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Memento: Localized Time‐Warping for Spatio‐Temporal Selection
(© 2020 Eurographics ‐ The European Association for Computer Graphics and John Wiley & Sons Ltd, 2020) Solteszova, V.; Smit, N. N.; Stoppel, S.; Grüner, R.; Bruckner, S.; Benes, Bedrich and Hauser, Helwig
Interaction techniques for temporal data are often focused on affecting the spatial aspects of the data, for instance through the use of transfer functions, camera navigation or clipping planes. However, the temporal aspect of the data interaction is often neglected. The temporal component is either visualized as individual time steps, an animation or a static summary over the temporal domain. When dealing with streaming data, these techniques are unable to cope with the task of re‐viewing an interesting local spatio‐temporal event, while continuing to observe the rest of the feed. We propose a novel technique that allows users to interactively specify areas of interest in the spatio‐temporal domain. By employing a time‐warp function, we are able to slow down time, freeze time or even travel back in time, around spatio‐temporal events of interest. The combination of such a (pre‐defined) time‐warp function and brushing directly in the data to select regions of interest allows for a detailed review of temporally and spatially localized events, while maintaining an overview of the global spatio‐temporal data. We demonstrate the utility of our technique with several usage scenarios.
LineageD: An Interactive Visual System for Plant Cell Lineage Assignments based on Correctable Machine Learning
(The Eurographics Association and John Wiley & Sons Ltd., 2022) Hong, Jiayi; Trubuil, Alain; Isenberg, Tobias; Borgo, Rita; Marai, G. Elisabeta; Schreck, Tobias
We describe LineageD-a hybrid web-based system to predict, visualize, and interactively adjust plant embryo cell lineages. Currently, plant biologists explore the development of an embryo and its hierarchical cell lineage manually, based on a 3D dataset that represents the embryo status at one point in time. This human decision-making process, however, is time-consuming, tedious, and error-prone due to the lack of integrated graphical support for specifying the cell lineage. To fill this gap, we developed a new system to support the biologists in their tasks using an interactive combination of 3D visualization, abstract data visualization, and correctable machine learning to modify the proposed cell lineage. We use existing manually established cell lineages to obtain a neural network model. We then allow biologists to use this model to repeatedly predict assignments of a single cell division stage. After each hierarchy level prediction, we allow them to interactively adjust the machine learning based assignment, which we then integrate into the pool of verified assignments for further predictions. In addition to building the hierarchy this way in a bottom-up fashion, we also offer users to divide the whole embryo and create the hierarchy tree in a top-down fashion for a few steps, improving the ML-based assignments by reducing the potential for wrong predictions. We visualize the continuously updated embryo and its hierarchical development using both 3D spatial and abstract tree representations, together with information about the model's confidence and spatial properties. We conducted case study validations with five expert biologists to explore the utility of our approach and to assess the potential for LineageD to be used in their daily workflow. We found that the visualizations of both 3D representations and abstract representations help with decision making and the hierarchy tree top-down building approach can reduce assignments errors in real practice.
Neural Flow Map Reconstruction
(The Eurographics Association and John Wiley & Sons Ltd., 2022) Sahoo, Saroj; Lu, Yuzhe; Berger, Matthew; Borgo, Rita; Marai, G. Elisabeta; Schreck, Tobias
In this paper we present a reconstruction technique for the reduction of unsteady flow data based on neural representations of time-varying vector fields. Our approach is motivated by the large amount of data typically generated in numerical simulations, and in turn the types of data that domain scientists can generate in situ that are compact, yet useful, for post hoc analysis. One type of data commonly acquired during simulation are samples of the flow map, where a single sample is the result of integrating the underlying vector field for a specified time duration. In our work, we treat a collection of flow map samples for a single dataset as a meaningful, compact, and yet incomplete, representation of unsteady flow, and our central objective is to find a representation that enables us to best recover arbitrary flow map samples. To this end, we introduce a technique for learning implicit neural representations of time-varying vector fields that are specifically optimized to reproduce flow map samples sparsely covering the spatiotemporal domain of the data. We show that, despite aggressive data reduction, our optimization problem - learning a function-space neural network to reproduce flow map samples under a fixed integration scheme - leads to representations that demonstrate strong generalization, both in the field itself, and using the field to approximate the flow map. Through quantitative and qualitative analysis across different datasets we show that our approach is an improvement across a variety of data reduction methods, and across a variety of measures ranging from improved vector fields, flow maps, and features derived from the flow map.
Implicit Modeling of Patient-Specific Aortic Dissections with Elliptic Fourier Descriptors
(The Eurographics Association and John Wiley & Sons Ltd., 2021) Mistelbauer, Gabriel; Rössl, Christian; Bäumler, Kathrin; Preim, Bernhard; Fleischmann, Dominik; Borgo, Rita and Marai, G. Elisabeta and Landesberger, Tatiana von
Aortic dissection is a life-threatening vascular disease characterized by abrupt formation of a new flow channel (false lumen) within the aortic wall. Survivors of the acute phase remain at high risk for late complications, such as aneurysm formation, rupture, and death. Morphologic features of aortic dissection determine not only treatment strategies in the acute phase (surgical vs. endovascular vs. medical), but also modulate the hemodynamics in the false lumen, ultimately responsible for late complications. Accurate description of the true and false lumen, any communications across the dissection membrane separating the two lumina, and blood supply from each lumen to aortic branch vessels is critical for risk prediction. Patient-specific surface representations are also a prerequisite for hemodynamic simulations, but currently require time-consuming manual segmentation of CT data. We present an aortic dissection cross-sectional model that captures the varying aortic anatomy, allowing for reliable measurements and creation of high-quality surface representations. In contrast to the traditional spline-based cross-sectional model, we employ elliptic Fourier descriptors, which allows users to control the accuracy of the cross-sectional contour of a flow channel. We demonstrate (i) how our approach can solve the requirements for generating surface and wall representations of the flow channels, (ii) how any number of communications between flow channels can be specified in a consistent manner, and (iii) how well branches connected to the respective flow channels are handled. Finally, we discuss how our approach is a step forward to an automated generation of surface models for aortic dissections from raw 3D imaging segmentation masks.
Curve Complexity Heuristic KD-trees for Neighborhood-based Exploration of 3D Curves
(The Eurographics Association and John Wiley & Sons Ltd., 2021) Lu, Yucheng; Cheng, Luyu; Isenberg, Tobias; Fu, Chi-Wing; Chen, Guoning; Liu, Hui; Deussen, Oliver; Wang, Yunhai; Mitra, Niloy and Viola, Ivan
We introduce the curve complexity heuristic (CCH), a KD-tree construction strategy for 3D curves, which enables interactive exploration of neighborhoods in dense and large line datasets. It can be applied to searches of k-nearest curves (KNC) as well as radius-nearest curves (RNC). The CCH KD-tree construction consists of two steps: (i) 3D curve decomposition that takes into account curve complexity and (ii) KD-tree construction, which involves a novel splitting and early termination strategy. The obtained KD-tree allows us to improve the speed of existing neighborhood search approaches by at least an order of magnitude (i. e., 28× for KNC and 12× for RNC with 98% accuracy) by considering local curve complexity. We validate this performance with a quantitative evaluation of the quality of search results and computation time. Also, we demonstrate the usefulness of our approach for supporting various applications such as interactive line queries, line opacity optimization, and line abstraction.
SurfNet: Learning Surface Representations via Graph Convolutional Network
(The Eurographics Association and John Wiley & Sons Ltd., 2022) Han, Jun; Wang, Chaoli; Borgo, Rita; Marai, G. Elisabeta; Schreck, Tobias
For scientific visualization applications, understanding the structure of a single surface (e.g., stream surface, isosurface) and selecting representative surfaces play a crucial role. In response, we propose SurfNet, a graph-based deep learning approach for representing a surface locally at the node level and globally at the surface level. By treating surfaces as graphs, we leverage a graph convolutional network to learn node embedding on a surface. To make the learned embedding effective, we consider various pieces of information (e.g., position, normal, velocity) for network input and investigate multiple losses. Furthermore, we apply dimensionality reduction to transform the learned embeddings into 2D space for understanding and exploration. To demonstrate the effectiveness of SurfNet, we evaluate the embeddings in node clustering (node-level) and surface selection (surface-level) tasks. We compare SurfNet against state-of-the-art node embedding approaches and surface selection methods. We also demonstrate the superiority of SurfNet by comparing it against a spectral-based mesh segmentation approach. The results show that SurfNet can learn better representations at the node and surface levels with less training time and fewer training samples while generating comparable or better clustering and selection results.
GO-Compass: Visual Navigation of Multiple Lists of GO terms
(The Eurographics Association and John Wiley & Sons Ltd., 2023) Harbig, Theresa; Witte Paz, Mathias; Nieselt, Kay; Bujack, Roxana; Archambault, Daniel; Schreck, Tobias
Analysis pipelines in genomics, transcriptomics, and proteomics commonly produce lists of genes, e.g., differentially expressed genes. Often these lists overlap only partly or not at all and contain too many genes for manual comparison. However, using background knowledge, such as the functional annotations of the genes, the lists can be abstracted to functional terms. One approach is to run Gene Ontology (GO) enrichment analyses to determine over- and/or underrepresented functions for every list of genes. Due to the hierarchical structure of the Gene Ontology, lists of enriched GO terms can contain many closely related terms, rendering the lists still long, redundant, and difficult to interpret for researchers. In this paper, we present GO-Compass (Gene Ontology list comparison using Semantic Similarity), a visual analytics tool for the dispensability reduction and visual comparison of lists of GO terms. For dispensability reduction, we adapted the REVIGO algorithm, a summarization method based on the semantic similarity of GO terms, to perform hierarchical dispensability clustering on multiple lists. In an interactive dashboard, GO-Compass offers several visualizations for the comparison and improved interpretability of GO terms lists. The hierarchical dispensability clustering is visualized as a tree, where users can interactively filter out dispensable GO terms and create flat clusters by cutting the tree at a chosen dispensability. The flat clusters are visualized in animated treemaps and are compared using a correlation heatmap, UpSet plots, and bar charts. With two use cases on published datasets from different omics domains, we demonstrate the general applicability and effectiveness of our approach. In the first use case, we show how the tool can be used to compare lists of differentially expressed genes from a transcriptomics pipeline and incorporate gene information into the analysis. In the second use case using genomics data, we show how GO-Compass facilitates the analysis of many hundreds of GO terms. For qualitative evaluation of the tool, we conducted feedback sessions with five domain experts and received positive comments. GO-Compass is part of the Tue- Vis Visualization Server as a web application available at https://go-compass-tuevis.cs.uni-tuebingen.de/
Progressive Rendering of Transparent Integral Surfaces
(The Eurographics Association, 2020) Tian, Xingze; Günther, Tobias; Kerren, Andreas and Garth, Christoph and Marai, G. Elisabeta
Integral surfaces are a useful method in illustrative and geometry-based flow visualization, as they convey shading, depth and geometric information better than their line-based counterparts. However, they are not as frequently used as line-based techniques due to the added complexity that arises from their computation. Frontline-based methods, such as stream surfaces and path surfaces require an adaptive subdivision of the frontline, whereas advected surfaces, such as streak surfaces and time surfaces, require refinement and possibly retriangulation of the entire surface after each time step. In this paper, we extend an image-space surface rendering technique to support transparency, which enables the application of illustrative surface rendering techniques without the need to adaptively refine frontlines or entire surfaces. We develop a pixel-based dynamic tree data structure that is progressively filled with integral curves and compactly stores the transparent layers arising in the rendering of the surfaces. We apply the method to the illustrative rendering of path surfaces and streak surfaces in a number of time-dependent vector fields.
Efficient High-Quality Rendering of Ribbons and Twisted Lines
(The Eurographics Association, 2022) Neuhauser, Christoph; Wang, Junpeng; Kern, Michael; Westermann, Rüdiger; Bender, Jan; Botsch, Mario; Keim, Daniel A.
Flat twisting ribbons are often used for visualizing twists along lines in 3D space. Flat ribbons can disappear when looking at them under oblique angles, and they introduce flickering due to aliasing during animations. We demonstrate that this limitation can be overcome by procedurally rendering generalized cylinders with elliptic profiles. By adjusting the length of the cylinder's semi-minor axis, the ribbon thickness can be controlled so that it always remains visible. The proposed rendering approach further enables the visualization of twists via the projection of a line spiralling around the cylinder's center line. In contrast to texture mapping, this keeps the line width fixed, regardless of the strength of the twist, and provides efficient control over the spiralling frequency and coloring between the twisting lines. The proposed rendering approach can be performed efficiently on recent GPUs by exploiting programmable pulling, mesh shaders and hardware-accelerated ray tracing.
4D Exploring System for Intuitive Understanding of 4D Space by Extending Familiar 3D Interfaces
(The Eurographics Association, 2023) Igarashi, Haruo; Sawada, Hideyuki; Jean-Marie Normand; Maki Sugimoto; Veronica Sundstedt
With the advancement of VR technology and the increasing demand for high-dimensional data, a variety of intuitive visualization and interaction methods for high-dimensional data have been proposed. In this paper, we propose a new 4D space interaction system aimed at not only being more intuitive but also making it easier for non-experts to understand 4D space. The proposed system functions as a familiar system for exploring 3D space, and when exploring the 4D space, a user is able to directly leverage the operations used for navigating the 3D space. This feature is achieved through a combination of displaying crosssections of 4D space by slicing through 3D screens and intuitive operation using motion controllers. By moving back and forth between exploring the 4D space and the 3D cross-sections, a user can observe and experience the relationships, aiding in the understanding of 4D space. From the maze exploration experiments, not only were promising results obtained, but interesting insights were also garnered regarding the field of high-dimensional space perception, an area with many unresolved aspects.

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