding from a composite hydrofoil: Experimental evidence of a novel "partial lock-in"

Mohamed Farhat, Thomas Antoine Nicolas Berger, Qin Wu, Yunqing Liu

Lock-in is of great importance in many engineering applications due to its practical implications for structural safety. The influence of composite bend-twist coupling on the wake dynamics and vortex-induced vibration around a carbon fiber composite hydrof ...

Aip Publishing2023

The JPEG AI Standard: Providing Efficient Human and Machine Visual Data Consumption

Touradj Ebrahimi

The Joint Photographic Experts Group (JPEG) AI learning-based image coding system is an ongoing joint standardization effort between International Organization for Standardization (ISO), International Electrotechnical Commission (IEC), and International Te ...

IEEE COMPUTER SOC2023

Three-dimensional nanoimaging of fuel cell catalyst layers

Vasiliki Tileli, Robin Pierre Alain Girod, Timon Lazaridis

Catalyst layers in proton exchange membrane fuel cells consist of platinum-group-metal nanocatalysts supported on carbon aggregates, forming a porous structure through which an ionomer network percolates. The local structural character of these heterogeneo ...

NATURE PORTFOLIO2023

Automatic Parameterization for Aerodynamic Shape Optimization via Deep Geometric Learning

Pascal Fua, Zhen Wei

We propose two deep learning models that fully automate shape parameterization for aerodynamic shape optimization. Both models are optimized to parameterize via deep geometric learning to embed human prior knowledge into learned geometric patterns, elimina ...

2023

Meshing of Spiny Neuronal Morphologies using Union Operators

Felix Schürmann, Marwan Muhammad Ahmed Abdellah, Elvis Boci, Nadir Roman Guerrero, Juan José García Cantero, Alessandro Enrico Foni

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 ...

2022

Sub-micrometer morphology of human atherosclerotic plaque revealed by synchrotron radiation-based mu CT-A comparison with histology

Goran Lovric, Anne Bonnin

Histology is a long standing and well-established gold standard for pathological characterizations. In recent years however, synchrotron radiation-based micro-computed tomography (SR mu CT) has become a tool for extending the imaging of two-dimensional thi ...

PUBLIC LIBRARY SCIENCE2022

New Capabilities of the FLUKA Multi-Purpose Code

Nikolaos Charitonidis, André Donadon Servelle, Philippe Jean Schoofs, Francesco Cerutti

FLUKA is a general purpose Monte Carlo code able to describe the transport and interaction of any particle and nucleus type in complex geometries over an energy range extending from thermal neutrons to ultrarelativistic hadron collisions. It has many diffe ...

FRONTIERS MEDIA SA2022

Landmarking for Navigational Streaming of Stored High-Dimensional Media

Pascal Frossard, Yuan Yuan

Modern media data such as 360 degrees videos and light field (LF) images are typically captured in much higher dimensions than the observers' visual displays. To efficiently browse high-dimensional media, a navigational streaming model is considered: a cli ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2022

Predicting visual stimuli from cortical response recorded with widefield imaging in a mouse

Silvestro Micera, Daniela De Luca

Optic nerve stimulation holds great potential for visual prostheses. Its effectiveness depends on the stimulation protocol, which can be optimized to achieve cortical activation similar to that evoked in response to visual stimuli. To identify a target cor ...

IEEE2022

Recent advances in trajectory inference from single-cell omics data

Bart Deplancke, Wouter Saelens

Trajectory inference methods have emerged as a novel class of single-cell bioinformatics tools to study cellular dynamics at unprecedented resolution. Initial development focused on adapting methods based on clustering or graph traversal, but recent advanc ...

ELSEVIER2021

Rapid screening of nanopore candidates in nanoporous single-layer graphene for selective separations using molecular visualization and interatomic potentials

Luc Sébastien Bondaz, Rohit Karnik

Nanoporous single-layer graphene is promising as an ideal membrane because of its extreme thinness, chemical resistance, and mechanical strength, provided that selective nanopores are successfully incorporated. However, screening and understanding the tran ...

AIP Publishing2021

A Non-Exponential Transmittance Model for Volumetric Scene Representations

Wenzel Alban Jakob, Delio Aleardo Vicini

We introduce a novel transmittance model to improve the volumetric representation of 3D scenes. The model can represent opaque surfaces in the volumetric light transport framework. Volumetric representations are useful for complex scenes, and become increa ...

ASSOC COMPUTING MACHINERY2021

Development of the RAPTOR suite of codes towards real-time reconstruction of JET discharges

Federico Alberto Alfredo Felici

The RAPTOR suite of codes combines real-time model-based predictions of the plasma state with the available diagnostic measurements. Following the work on TCV and ASDEX-Upgrade, this paper presents the implementation of the RAPTOR suite for JET. This suite ...

2021

Following spatial A beta aggregation dynamics in evolving Alzheimer's disease pathology by imaging stable isotope labeling kinetics

Anders Meibom, Stéphane Laurent Escrig, Melissa Kathleen Passarelli

beta-Amyloid (A beta) plaque formation is the major pathological hallmark of Alzheimer's disease (AD) and constitutes a potentially critical, early inducer driving AD pathogenesis as it precedes other pathological events and cognitive symptoms by decades. ...

AMER ASSOC ADVANCEMENT SCIENCE2021