DevLan/vispubs huggingface dataset:
Decision Graph Embedding for High-Resolution Manometry Diagnosis
Authors: Julian Kreiser, Alexander Hann, Eugen Zizer, Timo Ropinski
Published at SciVis, 2017

High-resolution manometry is an imaging modality which enables the categorization of esophageal motility disorders. Spatio-temporal pressure data along the esophagus is acquired using a tubular device and multiple test swallows are performed by the patient. Current approaches visualize these swallows as individual instances, despite the fact that aggregated metrics are relevant in the diagnostic process. Based on the current Chicago Classification, which serves as the gold standard in this area, we introduce a visualization supporting an efficient and correct diagnosis. To reach this goal, we propose a novel decision graph representing the Chicago Classification with workflow optimization in mind. Based on this graph, we are further able to prioritize the different metrics used during diagnosis and can exploit this prioritization in the actual data visualization. Thus, different disorders and their related parameters are directly represented and intuitively influence the appearance of our visualization. Within this paper, we introduce our novel visualization, justify the design decisions, and provide the results of a user study we performed with medical students as well as a domain expert. On top of the presented visualization, we further discuss how to derive a visual signature for individual patients that allows us for the first time to perform an intuitive comparison between subjects, in the form of small multiples.
Dynamic Load Balancing Based on Constrained K-D Tree Decomposition for Parallel Particle Tracing
Authors: Jiang Zhang 0002, Hanqi Guo 0001, Fan Hong, Xiaoru Yuan, Tom Peterka
Published at SciVis, 2017

We propose a dynamically load-balanced algorithm for parallel particle tracing, which periodically attempts to evenly redistribute particles across processes based on k-d tree decomposition. Each process is assigned with (1) a statically partitioned, axis-aligned data block that partially overlaps with neighboring blocks in other processes and (2) a dynamically determined k-d tree leaf node that bounds the active particles for computation; the bounds of the k-d tree nodes are constrained by the geometries of data blocks. Given a certain degree of overlap between blocks, our method can balance the number of particles as much as possible. Compared with other load-balancing algorithms for parallel particle tracing, the proposed method does not require any preanalysis, does not use any heuristics based on flow features, does not make any assumptions about seed distribution, does not move any data blocks during the run, and does not need any master process for work redistribution. Based on a comprehensive performance study up to 8K processes on a Blue Gene/Q system, the proposed algorithm outperforms baseline approaches in both load balance and scalability on various flow visualization and analysis problems.
Globe Browsing: Contextualized Spatio-Temporal Planetary Surface Visualization
Authors: Karl Bladin, Emil Axelsson, Erik Broberg, Carter Emmart, Patric Ljung, Alexander Bock 0002, Anders Ynnerman
Published at SciVis, 2017

Results of planetary mapping are often shared openly for use in scientific research and mission planning. In its raw format, however, the data is not accessible to non-experts due to the difficulty in grasping the context and the intricate acquisition process. We present work on tailoring and integration of multiple data processing and visualization methods to interactively contextualize geospatial surface data of celestial bodies for use in science communication. As our approach handles dynamic data sources, streamed from online repositories, we are significantly shortening the time between discovery and dissemination of data and results. We describe the image acquisition pipeline, the pre-processing steps to derive a 2.5D terrain, and a chunked level-of-detail, out-of-core rendering approach to enable interactive exploration of global maps and high-resolution digital terrain models. The results are demonstrated for three different celestial bodies. The first case addresses high-resolution map data on the surface of Mars. A second case is showing dynamic processes, such as concurrent weather conditions on Earth that require temporal datasets. As a final example we use data from the New Horizons spacecraft which acquired images during a single flyby of Pluto. We visualize the acquisition process as well as the resulting surface data. Our work has been implemented in the OpenSpace software [8], which enables interactive presentations in a range of environments such as immersive dome theaters, interactive touch tables, and virtual reality headsets.
Instant Construction and Visualization of Crowded Biological Environments
Authors: Tobias Klein, Ludovic Autin, Barbora Kozlíková, David S. Goodsell, Arthur J. Olson, M. Eduard Gröller, Ivan Viola
Published at SciVis, 2017

We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments distributed according to a Halton sequence. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.
Interactive Design and Visualization of Branched Covering Spaces
Authors: Lawrence Roy, Prashant Kumar, Sanaz Golbabaei, Yue Zhang 0009, Eugene Zhang
Published at SciVis, 2017

Branched covering spaces are a mathematical concept which originates from complex analysis and topology and has applications in tensor field topology and geometry remeshing. Given a manifold surface and an$N$-way rotational symmetry field, a branched covering space is a manifold surface that has an$N$-to-1 map to the original surface except at theramification points, which correspond to the singularities in the rotational symmetry field. Understanding the notion and mathematical properties of branched covering spaces is important to researchers in tensor field visualization and geometry processing, and their application areas. In this paper, we provide a framework to interactively design and visualize the branched covering space (BCS) of an input mesh surface and a rotational symmetry field defined on it. In our framework, the user can visualize not only the BCSs but also their construction process. In addition, our system allows the user to design the geometric realization of the BCS using mesh deformation techniques as well as connecting tubes. This enables the user to verify important facts about BCSs such as that they are manifold surfaces around singularities, as well as theRiemann-Hurwitz formulawhich relates the Euler characteristic of the BCS to that of the original mesh. Our system is evaluated by student researchers in scientific visualization and geometry processing as well as faculty members in mathematics at our university who teach topology. We include their evaluations and feedback in the paper.
Interactive Dynamic Volume Illumination with Refraction and Caustics
Authors: Jens G. Magnus, Stefan Bruckner
Published at SciVis, 2017

In recent years, significant progress has been made in developing high-quality interactive methods for realistic volume illumination. However, refraction - despite being an important aspect of light propagation in participating media - has so far only received little attention. In this paper, we present a novel approach for refractive volume illumination including caustics capable of interactive frame rates. By interleaving light and viewing ray propagation, our technique avoids memory-intensive storage of illumination information and does not require any precomputation. It is fully dynamic and all parameters such as light position and transfer function can be modified interactively without a performance penalty.
Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures
Authors: Haichao Miao, Elisa De Llano, Johannes Sorger, Yasaman Ahmadi, Tadija Kekic, Tobias Isenberg 0001, M. Eduard Gröller, Ivan Barisic, Ivan Viola
Published at SciVis, 2017

We present an approach to represent DNA nanostructures in varying forms of semantic abstraction, describe ways to smoothly transition between them, and thus create a continuous multiscale visualization and interaction space for applications in DNA nanotechnology. This new way of observing, interacting with, and creating DNA nanostructures enables domain experts to approach their work in any of the semantic abstraction levels, supporting both low-level manipulations and high-level visualization and modifications. Our approach allows them to deal with the increasingly complex DNA objects that they are designing, to improve their features, and to add novel functions in a way that no existing single-scale approach offers today. For this purpose we collaborated with DNA nanotechnology experts to design a set of ten semantic scales. These scales take the DNA's chemical and structural behavior into account and depict it from atoms to the targeted architecture with increasing levels of abstraction. To create coherence between the discrete scales, we seamlessly transition between them in a well-defined manner. We use special encodings to allow experts to estimate the nanoscale object's stability. We also add scale-adaptive interactions that facilitate the intuitive modification of complex structures at multiple scales. We demonstrate the applicability of our approach on an experimental use case. Moreover, feedback from our collaborating domain experts confirmed an increased time efficiency and certainty for analysis and modification tasks on complex DNA structures. Our method thus offers exciting new opportunities with promising applications in medicine and biotechnology.
On the Treatment of Field Quantities and Elemental Continuity in FEM Solutions
Authors: Ashok Jallepalli, Julia Docampo-Sánchez, Jennifer K. Ryan, Robert Haimes, Robert M. Kirby
Published at SciVis, 2017

As the finite element method (FEM) and the finite volume method (FVM), both traditional and high-order variants, continue their proliferation into various applied engineering disciplines, it is important that the visualization techniques and corresponding data analysis tools that act on the results produced by these methods faithfully represent the underlying data. To state this in another way: the interpretation of data generated by simulation needs to be consistent with the numerical schemes that underpin the specific solver technology. As the verifiable visualization literature has demonstrated: visual artifacts produced by the introduction of either explicit or implicit data transformations, such as data resampling, can sometimes distort or even obfuscate key scientific features in the data. In this paper, we focus on the handling of elemental continuity, which is often only$C^{0}$continuous or piecewise discontinuous, when visualizing primary or derived fields from FEM or FVM simulations. We demonstrate that traditional data handling and visualization of these fields introduce visual errors. In addition, we show how the use of the recently proposed line-SIAC filter provides a way of handling elemental continuity issues in an accuracy-conserving manner with the added benefit of casting the data in a smooth context even if the representation is element discontinuous.
Robust Detection and Visualization of Jet-Stream Core Lines in Atmospheric Flow
Authors: Michael Kern, Tim Hewson, Filip Sadlo, Rüdiger Westermann, Marc Rautenhaus
Published at SciVis, 2017

Jet-streams, their core lines and their role in atmospheric dynamics have been subject to considerable meteorological research since the first half of the twentieth century. Yet, until today no consistent automated feature detection approach has been proposed to identify jet-stream core lines from 3D wind fields. Such 3D core lines can facilitate meteorological analyses previously not possible. Although jet-stream cores can be manually analyzed by meteorologists in 2D as height ridges in the wind speed field, to the best of our knowledge no automated ridge detection approach has been applied to jet-stream core detection. In this work, we -a team of visualization scientists and meteorologists-propose a method that exploits directional information in the wind field to extract core lines in a robust and numerically less involved manner than traditional 3D ridge detection. For the first time, we apply the extracted 3D core lines to meteorological analysis, considering real-world case studies and demonstrating our method's benefits for weather forecasting and meteorological research.
Screen-Space Normal Distribution Function Caching for Consistent Multi-Resolution Rendering of Large Particle Data
Authors: Mohamed Ibrahim, Patrick Wickenhauser, Peter Rautek, Guido Reina, Markus Hadwiger
Published at SciVis, 2017

Molecular dynamics (MD) simulations are crucial to investigating important processes in physics and thermodynamics. The simulated atoms are usually visualized as hard spheres with Phong shading, where individual particles and their local density can be perceived well in close-up views. However, for large-scale simulations with 10 million particles or more, the visualization of large fields-of-view usually suffers from strong aliasing artifacts, because the mismatch between data size and output resolution leads to severe under-sampling of the geometry. Excessive super-sampling can alleviate this problem, but is prohibitively expensive. This paper presents a novel visualization method for large-scale particle data that addresses aliasing while enabling interactive high-quality rendering. We introduce the novel concept of screen-space normal distribution functions (S-NDFs) for particle data. S-NDFs represent the distribution of surface normals that map to a given pixel in screen space, which enables high-quality re-lighting without re-rendering particles. In order to facilitate interactive zooming, we cache S-NDFs in a screen-space mipmap (S-MIP). Together, these two concepts enable interactive, scale-consistent re-lighting and shading changes, as well as zooming, without having to re-sample the particle data. We show how our method facilitates the interactive exploration of real-world large-scale MD simulation data in different scenarios.
SparseLeap: Efficient Empty Space Skipping for Large-Scale Volume Rendering
Authors: Markus Hadwiger, Ali K. Al-Awami, Johanna Beyer, Marco Agus, Hanspeter Pfister
Published at SciVis, 2017

Recent advances in data acquisition produce volume data of very high resolution and large size, such as terabyte-sized microscopy volumes. These data often contain many fine and intricate structures, which pose huge challenges for volume rendering, and make it particularly important to efficiently skip empty space. This paper addresses two major challenges: (1) The complexity of large volumes containing fine structures often leads to highly fragmented space subdivisions that make empty regions hard to skip efficiently. (2) The classification of space into empty and non-empty regions changes frequently, because the user or the evaluation of an interactive query activate a different set of objects, which makes it unfeasible to pre-compute a well-adapted space subdivision. We describe the novel SparseLeap method for efficient empty space skipping in very large volumes, even around fine structures. The main performance characteristic of SparseLeap is that it moves the major cost of empty space skipping out of the ray-casting stage. We achieve this via a hybrid strategy that balances the computational load between determining empty ray segments in a rasterization (object-order) stage, and sampling non-empty volume data in the ray-casting (image-order) stage. Before ray-casting, we exploit the fast hardware rasterization of GPUs to create a ray segment list for each pixel, which identifies non-empty regions along the ray. The ray-casting stage then leaps over empty space without hierarchy traversal. Ray segment lists are created by rasterizing a set of fine-grained, view-independent bounding boxes. Frame coherence is exploited by re-using the same bounding boxes unless the set of active objects changes. We show that SparseLeap scales better to large, sparse data than standard octree empty space skipping.
StreetVizor: Visual Exploration of Human-Scale Urban Forms Based on Street Views
Authors: Qiaomu Shen, Wei Zeng 0004, Yu Ye, Stefan Müller Arisona, Simon Schubiger-Banz, Remo Aslak Burkhard, Huamin Qu
Published at SciVis, 2017

Urban forms at human-scale, i.e., urban environments that individuals can sense (e.g., sight, smell, and touch) in their daily lives, can provide unprecedented insights on a variety of applications, such as urban planning and environment auditing. The analysis of urban forms can help planners develop high-quality urban spaces through evidence-based design. However, such analysis is complex because of the involvement of spatial, multi-scale (i.e., city, region, and street), and multivariate (e.g., greenery and sky ratios) natures of urban forms. In addition, current methods either lack quantitative measurements or are limited to a small area. The primary contribution of this work is the design of StreetVizor, an interactive visual analytics system that helps planners leverage their domain knowledge in exploring human-scale urban forms based on street view images. Our system presents two-stage visual exploration: 1) an AOI Explorer for the visual comparison of spatial distributions and quantitative measurements in two areas-of-interest (AOIs) at city- and region-scales; 2) and a Street Explorer with a novel parallel coordinate plot for the exploration of the fine-grained details of the urban forms at the street-scale. We integrate visualization techniques with machine learning models to facilitate the detection of street view patterns. We illustrate the applicability of our approach with case studies on the real-world datasets of four cities, i.e., Hong Kong, Singapore, Greater London and New York City. Interviews with domain experts demonstrate the effectiveness of our system in facilitating various analytical tasks.
The Good, the Bad, and the Ugly: A Theoretical Framework for the Assessment of Continuous Colormaps
Authors: Roxana Bujack, Terece L. Turton, Francesca Samsel, Colin Ware, David H. Rogers 0001, James P. Ahrens
Published at SciVis, 2017

A myriad of design rules for what constitutes a “good” colormap can be found in the literature. Some common rules include order, uniformity, and high discriminative power. However, the meaning of many of these terms is often ambiguous or open to interpretation. At times, different authors may use the same term to describe different concepts or the same rule is described by varying nomenclature. These ambiguities stand in the way of collaborative work, the design of experiments to assess the characteristics of colormaps, and automated colormap generation. In this paper, we review current and historical guidelines for colormap design. We propose a specified taxonomy and provide unambiguous mathematical definitions for the most common design rules.
The Topology ToolKit
Authors: Julien Tierny, Guillaume Favelier, Joshua A. Levine, Charles Gueunet, Michael Michaux
Published at SciVis, 2017

This system paper presents the Topology ToolKit (TTK), a software platform designed for the topological analysis of scalar data in scientific visualization. While topological data analysis has gained in popularity over the last two decades, it has not yet been widely adopted as a standard data analysis tool for end users or developers. TTK aims at addressing this problem by providing a unified, generic, efficient, and robust implementation of key algorithms for the topological analysis of scalar data, including: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due to a tight integration with ParaView. It is also easily accessible to developers through a variety of bindings (Python, VTK/C++) for fast prototyping or through direct, dependency-free, C++, to ease integration into pre-existing complex systems. While developing TTK, we faced several algorithmic and software engineering challenges, which we document in this paper. In particular, we present an algorithm for the construction of a discrete gradient that complies to the critical points extracted in the piecewise-linear setting. This algorithm guarantees a combinatorial consistency across the topological abstractions supported by TTK, and importantly, a unified implementation of topological data simplification for multi-scale exploration and analysis. We also present a cached triangulation data structure, that supports time efficient and generic traversals, which self-adjusts its memory usage on demand for input simplicial meshes and which implicitly emulates a triangulation for regular grids with no memory overhead. Finally, we describe an original software architecture, which guarantees memory efficient and direct accesses to TTK features, while still allowing for researchers powerful and easy bindings and extensions. TTK is open source (BSD license) and its code. online documentation and video tutorials are available on TTK's website [108].
TopoAngler: Interactive Topology-Based Extraction of Fishes
Authors: Alexander Bock 0002, Harish Doraiswamy, Adam Summers, Cláudio T. Silva
Published at SciVis, 2017

We present TopoAngler, a visualization framework that enables an interactive user-guided segmentation of fishes contained in a micro-CT scan. The inherent noise in the CT scan coupled with the often disconnected (and sometimes broken) skeletal structure of fishes makes an automatic segmentation of the volume impractical. To overcome this, our framework combines techniques from computational topology with an interactive visual interface, enabling the human-in-the-Ioop to effectively extract fishes from the volume. In the first step, the join tree of the input is used to create a hierarchical segmentation of the volume. Through the use of linked views, the visual interface then allows users to interactively explore this hierarchy, and gather parts of individual fishes into a coherent sub-volume, thus reconstructing entire fishes. Our framework was primarily developed for its application to CT scans of fishes, generated as part of the ScanAllFish project, through close collaboration with their lead scientist. However, we expect it to also be applicable in other biological applications where a single dataset contains multiple specimen; a common routine that is now widely followed in laboratories to increase throughput of expensive CT scanners.