35-Issue 3

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https://diglib.eg.org/handle/10.2312/15270

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Cytosplore: Interactive Immune Cell Phenotyping for Large Single-Cell Datasets
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Höllt, Thomas; Pezzotti, Nicola; Unen, Vincent van; Koning, Frits; Eisemann, Elmar; Lelieveldt, Boudewijn P. F.; Vilanova, Anna; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
To understand how the immune system works, one needs to have a clear picture of its cellular compositon and the cells' corresponding properties and functionality. Mass cytometry is a novel technique to determine the properties of single-cells with unprecedented detail. This amount of detail allows for much finer differentiation but also comes at the cost of more complex analysis. In this work, we present Cytosplore, implementing an interactive workflow to analyze mass cytometry data in an integrated system, providing multiple linked views, showing different levels of detail and enabling the rapid definition of known and unknown cell types. Cytosplore handles millions of cells, each represented as a high-dimensional data point, facilitates hypothesis generation and confirmation, and provides a significant speed up of the current workflow. We show the effectiveness of Cytosplore in a case study evaluation.
Decoupled Shading for Real-time Heterogeneous Volume Illumination
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Zhang, Yubo; Ma, Kwan-Liu; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
Existing real-time volume rendering techniques which support global illumination are limited in modeling distinct realistic appearances for classified volume data, which is a desired capability in many fields of study for illustration and education. Directly extending the emission-absorption volume integral with heterogeneous material shading becomes unaffordable for real-time applications because the high-frequency view-dependent global lighting needs to be evaluated per sample along the volume integral. In this paper, we present a decoupled shading algorithm for multi-material volume rendering that separates global incident lighting evaluation from per-sample material shading under multiple light sources. We show how the incident lighting calculation can be optimized through a sparse volume integration method. The quality, performance and usefulness of our new multi-material volume rendering method is demonstrated through several examples.
Enhancing Scatterplots with Multi-Dimensional Focal Blur
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Staib, Joachim; Grottel, Sebastian; Gumhold, Stefan; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
Scatterplots directly depict two dimensions of multi-dimensional data points, discarding all other information. To visualize all data, these plots are extended to scatterplot matrices, which distribute the information of each data point over many plots. Problems arising from the resulting visual complexity are nowadays alleviated by concepts like filtering and focus and context. We present a method based on depth of field that contains both aspects and injects information from all dimensions into each scatterplot. Our approach is a natural generalization of the commonly known focus effects from optics. It is based on a multidimensional focus selection body. Points outside of this body are defocused depending on their distance. Our method allows for a continuous transition from data points in focus, over regions of blurry points providing contextual information, to visually filtered data. Our algorithm supports different focus selection bodies, blur kernels, and point shapes. We present an optimized GPU-based implementation for interactive exploration and show the usefulness of our approach on several data sets.
GEMSe: Visualization-Guided Exploration of Multi-channel Segmentation Algorithms
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Fröhler, Bernhard; Möller, Torsten; Heinzl, Christoph; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
We present GEMSe, an interactive tool for exploring and analyzing the parameter space of multi-channel segmentation algorithms. Our targeted user group are domain experts who are not necessarily segmentation specialists. GEMSe allows the exploration of the space of possible parameter combinations for a segmentation framework and its ensemble of results. Users start with sampling the parameter space and computing the corresponding segmentations. A hierarchically clustered image tree provides an overview of variations in the resulting space of label images. Details are provided through exemplary images from the selected cluster and histograms visualizing the parameters and the derived output in the selected cluster. The correlation between parameters and derived output as well as the effect of parameter changes can be explored through interactive filtering and scatter plots. We evaluate the usefulness of GEMSe through expert reviews and case studies based on three different kinds of datasets: A synthetic dataset emulating the combination of 3D X-ray computed tomography with data from K-Edge spectroscopy, a three-channel scan of a rock crystal acquired by a Talbot-Lau grating interferometer X-ray computed tomography device, as well as a hyperspectral image.
Glyphs for Asymmetric Second-Order 2D Tensors
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Seltzer, Nicholas; Kindlmann, Gordon; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
Tensors model a wide range of physical phenomena. While symmetric tensors are sufficient for some applications (such as diffusion), asymmetric tensors are required, for example, to describe differential properties of fluid flow. Glyphs permit inspecting individual tensor values, but existing tensor glyphs are fully defined only for symmetric tensors. We propose a glyph to visualize asymmetric second-order two-dimensional tensors. The glyph includes visual encoding for physically significant attributes of the tensor, including rotation, anisotropic stretching, and isotropic dilation. Our glyph design conserves the symmetry and continuity properties of the underlying tensor, in that transformations of a tensor (such as rotation or negation) correspond to analogous transformations of the glyph. We show results with synthetic data from computational fluid dynamics.
Interactive 3D Force-Directed Edge Bundling
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Zielasko, Daniel; Weyers, Benjamin; Hentschel, Bernd; Kuhlen, Torsten W.; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
Interactive analysis of 3D relational data is challenging. A common way of representing such data are node-link diagrams as they support analysts in achieving a mental model of the data. However, naïve 3D depictions of complex graphs tend to be visually cluttered, even more than in a 2D layout. This makes graph exploration and data analysis less efficient. This problem can be addressed by edge bundling. We introduce a 3D cluster-based edge bundling algorithm that is inspired by the force-directed edge bundling (FDEB) algorithm [HvW09b] and fulfills the requirements to be embedded in an interactive framework for spatial data analysis. It is parallelized and scales with the size of the graph regarding the runtime. Furthermore, it maintains the edge's model and thus supports rendering the graph in different structural styles. We demonstrate this with a graph originating from a simulation of the function of a macaque brain.
Semi-automatic Vortex Flow Classification in 4D PC-MRI Data of the Aorta
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Meuschke, Monique; Köhler, Benjamin; Preim, Uta; Preim, Bernhard; Lawonn, Kai; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
We present an Aortic Vortex Classification (AVOCLA) that allows to classify vortices in the human aorta semi-automatically. Current medical studies assume a strong relation between cardiovascular diseases and blood flow patterns such as vortices. Such vortices are extracted and manually classified according to specific, unstandardized properties. We employ an agglomerative hierarchical clustering to group vortex-representing path lines as basis for the subsequent classification. Classes are based on the vortex' size, orientation and shape, its temporal occurrence relative to the cardiac cycle as well as its spatial position relative to the vessel course. The classification results are presented by a 2D and 3D visualization technique. To confirm the usefulness of both approaches, we report on the results of a user study. Moreover, AVOCLA was applied to 15 datasets of healthy volunteers and patients with different cardiovascular diseases. The results of the semi-automatic classification were qualitatively compared to a manually generated ground truth of two domain experts considering the vortex number and five specific properties.
Visual Analysis of Governing Topological Structures in Excitable Network Dynamics
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Ngo, Quynh Quang; Hütt, Marc-Thorsten; Linsen, Lars; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
To understand how topology shapes the dynamics in excitable networks is one of the fundamental problems in network science when applied to computational systems biology and neuroscience. Recent advances in the field discovered the influential role of two macroscopic topological structures, namely hubs and modules. We propose a visual analytics approach that allows for a systematic exploration of the role of those macroscopic topological structures on the dynamics in excitable networks. Dynamical patterns are discovered using the dynamical features of excitation ratio and co-activation. Our approach is based on the interactive analysis of the correlation of topological and dynamical features using coordinated views. We designed suitable visual encodings for both the topological and the dynamical features. A degree map and an adjacency matrix visualization allow for the interaction with hubs and modules, respectively. A barycentric-coordinates layout and a multi-dimensional scaling approach allow for the analysis of excitation ratio and co-activation, respectively. We demonstrate how the interplay of the visual encodings allows us to quickly reconstruct recent findings in the field within an interactive analysis and even discovered new patterns. We apply our approach to network models of commonly investigated topologies as well as to the structural networks representing the connectomes of different species. We evaluate our approach with domain experts in terms of its intuitiveness, expressiveness, and usefulness.
Visual Analysis of Tumor Control Models for Prediction of Radiotherapy Response
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Raidou, Renata Georgia; Casares-Magaz, Oscar; Muren, Ludvig Paul; Heide, Uulke A. van der; Rørvik, Jarle; Breeuwer, Marcel; Vilanova, Anna; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
In radiotherapy, tumors are irradiated with a high dose, while surrounding healthy tissues are spared. To quantify the probability that a tumor is effectively treated with a given dose, statistical models were built and employed in clinical research. These are called tumor control probability (TCP) models. Recently, TCP models started incorporating additional information from imaging modalities. In this way, patient-specific properties of tumor tissues are included, improving the radiobiological accuracy of models. Yet, the employed imaging modalities are subject to uncertainties with significant impact on the modeling outcome, while the models are sensitive to a number of parameter assumptions. Currently, uncertainty and parameter sensitivity are not incorporated in the analysis, due to time and resource constraints. To this end, we propose a visual tool that enables clinical researchers working on TCP modeling, to explore the information provided by their models, to discover new knowledge and to confirm or generate hypotheses within their data. Our approach incorporates the following four main components: (1) It supports the exploration of uncertainty and its effect on TCP models; (2) It facilitates parameter sensitivity analysis to common assumptions; (3) It enables the identification of inter-patient response variability; (4) It allows starting the analysis from the desired treatment outcome, to identify treatment strategies that achieve it. We conducted an evaluation with nine clinical researchers. All participants agreed that the proposed visual tool provides better understanding and new opportunities for the exploration and analysis of TCP modeling.
Visualizing the Impact of Geographical Variations on Multivariate Clustering
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Zhang, Yifan; Luo, Wei; Mack, Elizabeth A.; Maciejewski, Ross; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
Traditional multivariate clustering approaches are common in many geovisualization applications. These algorithms are used to define geodemographic profiles, ecosystems and various other land use patterns that are based on multivariate measures. Cluster labels are then projected onto a choropleth map to enable analysts to explore spatial dependencies and heterogeneity within the multivariate attributes. However, local variations in the data and choices of clustering parameters can greatly impact the resultant visualization. In this work, we develop a visual analytics framework for exploring and comparing the impact of geographical variations for multivariate clustering. Our framework employs a variety of graphical configurations and summary statistics to explore the spatial extents of clustering. It also allows users to discover patterns that can be concealed by traditional global clustering via several interactive visualization techniques including a novel drag & drop clustering difference view. We demonstrate the applicability of our framework over a demographics dataset containing quick facts about counties in the continental United States and demonstrate the need for analytical tools that can enable users to explore and compare clustering results over varying geographical features and scales.

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