Browsing by Author "Krone, Michael"
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Item Distance Visualizations for Vascular Structures in Desktop and VR: Overview and Implementation(The Eurographics Association, 2022) Hombeck, Jan; Meuschke, Monique; Lieb, Simon; Lichtenberg, Nils; Datta, Rabi; Krone, Michael; Hansen, Christian; Preim, Bernhard; Lawonn, Kai; Renata G. Raidou; Björn Sommer; Torsten W. Kuhlen; Michael Krone; Thomas Schultz; Hsiang-Yun WuThe role of expressive surface visualizations in rendering vascular structures has seen an increased impact over the last years. Surface visualizations provide an overview of complex anatomical structures and support treatment planning as well as medical education. To support decision-making, physicians need visualizations that depict anatomical structures and their spatial relations to each other, i.e., well perceivable visual encodings of egocentric and endocentric distances. We give an overview of common techniques for encoding distance information of 3D vessel surfaces. We also provide an implementation of all the visualizations presented as a starting point for other researchers. Therefore, we provide a Unity environment for each visualization, as well as implementation instructions. Thirteen different visualizations are included in this work, which can be divided into fundamental, surface-based, auxiliary and illustrative visualizations.Item EuroVis 2023 Posters: Frontmatter(The Eurographics Association, 2023) Gillmann, Christina; Krone, Michael; Lenti, Simone; Gillmann, Christina; Krone, Michael; Lenti, SimoneItem Hybrid Visualization of Protein-Lipid and Protein-Protein Interaction(The Eurographics Association, 2019) Alharbi, Naif; Krone, Michael; Chavent, Matthieu; Laramee, Robert S.; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata GeorgiaIn the Molecular Dynamics (MD) visualization literature, different approaches are utilized to study protein-lipid interactions (PLI) and protein-protein interaction (PPI) in decoupled contexts. However, the two types of interaction occur in the same space-time domain. It is beneficial to study the PLI and PPI in a unified context. Nevertheless, the simulation's size, length, and complexity increase the challenge of understanding the dynamic behavior. We propose a novel framework consisting of four linked views, a time-dependent 3D view, a novel hybrid view, a clustering timeline, and a details-on-demand window. We introduce a selection of visual designs to convey the behavior of PLI and PPI through a unified coordinate system. Abstraction is used to present proteins in hybrid 2D space, a projected tiled space is used to present both PLI and PPI at the particle level in a heat-map style visual design while glyphs are used to represent PPI at the molecular level. We couple visually separable visual designs in a unified coordinate space. The result lets the user study both PLI and PPI separately or together in a unified visual analysis framework. We also exemplify its use with case studies focusing on protein clustering and we report domain expert feedback.Item MolVa 2019: Frontmatter(The Eurographics Association, 2019) Byska, Jan; Krone, Michael; Sommer, Björn; Byska, Jan and Krone, Michael and Sommer, BjörnItem MolVa 2020: Frontmatter(The Eurographics Association, 2020) Byška, Jan; Krone, Michael; Sommer, Björn; Byška, Jan and Krone, Michael and Sommer, BjörnItem MolVa 2021: Frontmatter(The Eurographics Association, 2021) Byška, Jan; Krone, Michael; Sommer, Björn; Byška, Jan and Krone, Michael and Sommer, BjörnItem MolVa 2023: Frontmatter(The Eurographics Association, 2023) Byška, Jan; Krone, Michael; Sommer, Björn; Byška, Jan; Krone, Michael; Sommer, BjörnItem Perceptual Evaluation of Common Line Variables for Displaying Uncertainty on Molecular Surfaces(The Eurographics Association, 2022) Sterzik, Anna; Lichtenberg, Nils; Krone, Michael; Cunningham, Douglas W.; Lawonn, Kai; Renata G. Raidou; Björn Sommer; Torsten W. Kuhlen; Michael Krone; Thomas Schultz; Hsiang-Yun WuData are often subject to some degree of uncertainty, whether aleatory or epistemic. This applies both to experimental data acquired with sensors as well as to simulation data. Displaying these data and their uncertainty faithfully is crucial for gaining knowledge. Specifically, the effective communication of the uncertainty can influence the interpretation of the data and the users' trust in the visualization. However, uncertainty-aware visualization has gotten little attention in molecular visualization. When using the established molecular representations, the physicochemical attributes of the molecular data usually already occupy the common visual channels like shape, size, and color. Consequently, to encode uncertainty information, we need to open up another channel by using feature lines. Even though various line variables have been proposed for uncertainty visualizations, they have so far been primarily used for two-dimensional data and there has been little perceptual evaluation. Therefore, we conducted a perceptual study to determine the suitability of the line variables sketchiness, dashing, grayscale, and width for distinguishing several uncertainty values on molecular surfaces.Item QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces(The Eurographics Association, 2019) Martinez, Xavier; Krone, Michael; Baaden, Marc; Byska, Jan and Krone, Michael and Sommer, BjörnRecently, several fast methods to compute Solvent Excluded Surfaces (SES) on GPUs have been presented. While these published methods reportedly yield interesting and useful results, up to now no public, freely accessible implementation of a fast and opensource SES mesh computation method that runs on GPUs is available. Most molecular viewers, therefore, still use legacy CPU methods that run only on a single core, without GPU acceleration. In this paper, we present an in-depth explanation and a fully open-source CUDA implementation of the fast, grid-based computation method proposed by Hermosilla et al. [HKG*17]. Our library called QuickSES runs on GPUs and is distributed with a permissive license. It comes with a standalone program that reads Protein Data Bank (PDB) files and outputs a complete SES mesh as a Wavefront OBJ file. Alternatively it can directly be integrated in classical molecular viewers as shared library. We demonstrate the low memory consumption to enable execution on lower-end GPUs, and compare the runtime speed-up to available state-of-the-art tools.Item State of the Art of Molecular Visualization in Immersive Virtual Environments(© 2023 Eurographics ‐ The European Association for Computer Graphics and John Wiley & Sons Ltd., 2023) Kuťák, David; Vázquez, Pere‐Pau; Isenberg, Tobias; Krone, Michael; Baaden, Marc; Byška, Jan; Kozlíková, Barbora; Miao, Haichao; Hauser, Helwig and Alliez, PierreVisualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head‐mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.Item VisGap 2022: Frontmatter(The Eurographics Association, 2022) Gillmann, Christina; Krone, Michael; Reina, Guido; Wischgoll, Thomas; Gillmann, Christina; Krone, Michael; Reina, Guido; Wischgoll, ThomasItem A Web-based Visual Analytics Application for Biological Networks(The Eurographics Association, 2020) Krone, Michael; Dräger, Andreas; Cobanoglu, Ebru; Harke, Manuel Otto; Hoene, Miriam; Weigert, Cora; Lehmann, Rainer; Byška, Jan and Jänicke, StefanModern high-throughput methods enable rapidly obtaining transcriptomics data, which includes information about the expression rate of genes. The expression rates are usually given as fold change, which describes the over- or under-expression of each gene. Each gene can be part of one or more biological pathways. A pathway models the interactions between molecules in an organism that lead to a particular chemical change. Consequently, many applications in medical research need to analyze the impact of gene expression changes on the biological pathways of an organism. It allows concluding diseases or other conditions of the organism. We present a web-based visual analytics application that facilitates exploring the network of biological pathways corresponding to a given set of genes. The network is constructed from pathways derived from an external database. Users can interactively zoom and filter the network and get details on demand. Our application is currently work in progress and is developed in close collaboration with medical researchers. In subsequent steps, we strive to add more features, such as the ability to compare data from different individuals or to visualize time series data. Furthermore, we want to extend our application to visualize not just transcriptomics but multi-omics data.Item Web-based Volume Rendering using Progressive Importance-based Data Transfer(The Eurographics Association, 2018) Mwalongo, Finian; Krone, Michael; Reina, Guido; Ertl, Thomas; Beck, Fabian and Dachsbacher, Carsten and Sadlo, FilipWebGL 2.0 makes it possible to implement efficient volume rendering that runs in browsers using 3D textures and complex fragment shaders. However, a typical bottleneck for web-based volume rendering is the size of the volumetric data sets. Transferring these data to the client for rendering can take a substantial amount of time, depending on the network speed. This can introduce latency that can in turn affect interactive rendering at the client. We address this challenge by introducing a multi-resolution bricked volume rendering, where data is transferred progressively. Similar to MIP-Mapping, the volume data is divided into multiple levels of detail. Each level of detail is broken down into bricks. The client requests the data brick by brick starting with the lowest resolution and renders each brick immediately as it is received. The 3D volume texture is updated as bricks with higher resolution are received asynchronously from the server. The advantages of this algorithm are that it reduces latency, the user can see at least a reduced-detail version of the data almost immediately, and the application always stays responsive while the data is updated. We also implemented a prioritization scheme for the bricks, where each brick can be assigned an importance value. Using this information, the client can request more important bricks first. Furthermore, we investigated the influence of data compression on the transfer and processing times.