Publications

Papers

Aryaman Gupta, Pietro Incardona, Paul Hunt, Guido Reina, Steffen Frey, Stefan Gumhold, Ulrik Günther, Ivo F. Sbalzarini
Content-adaptive generation and parallel compositing of volumetric depth images for responsive visualization of large volume data.
Submitted to LDAV 2022 / arXiv preprint / GitHub repository

Aryaman Gupta, Ulrik Günther, Pietro Incardona, Guido Reina, Steffen Frey, Stefan Gumhold, Ivo F. Sbalzarini
Efficient Raycasting of View-Dependent Piecewise Constant Representations of Volumetric Data.
arXiv preprint / GitHub repository

Cameron Arshadi, Ulrik Günther, Marc Eddison, Kyle I.S. Harrington, Tiago A. Ferreira
SNT: A Unifying Toolbox for Quantification of Neuronal Anatomy.
Nature Methods, 2021 / bioRxiv preprint 2020.07.13.179325 / GitHub repository

Aryaman Gupta, Pietro Incardona, Ata Deniz Aydin, Stefan Gumhold, Ulrik Günther, Ivo F. Sbalzarini
An Architecture for Interactive In Situ Visualization and its Transparent Implementation in OpenFPM.
ISAV’20 – In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization at SuperComputing 2020. arXiv preprint / GitHub repository

Aryaman Gupta, Ulrik Günther, Pietro Incardona, Guido Reina, Steffen Frey, Stefan Gumhold, Ivo F. Sbalzarini
Parallel Compositing of Volumetric Depth Images for Interactive Distributed Volume Rendering.
Submitted to LDAV 2020.

Ulrik Günther, Kyle I.S. Harrington, Raimund Dachselt, Ivo F. Sbalzarini
Bionic Tracking: Using Eye Tracking to Track Biological Cells in Virtual Reality.
BioImage Computing at ECCV 2020. arXiv preprint / Supplementary Video / GitHub repository

Ulrik Günther, Kyle I.S. Harrington
Tales from the Trenches – Developing sciview, a new 3D Viewer for the ImageJ Community.
VisGap, Eurographics/Eurovis, 2020 / Talk Recording / arXiv preprint

Ulrik Günther, Tobias Pietzsch, Aryaman Gupta, Kyle I.S. Harrington, Pavel Tomancak, Stefan Gumhold, and Ivo F. Sbalzarini
scenery – Flexible Virtual Reality Visualisation on the Java VM.
IEEE VIS, 2019 / Talk Recording / arXiv preprint / GitHub repository / Documentation

Stephan Daetwyler Ulrik Günther, Carl D. Modes, Kyle I.S. Harrington, and Jan Huisken
Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish.
Development, 2019 / bioRxiv preprint

Bevan L. Cheeseman, Ulrik Günther, Mateusz Susik, Kryzstof Gonciarz and Ivo F. Sbalzarini
Adaptive Particle Representation of Fluorescence Microscopy Images.
Nature Communications, 2019 / bioRxiv preprint / GitHub repository

Loïc A. Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini and Eugene W. Myers
ClearVolume: open-source live 3D visualization for light-sheet microscopy.
Nature Methods, 2015 / GitHub repository / Website

Talks

Ulrik Günther: Bionic Tracking: Making cell tracking tasks easier and more ergonomic with eye tracking in VR (invited talk).
EuroBioImaging Virtual Pub, 2021.

Ulrik Günther: towards visualisation and modelling in virtual reality with scenery and sciview.
Image-based Modelling & Simulation of Morphogenesis, Dresden, 2019.

Ulrik Günther, Loïc A. Royer: Smart Microscopy / Smart Visualisation (invited talk).
5th Swiss Microscopy Core Facility Day, Fribourg, 2017.

Peer-reviewed Posters

Aryaman Gupta, Ulrik Günther, Pietro Incardona, Ata Deniz Aydin, Raimund Dachselt, Stefan Gumhold,  Ivo F. Sbalzarini
A Framework for Interactive Virtual Reality In Situ Visual- isation of Parallel Numerical Simulations
The 9th IEEE Symposium on Large Data Analysis and Visualization at IEEE VIS, 2019 (accepted) / arXiv preprint

Aryaman Gupta, Ulrik Günther, Pietro Incardona, and Ivo F. Sbalzarini
Virtual Reality In Situ Visualization with Interactive Steering for Numerical Simulations
International Supercomputing Conference PhD Forum, 2019

Posters

Ulrik Günther, Tobias Pietzsch, Curtis Rueden, Stephan Daetwyler, Jan Huisken, Kevin Elicieri, Pavel Tomancak, Ivo F. Sbalzarini, and Kyle I.S. Harrington
sciview - Next-generation 3D visualisation for ImageJ & Fiji
From Images to Knowledge with ImageJ and Friends, EMBL Heidelberg, 2018

Ulrik Günther, Kyle I.S. Harrington, and Ivo F. Sbalzarini
Exploring the scenery of lightsheet microscopy with virtual reality
LSFM2018, Dresden, 2018

Ulrik Günther, Loïc A. Royer, Martin Weigert, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini, and Eugene W. Myers
ClearVolume - from microscope to visualisation in seconds
VizBi, EMBL Heidelberg, 2016

Loïc A. Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini, and Eugene W. Myers
ClearVolume - open-source 4D live visualisation for light-sheet microscopy.
Focus on Microscopy, Göttingen, 2015

Ulrik Günther, Bevan L. Cheeseman, Pavel Tomancak, and Ivo F. Sbalzarini
dive into data— immersive 3D particle visualisation
BioImageInformatics, Leuven, 2014