DevLan/vispubs huggingface dataset:
Hairy Slices: Evaluating the Perceptual Effectiveness of Cutting Plane Glyphs for 3D Vector Fields
Authors: Andrew H. Stevens, Thomas Butkiewicz, Colin Ware
Published at SciVis, 2016

Three-dimensional vector fields are common datasets throughout the sciences. Visualizing these fields is inherently difficult due to issues such as visual clutter and self-occlusion. Cutting planes are often used to overcome these issues by presenting more manageable slices of data. The existing literature provides many techniques for visualizing the flow through these cutting planes; however, there is a lack of empirical studies focused on the underlying perceptual cues that make popular techniques successful. This paper presents a quantitative human factors study that evaluates static monoscopic depth and orientation cues in the context of cutting plane glyph designs for exploring and analyzing 3D flow fields. The goal of the study was to ascertain the relative effectiveness of various techniques for portraying the direction of flow through a cutting plane at a given point, and to identify the visual cues and combinations of cues involved, and how they contribute to accurate performance. It was found that increasing the dimensionality of line-based glyphs into tubular structures enhances their ability to convey orientation through shading, and that increasing their diameter intensifies this effect. These tube-based glyphs were also less sensitive to visual clutter issues at higher densities. Adding shadows to lines was also found to increase perception of flow direction. Implications of the experimental results are discussed and extrapolated into a number of guidelines for designing more perceptually effective glyphs for 3D vector field visualizations.
Hybrid Tactile/Tangible Interaction for 3D Data Exploration
Authors: Lonni Besançon, Paul Issartel, Mehdi Ammi, Tobias Isenberg 0001
Published at SciVis, 2016

We present the design and evaluation of an interface that combines tactile and tangible paradigms for 3D visualization. While studies have demonstrated that both tactile and tangible input can be efficient for a subset of 3D manipulation tasks, we reflect here on the possibility to combine the two complementary input types. Based on a field study and follow-up interviews, we present a conceptual framework of the use of these different interaction modalities for visualization both separately and combined-focusing on free exploration as well as precise control. We present a prototypical application of a subset of these combined mappings for fluid dynamics data visualization using a portable, position-aware device which offers both tactile input and tangible sensing. We evaluate our approach with domain experts and report on their qualitative feedback.
In Situ Distribution Guided Analysis and Visualization of Transonic Jet Engine Simulations
Authors: Soumya Dutta, Chun-Ming Chen, Gregory Heinlein, Han-Wei Shen, Jen-Ping Chen
Published at SciVis, 2016

Study of flow instability in turbine engine compressors is crucial to understand the inception and evolution of engine stall. Aerodynamics experts have been working on detecting the early signs of stall in order to devise novel stall suppression technologies. A state-of-the-art Navier-Stokes based, time-accurate computational fluid dynamics simulator, TURBO, has been developed in NASA to enhance the understanding of flow phenomena undergoing rotating stall. Despite the proven high modeling accuracy of TURBO, the excessive simulation data prohibits post-hoc analysis in both storage and I/O time. To address these issues and allow the expert to perform scalable stall analysis, we have designed an in situ distribution guided stall analysis technique. Our method summarizes statistics of important properties of the simulation data in situ using a probabilistic data modeling scheme. This data summarization enables statistical anomaly detection for flow instability in post analysis, which reveals the spatiotemporal trends of rotating stall for the expert to conceive new hypotheses. Furthermore, the verification of the hypotheses and exploratory visualization using the summarized data are realized using probabilistic visualization techniques such as uncertain isocontouring. Positive feedback from the domain scientist has indicated the efficacy of our system in exploratory stall analysis.
Jacobi Fiber Surfaces for Bivariate Reeb Space Computation
Authors: Julien Tierny, Hamish A. Carr
Published at SciVis, 2016

This paper presents an efficient algorithm for the computation of the Reeb space of an input bivariate piecewise linear scalar function f defined on a tetrahedral mesh. By extending and generalizing algorithmic concepts from the univariate case to the bivariate one, we report the first practical, output-sensitive algorithm for the exact computation of such a Reeb space. The algorithm starts by identifying the Jacobi set of f, the bivariate analogs of critical points in the univariate case. Next, the Reeb space is computed by segmenting the input mesh along the new notion of Jacobi Fiber Surfaces, the bivariate analog of critical contours in the univariate case. We additionally present a simplification heuristic that enables the progressive coarsening of the Reeb space. Our algorithm is simple to implement and most of its computations can be trivially parallelized. We report performance numbers demonstrating orders of magnitude speedups over previous approaches, enabling for the first time the tractable computation of bivariate Reeb spaces in practice. Moreover, unlike range-based quantization approaches (such as the Joint Contour Net), our algorithm is parameter-free. We demonstrate the utility of our approach by using the Reeb space as a semi-automatic segmentation tool for bivariate data. In particular, we introduce continuous scatterplot peeling, a technique which enables the reduction of the cluttering in the continuous scatterplot, by interactively selecting the features of the Reeb space to project. We provide a VTK-based C++ implementation of our algorithm that can be used for reproduction purposes or for the development of new Reeb space based visualization techniques.
Molecular Surface Maps
Authors: Michael Krone, Florian Frieß, Katrin Scharnowski, Guido Reina, Silvia Fademrecht, Tobias Kulschewski, Jürgen Pleiss, Thomas Ertl
Published at SciVis, 2016

We present Molecular Surface Maps, a novel, view-independent, and concise representation for molecular surfaces. It transfers the well-known world map metaphor to molecular visualization. Our application maps the complex molecular surface to a simple 2D representation through a spherical intermediate, the Molecular Surface Globe. The Molecular Surface Map concisely shows arbitrary attributes of the original molecular surface, such as biochemical properties or geometrical features. This results in an intuitive overview, which allows researchers to assess all molecular surface attributes at a glance. Our representation can be used as a visual summarization of a molecule's interface with its environment. In particular, Molecular Surface Maps simplify the analysis and comparison of different data sets or points in time. Furthermore, the map representation can be used in a Space-time Cube to analyze time-dependent data from molecular simulations without the need for animation. We show the feasibility of Molecular Surface Maps for different typical analysis tasks of biomolecular data.
OSPRay - A CPU Ray Tracing Framework for Scientific Visualization
Authors: Ingo Wald, Gregory P. Johnson, Jefferson Amstutz, Carson Brownlee, Aaron Knoll, Jim Jeffers, Johannes Günther 0001, Paul A. Navrátil
Published at SciVis, 2016

Scientific data is continually increasing in complexity, variety and size, making efficient visualization and specifically rendering an ongoing challenge. Traditional rasterization-based visualization approaches encounter performance and quality limitations, particularly in HPC environments without dedicated rendering hardware. In this paper, we present OSPRay, a turn-key CPU ray tracing framework oriented towards production-use scientific visualization which can utilize varying SIMD widths and multiple device backends found across diverse HPC resources. This framework provides a high-quality, efficient CPU-based solution for typical visualization workloads, which has already been integrated into several prevalent visualization packages. We show that this system delivers the performance, high-level API simplicity, and modular device support needed to provide a compelling new rendering framework for implementing efficient scientific visualization workflows.
PelVis: Atlas-based Surgical Planning for Oncological Pelvic Surgery
Authors: Noeska N. Smit, Kai Lawonn, Annelot Kraima, Marco C. DeRuiter, Hessam Sokooti, Stefan Bruckner, Elmar Eisemann, Anna Vilanova
Published at SciVis, 2016

Due to the intricate relationship between the pelvic organs and vital structures, such as vessels and nerves, pelvic anatomy is often considered to be complex to comprehend. In oncological pelvic surgery, a trade-off has to be made between complete tumor resection and preserving function by preventing damage to the nerves. Damage to the autonomic nerves causes undesirable post-operative side-effects such as fecal and urinal incontinence, as well as sexual dysfunction in up to 80 percent of the cases. Since these autonomic nerves are not visible in pre-operative MRI scans or during surgery, avoiding nerve damage during such a surgical procedure becomes challenging. In this work, we present visualization methods to represent context, target, and risk structures for surgical planning. We employ distance-based and occlusion management techniques in an atlas-based surgical planning tool for oncological pelvic surgery. Patient-specific pre-operative MRI scans are registered to an atlas model that includes nerve information. Through several interactive linked views, the spatial relationships and distances between the organs, tumor and risk zones are visualized to improve understanding, while avoiding occlusion. In this way, the surgeon can examine surgically relevant structures and plan the procedure before going into the operating theater, thus raising awareness of the autonomic nerve zone regions and potentially reducing post-operative complications. Furthermore, we present the results of a domain expert evaluation with surgical oncologists that demonstrates the advantages of our approach.
Physics-Based Visual Characterization of Molecular Interaction Forces
Authors: Pedro Hermosilla, Jorge Estrada, Victor Guallar, Timo Ropinski, Àlvar Vinacua, Pere-Pau Vázquez
Published at SciVis, 2016

Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.
Progressive Direct Volume-to-Volume Transformation
Authors: Steffen Frey, Thomas Ertl
Published at SciVis, 2016

We present a novel technique to generate transformations between arbitrary volumes, providing both expressive distances and smooth interpolates. In contrast to conventional morphing or warping approaches, our technique requires no user guidance, intermediate representations (like extracted features), or blending, and imposes no restrictions regarding shape or structure. Our technique operates directly on the volumetric data representation, and while linear programming approaches could solve the underlying problem optimally, their polynomial complexity makes them infeasible for high-resolution volumes. We therefore propose a progressive refinement approach designed for parallel execution that is able to quickly deliver approximate results that are iteratively improved toward the optimum. On this basis, we further present a new approach for the streaming selection of time steps in temporal data that allows for the reconstruction of the full sequence with a user-specified error bound. We finally demonstrate the utility of our technique for different applications, compare our approach against alternatives, and evaluate its characteristics with a variety of different data sets.
Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution
Authors: Chris Bryan, Gregory Guterman, Kwan-Liu Ma, Harris A. Lewin, Denis M. Larkin, Jaebum Kim, Jian Ma 0004, Marta Farre
Published at SciVis, 2016

Rapid advances in biology demand new tools for more active research dissemination and engaged teaching. This paper presents Synteny Explorer, an interactive visualization application designed to let college students explore genome evolution of mammalian species. The tool visualizes synteny blocks: segments of homologous DNA shared between various extant species that can be traced back or reconstructed in extinct, ancestral species. We take a karyogram-based approach to create an interactive synteny visualization, leading to a more appealing and engaging design for undergraduate-level genome evolution education. For validation, we conduct three user studies: two focused studies on color and animation design choices and a larger study that performs overall system usability testing while comparing our karyogram-based designs with two more common genome mapping representations in an educational context. While existing views communicate the same information, study participants found the interactive, karyogram-based views much easier and likable to use. We additionally discuss feedback from biology and genomics faculty, who judge Synteny Explorer's fitness for use in classrooms.
Time-Hierarchical Clustering and Visualization of Weather Forecast Ensembles
Authors: Florian Ferstl, Mathias Kanzler, Marc Rautenhaus, Rüdiger Westermann
Published at SciVis, 2016

We propose a new approach for analyzing the temporal growth of the uncertainty in ensembles of weather forecasts which are started from perturbed but similar initial conditions. As an alternative to traditional approaches in meteorology, which use juxtaposition and animation of spaghetti plots of iso-contours, we make use of contour clustering and provide means to encode forecast dynamics and spread in one single visualization. Based on a given ensemble clustering in a specified time window, we merge clusters in time-reversed order to indicate when and where forecast trajectories start to diverge. We present and compare different visualizations of the resulting time-hierarchical grouping, including space-time surfaces built by connecting cluster representatives over time, and stacked contour variability plots. We demonstrate the effectiveness of our visual encodings with forecast examples of the European Centre for Medium-Range Weather Forecasts, which convey the evolution of specific features in the data as well as the temporally increasing spatial variability.
Topological Analysis of Inertial Dynamics
Authors: Antoni Sagristà, Stefan Jordan, Andreas Just, Fabio Dias, Luis Gustavo Nonato, Filip Sadlo
Published at SciVis, 2016

Traditional vector field visualization has a close focus on velocity, and is typically constrained to the dynamics of massless particles. In this paper, we present a novel approach to the analysis of the force-induced dynamics of inertial particles. These forces can arise from acceleration fields such as gravitation, but also be dependent on the particle dynamics itself, as in the case of magnetism. Compared to massless particles, the velocity of an inertial particle is not determined solely by its position and time in a vector field. In contrast, its initial velocity can be arbitrary and impacts the dynamics over its entire lifetime. This leads to a four-dimensional problem for 2D setups, and a six-dimensional problem for the 3D case. Our approach avoids this increase in dimensionality and tackles the visualization by an integrated topological analysis approach. We demonstrate the utility of our approach using a synthetic time-dependent acceleration field, a system of magnetic dipoles, and N-body systems both in 2D and 3D.
Urban Pulse: Capturing the Rhythm of Cities
Authors: Fabio Miranda 0001, Harish Doraiswamy, Marcos Lage, Kai Zhao, Bruno Gonçalves, Luc Wilson, Mondrian Hsieh, Cláudio T. Silva
Published at SciVis, 2016

Cities are inherently dynamic. Interesting patterns of behavior typically manifest at several key areas of a city over multiple temporal resolutions. Studying these patterns can greatly help a variety of experts ranging from city planners and architects to human behavioral experts. Recent technological innovations have enabled the collection of enormous amounts of data that can help in these studies. However, techniques using these data sets typically focus on understanding the data in the context of the city, thus failing to capture the dynamic aspects of the city. The goal of this work is to instead understand the city in the context of multiple urban data sets. To do so, we define the concept of an “urban pulse” which captures the spatio-temporal activity in a city across multiple temporal resolutions. The prominent pulses in a city are obtained using the topology of the data sets, and are characterized as a set of beats. The beats are then used to analyze and compare different pulses. We also design a visual exploration framework that allows users to explore the pulses within and across multiple cities under different conditions. Finally, we present three case studies carried out by experts from two different domains that demonstrate the utility of our framework.
Visualization and Extraction of Carvings for Heritage Conservation
Authors: Kai Lawonn, Erik Trostmann, Bernhard Preim, Klaus Hildebrandt
Published at SciVis, 2016

We present novel techniques for visualizing, illustrating, analyzing, and generating carvings in surfaces. In particular, we consider the carvings in the plaster of the cloister of the Magdeburg cathedral, which dates to the 13th century. Due to aging and weathering, the carvings have flattened. Historians and restorers are highly interested in using digitalization techniques to analyze carvings in historic artifacts and monuments and to get impressions and illustrations of their original shape and appearance. Moreover, museums and churches are interested in such illustrations for presenting them to visitors. The techniques that we propose allow for detecting, selecting, and visualizing carving structures. In addition, we introduce an example-based method for generating carvings. The resulting tool, which integrates all techniques, was evaluated by three experienced restorers to assess the usefulness and applicability. Furthermore, we compared our approach with exaggerated shading and other state-of-the-art methods.
Visualization as Seen through its Research Paper Keywords
Authors: Petra Isenberg, Tobias Isenberg 0001, Michael Sedlmair, Jian Chen 0006, Torsten Möller
Published at SciVis, 2016

We present the results of a comprehensive multi-pass analysis of visualization paper keywords supplied by authors for their papers published in the IEEE Visualization conference series (now called IEEE VIS) between 1990-2015. From this analysis we derived a set of visualization topics that we discuss in the context of the current taxonomy that is used to categorize papers and assign reviewers in the IEEE VIS reviewing process. We point out missing and overemphasized topics in the current taxonomy and start a discussion on the importance of establishing common visualization terminology. Our analysis of research topics in visualization can, thus, serve as a starting point to (a) help create a common vocabulary to improve communication among different visualization sub-groups, (b) facilitate the process of understanding differences and commonalities of the various research sub-fields in visualization, (c) provide an understanding of emerging new research trends, (d) facilitate the crucial step of finding the right reviewers for research submissions, and (e) it can eventually lead to a comprehensive taxonomy of visualization research. One additional tangible outcome of our work is an online query tool (http://keyvis.org/) that allows visualization researchers to easily browse the 3952 keywords used for IEEE VIS papers since 1990 to find related work or make informed keyword choices.
Visualization of Time-Varying Weather Ensembles across Multiple Resolutions
Authors: Ayan Biswas, Guang Lin, Xiaotong Liu, Han-Wei Shen
Published at SciVis, 2016

Uncertainty quantification in climate ensembles is an important topic for the domain scientists, especially for decision making in the real-world scenarios. With powerful computers, simulations now produce time-varying and multi-resolution ensemble data sets. It is of extreme importance to understand the model sensitivity given the input parameters such that more computation power can be allocated to the parameters with higher influence on the output. Also, when ensemble data is produced at different resolutions, understanding the accuracy of different resolutions helps the total time required to produce a desired quality solution with improved storage and computation cost. In this work, we propose to tackle these non-trivial problems on the Weather Research and Forecasting (WRF) model output. We employ a moment independent sensitivity measure to quantify and analyze parameter sensitivity across spatial regions and time domain. A comparison of clustering structures across three resolutions enables the users to investigate the sensitivity variation over the spatial regions of the five input parameters. The temporal trend in the sensitivity values is explored via an MDS view linked with a line chart for interactive brushing. The spatial and temporal views are connected to provide a full exploration system for complete spatio-temporal sensitivity analysis. To analyze the accuracy across varying resolutions, we formulate a Bayesian approach to identify which regions are better predicted at which resolutions compared to the observed precipitation. This information is aggregated over the time domain and finally encoded in an output image through a custom color map that guides the domain experts towards an adaptive grid implementation given a cost model. Users can select and further analyze the spatial and temporal error patterns for multi-resolution accuracy analysis via brushing and linking on the produced image. In this work, we collaborate with a domain expert whose feedback shows the effectiveness of our proposed exploration work-flow.