DevLan/vispubs huggingface dataset:
Interactive Visualization of RNA and DNA Structures
Authors: Norbert Lindow, Daniel Baum, Morgan Leborgne, Hans-Christian Hege
Published at SciVis, 2018

The analysis and visualization of nucleic acids (RNA and DNA) is playing an increasingly important role due to their fundamental importance for all forms of life and the growing number of known 3D structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. We present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables for the first time real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization.
Labels on Levels: Labeling of Multi-Scale Multi-Instance and Crowded 3D Biological Environments
Authors: David Kouril, Ladislav Cmolík, Barbora Kozlíková, Hsiang-Yun Wu, Graham Johnson, David S. Goodsell, Arthur J. Olson, M. Eduard Gröller, Ivan Viola
Published at SciVis, 2018

Labeling is intrinsically important for exploring and understanding complex environments and models in a variety of domains. We present a method for interactive labeling of crowded 3D scenes containing very many instances of objects spanning multiple scales in size. In contrast to previous labeling methods, we target cases where many instances of dozens of types are present and where the hierarchical structure of the objects in the scene presents an opportunity to choose the most suitable level for each placed label. Our solution builds on and goes beyond labeling techniques in medical 3D visualization, cartography, and biological illustrations from books and prints. In contrast to these techniques, the main characteristics of our new technique are: 1) a novel way of labeling objects as part of a bigger structure when appropriate, 2) visual clutter reduction by labeling only representative instances for each type of an object, and a strategy of selecting those. The appropriate level of label is chosen by analyzing the scene's depth buffer and the scene objects' hierarchy tree. We address the topic of communicating the parent-children relationship between labels by employing visual hierarchy concepts adapted from graphic design. Selecting representative instances considers several criteria tailored to the character of the data and is combined with a greedy optimization approach. We demonstrate the usage of our method with models from mesoscale biology where these two characteristics-multi-scale and multi-instance-are abundant, along with the fact that these scenes are extraordinarily dense.
Objective Vortex Corelines of Finite-sized Objects in Fluid Flows
Authors: Tobias Günther, Holger Theisel
Published at SciVis, 2018

Vortices are one of the most-frequently studied phenomena in fluid flows. The center of the rotating motion is called the vortex coreline and its successful detection strongly depends on the choice of the reference frame. The optimal frame moves with the center of the vortex, which incidentally makes the observed fluid flow steady and thus standard vortex coreline extractors such as Sujudi-Haimes become applicable. Recently, an objective optimization framework was proposed that determines a near-steady reference frame for tracer particles. In this paper, we extend this technique to the detection of vortex corelines of inertial particles. An inertial particle is a finite-sized object that is carried by a fluid flow. In contrast to the usual tracer particles, they do not move tangentially with the flow, since they are subject to gravity and exhibit mass-dependent inertia. Their particle state is determined by their position and own velocity, which makes the search for the optimal frame a high-dimensional problem. We demonstrate in this paper that the objective detection of an inertial vortex coreline can be reduced in 2D to a critical point search in 2D. For 3D flows, however, the vortex coreline criterion remains a parallel vectors condition in 6D. To detect the vortex corelines we propose a recursive subdivision approach that is tailored to the underlying structure of the 6D vectors. The resulting algorithm is objective, and we demonstrate the vortex coreline extraction in a number of 2D and 3D vector fields.
Persistence Atlas for Critical Point Variability in Ensembles
Authors: Guillaume Favelier, Noura Faraj, Brian Summa, Julien Tierny
Published at SciVis, 2018

This paper presents a new approach for the visualization and analysis of the spatial variability of features of interest represented by critical points in ensemble data. Our framework, called Persistence Atlas, enables the visualization of the dominant spatial patterns of critical points, along with statistics regarding their occurrence in the ensemble. The persistence atlas represents in the geometrical domain each dominant pattern in the form of a confidence map for the appearance of critical points. As a by-product, our method also provides 2-dimensional layouts of the entire ensemble, highlighting the main trends at a global level. Our approach is based on the new notion of Persistence Map, a measure of the geometrical density in critical points which leverages the robustness to noise of topological persistence to better emphasize salient features. We show how to leverage spectral embedding to represent the ensemble members as points in a low-dimensional Euclidean space, where distances between points measure the dissimilarities between critical point layouts and where statistical tasks, such as clustering, can be easily carried out. Further, we show how the notion of mandatory critical point can be leveraged to evaluate for each cluster confidence regions for the appearance of critical points. Most of the steps of this framework can be trivially parallelized and we show how to efficiently implement them. Extensive experiments demonstrate the relevance of our approach. The accuracy of the confidence regions provided by the persistence atlas is quantitatively evaluated and compared to a baseline strategy using an off-the-shelf clustering approach. We illustrate the importance of the persistence atlas in a variety of real-life datasets, where clear trends in feature layouts are identified and analyzed. We provide a lightweight VTK-based C++ implementation of our approach that can be used for reproduction purposes.
Probabilistic Asymptotic Decider for Topological Ambiguity Resolution in Level-Set Extraction for Uncertain 2D Data
Authors: Tushar M. Athawale, Christopher R. Johnson 0001
Published at SciVis, 2018

We present a framework for the analysis of uncertainty in isocontour extraction. The marching squares (MS) algorithm for isocontour reconstruction generates a linear topology that is consistent with hyperbolic curves of a piecewise bilinear interpolation. The saddle points of the bilinear interpolant cause topological ambiguity in isocontour extraction. The midpoint decider and the asymptotic decider are well-known mathematical techniques for resolving topological ambiguities. The latter technique investigates the data values at the cell saddle points for ambiguity resolution. The uncertainty in data, however, leads to uncertainty in underlying bilinear interpolation functions for the MS algorithm, and hence, their saddle points. In our work, we study the behavior of the asymptotic decider when data at grid vertices is uncertain. First, we derive closed-form distributions characterizing variations in the saddle point values for uncertain bilinear interpolants. The derivation assumes uniform and nonparametric noise models, and it exploits the concept of ratio distribution for analytic formulations. Next, the probabilistic asymptotic decider is devised for ambiguity resolution in uncertain data using distributions of the saddle point values derived in the first step. Finally, the confidence in probabilistic topological decisions is visualized using a colormapping technique. We demonstrate the higher accuracy and stability of the probabilistic asymptotic decider in uncertain data with regard to existing decision frameworks, such as deciders in the mean field and the probabilistic midpoint decider, through the isocontour visualization of synthetic and real datasets.
Recirculation Surfaces for Flow Visualization
Authors: Thomas Wilde, Christian Rössl, Holger Theisel
Published at SciVis, 2018

We present a formal approach to the visual analysis of recirculation in flows by introducing recirculation surfaces for 3D unsteady flow fields. Recirculation surfaces are the loci where massless particle integration returns to its starting point after some variable, finite integration. We give a rigorous definition of recirculation surfaces as 2-manifolds embedded in 5D space and study their properties. Based on this we construct an algorithm for their extraction, which searches for intersections of a recirculation surface with lines defined in 3D. This reduces the problem to a repeated search for critical points in 3D vector fields. We provide a uniform sampling of the search space paired with a surface reconstruction and visualize results. This way, we present the first algorithm for a comprehensive feature extraction in the 5D flow map of a 3D flow. The problem of finding isolated closed orbits in steady vector fields occurs as a special case of recirculation surfaces. This includes isolated closed orbits with saddle behavior. We show recirculation surfaces for a number of artificial and real flow data sets.
Robust and Fast Extraction of 3D Symmetric Tensor Field Topology
Authors: Lawrence Roy, Prashant Kumar, Yue Zhang 0009, Eugene Zhang
Published at SciVis, 2018

3D symmetric tensor fields appear in many science and engineering fields, and topology-driven analysis is important in many of these application domains, such as solid mechanics and fluid dynamics. Degenerate curves and neutral surfaces are important topological features in 3D symmetric tensor fields. Existing methods to extract degenerate curves and neutral surfaces often miss parts of the curves and surfaces, respectively. Moreover, these methods are computationally expensive due to the lack of knowledge of structures of degenerate curves and neutral surfaces.&lt;;/p&gt; &lt;;p&gt;In this paper, we provide theoretical analysis on the geometric and topological structures of degenerate curves and neutral surfaces of 3D linear tensor fields. These structures lead to parameterizations for degenerate curves and neutral surfaces that can not only provide more robust extraction of these features but also incur less computational cost.&lt;;/p&gt; &lt;;p&gt;We demonstrate the benefits of our approach by applying our degenerate curve and neutral surface detection techniques to solid mechanics simulation data sets.
Shared-Memory Parallel Computation of Morse-Smale Complexes with Improved Accuracy
Authors: Attila Gyulassy, Peer-Timo Bremer, Valerio Pascucci
Published at SciVis, 2018

Topological techniques have proven to be a powerful tool in the analysis and visualization of large-scale scientific data. In particular, the Morse-Smale complex and its various components provide a rich framework for robust feature definition and computation. Consequently, there now exist a number of approaches to compute Morse-Smale complexes for large-scale data in parallel. However, existing techniques are based on discrete concepts which produce the correct topological structure but are known to introduce grid artifacts in the resulting geometry. Here, we present a new approach that combines parallel streamline computation with combinatorial methods to construct a high-quality discrete Morse-Smale complex. In addition to being invariant to the orientation of the underlying grid, this algorithm allows users to selectively build a subset of features using high-quality geometry. In particular, a user may specifically select which ascending/descending manifolds are reconstructed with improved accuracy, focusing computational effort where it matters for subsequent analysis. This approach computes Morse-Smale complexes for larger data than previously feasible with significant speedups. We demonstrate and validate our approach using several examples from a variety of different scientific domains, and evaluate the performance of our method.
Tensor Field Visualization using Fiber Surfaces of Invariant Space
Authors: Felix Raith, Christian Blecha, Thomas Nagel, Francesco Parisio, Olaf Kolditz, Fabian Günther, Markus Stommel, Gerik Scheuermann
Published at SciVis, 2018

Scientific visualization developed successful methods for scalar and vector fields. For tensor fields, however, effective, interactive visualizations are still missing despite progress over the last decades. We present a general approach for the generation of separating surfaces in symmetric, second-order, three-dimensional tensor fields. These surfaces are defined as fiber surfaces of the invariant space, i.e. as pre-images of surfaces in the range of a complete set of invariants. This approach leads to a generalization of the fiber surface algorithm by Klacansky et al. [16] to three dimensions in the range. This is due to the fact that the invariant space is three-dimensional for symmetric second-order tensors over a spatial domain. We present an algorithm for surface construction for simplicial grids in the domain and simplicial surfaces in the invariant space. We demonstrate our approach by applying it to stress fields from component design in mechanical engineering.
Time-Dependent Flow seen through Approximate Observer Killing Fields
Authors: Markus Hadwiger, Matej Mlejnek, Thomas Theußl, Peter Rautek
Published at SciVis, 2018

Flow fields are usually visualized relative to a global observer, i.e., a single frame of reference. However, often no global frame can depict all flow features equally well. Likewise, objective criteria for detecting features such as vortices often use either a global reference frame, or compute a separate frame for each point in space and time. We propose the first general framework that enables choosing a smooth trade-off between these two extremes. Using global optimization to minimize specific differential geometric properties, we compute a time-dependent observer velocity field that describes the motion of a continuous field of observers adapted to the input flow. This requires developing the novel notion of an observed time derivative. While individual observers are restricted to rigid motions, overall we compute an approximate Killing field, corresponding to almost-rigid motion. This enables continuous transitions between different observers. Instead of focusing only on flow features, we furthermore develop a novel general notion of visualizing how all observers jointly perceive the input field. This in fact requires introducing the concept of an observation time, with respect to which a visualization is computed. We develop the corresponding notions of observed stream, path, streak, and time lines. For efficiency, these characteristic curves can be computed using standard approaches, by first transforming the input field accordingly. Finally, we prove that the input flow perceived by the observer field is objective. This makes derived flow features, such as vortices, objective as well.
Visual Analysis of Aneurysm Data using Statistical Graphics
Authors: Monique Meuschke, Tobias Günther, Philipp Berg, Ralph Wickenhöfer, Bernhard Preim, Kai Lawonn
Published at SciVis, 2018

This paper presents a framework to explore multi-field data of aneurysms occurring at intracranial and cardiac arteries by using statistical graphics. The rupture of an aneurysm is often a fatal scenario, whereas during treatment serious complications for the patient can occur. Whether an aneurysm ruptures or whether a treatment is successful depends on the interaction of different morphological such as wall deformation and thickness, and hemodynamic attributes like wall shear stress and pressure. Therefore, medical researchers are very interested in better understanding these relationships. However, the required analysis is a time-consuming process, where suspicious wall regions are difficult to detect due to the time-dependent behavior of the data. Our proposed visualization framework enables medical researchers to efficiently assess aneurysm risk and treatment options. This comprises a powerful set of views including 2D and 3D depictions of the aneurysm morphology as well as statistical plots of different scalar fields. Brushing and linking aids the user to identify interesting wall regions and to understand the influence of different attributes on the aneurysm's state. Moreover, a visual comparison of pre- and post-treatment as well as different treatment options is provided. Our analysis techniques are designed in collaboration with domain experts, e.g., physicians, and we provide details about the evaluation.
Visual Analysis of Spatia-temporal Relations of Pairwise Attributes in Unsteady Flow
Authors: Marzieh Berenjkoub, Rodolfo Ostilla Monico, Robert S. Laramee, Guoning Chen
Published at SciVis, 2018

Despite significant advances in the analysis and visualization of unsteady flow, the interpretation of it's behavior still remains a challenge. In this work, we focus on the linear correlation and non-linear dependency of different physical attributes of unsteady flows to aid their study from a new perspective. Specifically, we extend the existing spatial correlation quantification, i.e. the Local Correlation Coefficient (LCC), to the spatio-temporal domain to study the correlation of attribute-pairs from both the Eulerian and Lagrangian views. To study the dependency among attributes, which need not be linear, we extend and compute the mutual information (MI) among attributes over time. To help visualize and interpret the derived correlation and dependency among attributes associated with a particle, we encode the correlation and dependency values on individual pathlines. Finally, to utilize the correlation and MI computation results to identify regions with interesting flow behavior, we propose a segmentation strategy of the flow domain based on the ranking of the strength of the attributes relations. We have applied our correlation and dependency metrics to a number of 2D and 3D unsteady flows with varying spatio-temporal kernel sizes to demonstrate and assess their effectiveness.
Visualization of Bubble Formation in Porous Media
Authors: Hui Zhang 0027, Steffen Frey, Holger Steeb, David Uribe, Thomas Ertl, Wenping Wang
Published at SciVis, 2018

We present a visualization approach for the analysis of CO2bubble-induced attenuation in porous rock formations. As a basis for this, we introduce customized techniques to extract CO2bubbles and their surrounding porous structure from X-ray computed tomography data (XCT) measurements. To understand how the structure of porous media influences the occurrence and the shape of formed bubbles, we automatically classify and relate them in terms of morphology and geometric features, and further directly support searching for promising porous structures. To allow for the meaningful direct visual comparison of bubbles and their structures, we propose a customized registration technique considering the bubble shape as well as its points of contact with the porous media surface. With our quantitative extraction of geometric bubble features, we further support the analysis as well as the creation of a physical model. We demonstrate that our approach was successfully used to answer several research questions in the domain, and discuss its high practical relevance to identify critical seismic characteristics of fluid-saturated rock that govern its capability to store CO2.
Visualization of Large Molecular Trajectories
Authors: David Duran, Pedro Hermosilla, Timo Ropinski, Barbora Kozlíková, Àlvar Vinacua, Pere-Pau Vázquez
Published at SciVis, 2018

The analysis of protein-ligand interactions is a time-intensive task. Researchers have to analyze multiple physico-chemical properties of the protein at once and combine them to derive conclusions about the protein-ligand interplay. Typically, several charts are inspected, and 3D animations can be played side-by-side to obtain a deeper understanding of the data. With the advances in simulation techniques, larger and larger datasets are available, with up to hundreds of thousands of steps. Unfortunately, such large trajectories are very difficult to investigate with traditional approaches. Therefore, the need for special tools that facilitate inspection of these large trajectories becomes substantial. In this paper, we present a novel system for visual exploration of very large trajectories in an interactive and user-friendly way. Several visualization motifs are automatically derived from the data to give the user the information about interactions between protein and ligand. Our system offers specialized widgets to ease and accelerate data inspection and navigation to interesting parts of the simulation. The system is suitable also for simulations where multiple ligands are involved. We have tested the usefulness of our tool on a set of datasets obtained from protein engineers, and we describe the expert feedback.
Visualization of Neuronal Structures in Wide-Field Microscopy Brain Images
Authors: Saeed Boorboor, Shreeraj Jadhav, Mala Ananth 0001, David Talmage, Lorna Role, Arie E. Kaufman
Published at SciVis, 2018

Wide-field microscopes are commonly used in neurobiology for experimental studies of brain samples. Available visualization tools are limited to electron, two-photon, and confocal microscopy datasets, and current volume rendering techniques do not yield effective results when used with wide-field data. We present a workflow for the visualization of neuronal structures in wide-field microscopy images of brain samples. We introduce a novel gradient-based distance transform that overcomes the out-of-focus blur caused by the inherent design of wide-field microscopes. This is followed by the extraction of the 3D structure of neurites using a multi-scale curvilinear filter and cell-bodies using a Hessian-based enhancement filter. The response from these filters is then applied as an opacity map to the raw data. Based on the visualization challenges faced by domain experts, our workflow provides multiple rendering modes to enable qualitative analysis of neuronal structures, which includes separation of cell-bodies from neurites and an intensity-based classification of the structures. Additionally, we evaluate our visualization results against both a standard image processing deconvolution technique and a confocal microscopy image of the same specimen. We show that our method is significantly faster and requires less computational resources, while producing high quality visualizations. We deploy our workflow in an immersive gigapixel facility as a paradigm for the processing and visualization of large, high-resolution, wide-field microscopy brain datasets.