arXiv subjects

Ulrik Günther

Publications and source records attributed to Ulrik Günther.

11 recordsLinked to original sources

arXiv2026

Metric-Guided Synthetic Image Data Rendering for Deep Learning compatible with Agentic AI

Deep learning computer vision for scientific applications requires collecting and annotating large datasets in a laborious, expensive and error-prone process. Synthetic data generation through 3D modelling and rendering may simplify this process and increase the accuracy of annotations by generating them programmatically. However, minimising the domain gap between real and synthetic images visually is subjective and lacks systematic quantitative guidance. We present GraNatPy, a Python package with metrics to guide improvement of the rendered scene. We show that quantifiable increase in realism, diversity and size of rendered dataset correlates with improved visual perception of the scene and higher zero-shot performance of an object detection model. Furthermore, we demonstrated using photographs of virological plaque assays that gradient similarity affects performance on small object detection, which can be improved by mixing real and synthetic data. Finally, we turn procedural data rendering into an agentic skill (SynthClaw) to automate the procedural parameter optimisation.

cs.CV↗

arXiv2026

SciFi-VIS: Way Out There -- How SciFi and Visualization Influence Each Other

We propose a hybrid half-day workshop at IEEE VIS 2026, calling for participation from visualization researchers and science fiction creators in order to develop a systematic understanding of the two-way relationship these communities have long shared. We invite submissions of creative formats showcasing connections and inspiring future research. Our workshop plan includes a keynote, lightning talks, brainstorming, cross-community critique, affinity mapping, and discussion around identified themes.

cs.HC↗

arXiv2026

Honey, I shrunk the scientist -- Evaluating 2D, 3D, and VR interfaces for navigating samples under the microscope

In contemporary biology and medicine, 3D microscopy is one of the most widely-used techniques for imaging and manipulation of various kinds of samples. Navigating such a micrometer-sized, 3-dimensional sample under the microscope -- e.g. to find relevant imaging regions -- can pose a tedious challenge for the experimenter. In this paper, we examine whether 2D desktop, 3D desktop, or Virtual Reality (VR) interfaces provide the best user experience and performance for the exploration of 3D samples. We invited 12 skilled microscope operators to perform two different exploration tasks in 2D, 3D and VR and compared all conditions in terms speed, usability, and completion. Our results show a clear benefit when using VR -- in terms of task efficiency, usability, and user acceptance. Intriguingly, while VR outperformed desktop 2D and 3D in all scenarios, 3D desktop did not outperform 2D desktop.

cs.HC↗

arXiv2026

manvr3d: A Platform for Human-in-the-loop Cell Tracking in Virtual Reality

We propose manvr3d, a novel VR-ready platform for interactive human-in-the-loop cell tracking. We utilize VR controllers and eye-tracking hardware to facilitate rapid ground truth generation and proofreading for deep learning-based cell tracking models. Life scientists reconstruct the developmental history of organisms on the cellular level by analyzing 3D time-lapse microscopy images acquired at high spatio-temporal resolution. The reconstruction of such cell lineage trees traditionally involves tracking individual cells through all recorded time points, manually annotating their positions, and then linking them over time to create complete trajectories. Deep learning-based algorithms accelerate this process, yet depend heavily on manually-annotated high-quality ground truth data and curation. Visual representation of the image data in this process still relies primarily on 2D renderings, which greatly limits spatial understanding and navigation. In this work, we bridge the gap between deep learning-based cell tracking software and 3D/VR visualization to create a human-in-the-loop cell tracking system. We lift the incremental annotation, training and proofreading loop of the deep learning model into the 3rd dimension and apply natural user interfaces like hand gestures and eye tracking to accelerate the cell tracking workflow for life scientists.

cs.HC↗

arXiv2024

Parallel Compositing of Volumetric Depth Images for Interactive Visualization of Distributed Volumes at High Frame Rates

We present a parallel compositing algorithm for Volumetric Depth Images (VDIs) of large three-dimensional volume data. Large distributed volume data are routinely produced in both numerical simulations and experiments, yet it remains challenging to visualize them at smooth, interactive frame rates. VDIs are view-dependent piecewise constant representations of volume data that offer a potential solution. They are more compact and less expensive to render than the original data. So far, however, there is no method for generating VDIs from distributed data. We propose an algorithm that enables this by sort-last parallel generation and compositing of VDIs with automatically chosen content-adaptive parameters. The resulting composited VDI can then be streamed for remote display, providing responsive visualization of large, distributed volume data.

cs.GR↗

arXiv2023

Efficient Raycasting of Volumetric Depth Images for Remote Visualization of Large Volumes at High Frame Rates

We present an efficient raycasting algorithm for rendering Volumetric Depth Images (VDIs), and we show how it can be used in a remote visualization setting with VDIs generated and streamed from a remote server. VDIs are compact view-dependent volume representations that enable interactive visualization of large volumes at high frame rates by decoupling viewpoint changes from expensive rendering calculations. However, current rendering approaches for VDIs struggle with achieving interactive frame rates at high image resolutions. Here, we exploit the properties of perspective projection to simplify intersections of rays with the view-dependent frustums in a VDI and leverage spatial smoothness in the volume data to minimize memory accesses. Benchmarks show that responsive frame rates can be achieved close to the viewpoint of generation for HD display resolutions, providing high-fidelity approximate renderings of Gigabyte-sized volumes. We also propose a method to subsample the VDI for preview rendering, maintaining high frame rates even for large viewpoint deviations. We provide our implementation as an extension of an established open-source visualization library.

cs.GR↗

arXiv2022

Corvo: Visualizing CellxGene Single-Cell Datasets in Virtual Reality

The CellxGene project has enabled access to single-cell data in the scientific community, providing tools for browsed-based no-code analysis of more than 500 annotated datasets. However, single-cell data requires dimensional reduction to visualize, and 2D embedding does not take full advantage of three-dimensional human spatial understanding and cognition. Compared to a 2D visualization that could potentially hide gene expression patterns, 3D Virtual Reality may enable researchers to make better use of the information contained within the datasets. For this purpose, we present \emph{Corvo}, a fully free and open-source software tool that takes the visualization and analysis of CellxGene single-cell datasets to 3D Virtual Reality. Similar to CellxGene, Corvo takes a no-code approach for the end user, but also offers multimodal user input to facilitate fast navigation and analysis, and is interoperable with the existing Python data science ecosystem. In this paper, we explain the design goals of Corvo, detail its approach to the Virtual Reality visualization and analysis of single-cell data, and briefly discuss limitations and future extensions.

cs.HC↗

arXiv2020

Bionic Tracking: Using Eye Tracking to Track Biological Cells in Virtual Reality

We present Bionic Tracking, a novel method for solving biological cell tracking problems with eye tracking in virtual reality using commodity hardware. Using gaze data, and especially smooth pursuit eye movements, we are able to track cells in time series of 3D volumetric datasets. The problem of tracking cells is ubiquitous in developmental biology, where large volumetric microscopy datasets are acquired on a daily basis, often comprising hundreds or thousands of time points that span hours or days. The image data, however, is only a means to an end, and scientists are often interested in the reconstruction of cell trajectories and cell lineage trees. Reliably tracking cells in crowded three-dimensional space over many timepoints remains an open problem, and many current approaches rely on tedious manual annotation and curation. In our Bionic Tracking approach, we substitute the usual 2D point-and-click annotation to track cells with eye tracking in a virtual reality headset, where users simply have to follow a cell with their eyes in 3D space in order to track it. We detail the interaction design of our approach and explain the graph-based algorithm used to connect different time points, also taking occlusion and user distraction into account. We demonstrate our cell tracking method using the example of two different biological datasets. Finally, we report on a user study with seven cell tracking experts, demonstrating the benefits of our approach over manual point-and-click tracking.

cs.HC↗

arXiv2020

Tales from the Trenches: Developing sciview, a new 3D viewer for the ImageJ community

ImageJ/Fiji is a widely-used tool in the biomedical community for performing everyday image analysis tasks. However, its 3D viewer component (aptly named 3D Viewer) has become dated and is no longer actively maintained. We set out to create an alternative tool that not only brings modern concepts and APIs from computer graphics to ImageJ, but is designed to be robust to long-term, open-source development. To achieve this we divided the visualization logic into two parts: the rendering framework, scenery, and the user-facing application, sciview. In this paper we describe the development process and design decisions made, putting an emphasis on sustainable development, community building, and software engineering best practises. We highlight the motivation for the Java Virtual Machine (JVM) as a target platform for visualisation applications. We conclude by discussing the remaining milestones and strategy for long-term sustainability.

cs.GR↗

arXiv2020

scenery: Flexible Virtual Reality Visualization on the Java VM

Life science today involves computational analysis of a large amount and variety of data, such as volumetric data acquired by state-of-the-art microscopes, or mesh data from analysis of such data or simulations. Visualization is often the first step in making sense of data, and a crucial part of building and debugging analysis pipelines. It is therefore important that visualizations can be quickly prototyped, as well as developed or embedded into full applications. In order to better judge spatiotemporal relationships, immersive hardware, such as Virtual or Augmented Reality (VR/AR) headsets and associated controllers are becoming invaluable tools. In this work we introduce scenery, a flexible VR/AR visualization framework for the Java VM that can handle mesh and large volumetric data, containing multiple views, timepoints, and color channels. scenery is free and open-source software, works on all major platforms, and uses the Vulkan or OpenGL rendering APIs. We introduce scenery's main features and example applications, such as its use in VR for microscopy, in the biomedical image analysis software Fiji, or for visualizing agent-based simulations.

cs.GR↗

arXiv2019

A Proposed Framework for Interactive Virtual Reality In Situ Visualization of Parallel Numerical Simulations

As computer simulations progress to increasingly complex, non-linear, and three-dimensional systems and phenomena, intuitive and immediate visualization of their results is becoming crucial. While Virtual Reality (VR) and Natural User Interfaces (NUIs) have been shown to improve understanding of complex 3D data, their application to live in situ visualization and computational steering is hampered by performance requirements. Here, we present the design of a software framework for interactive VR in situ visualization of parallel numerical simulations, as well as a working prototype implementation. Our design is targeted towards meeting the performance requirements for VR, and our work is packaged in a framework that allows for easy instrumentation of simulations. Our preliminary results inform about the technical feasibility of the architecture, as well as the challenges that remain.

cs.DC↗