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Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Large scale visualization on the Powerwall.
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

Visualization

Visualization, sometimes referred to as visual data analysis, uses the graphical representation of data as a means of gaining understanding and insight into the data. Visualization research at SCI has focused on applications spanning computational fluid dynamics, medical imaging and analysis, biomedical data analysis, healthcare data analysis, weather data analysis, poetry, network and graph analysis, financial data analysis, etc.

Research involves novel algorithm and technique development to building tools and systems that assist in the comprehension of massive amounts of (scientific) data. We also research the process of creating successful visualizations.

We strongly believe in the role of interactivity in visual data analysis. Therefore, much of our research is concerned with creating visualizations that are intuitive to interact with and also render at interactive rates.

Visualization at SCI includes the academic subfields of Scientific Visualization, Information Visualization and Visual Analytics.


chuck

Charles Hansen

Volume Rendering
Ray Tracing
Graphics
pascucci

Valerio Pascucci

Topological Methods
Data Streaming
Big Data
chris

Chris Johnson

Scalar, Vector, and
Tensor Field Visualization,
Uncertainty Visualization
mike

Mike Kirby

Uncertainty Visualization
ross

Ross Whitaker

Topological Methods
Uncertainty Visualization
miriah

Miriah Meyer

Information Visualization
yarden

Yarden Livnat

Information Visualization
alex lex

Alex Lex

Information Visualization
bei

Bei Wang

Information Visualization
Scientific Visualization
Topological Data Analysis
 

Visualization Project Sites:


Associated Labs:


Publications in Visualization:


A statistical framework for quantification and visualisation of positional uncertainty in deep brain stimulation electrodes,
T. M. Athawale, K. A. Johnson, C. R. Butson, C. R. Johnson. In Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, Taylor & Francis, pp. 1-12. 2018.
DOI: doi:10.1080/21681163.2018.1523750

Deep brain stimulation (DBS) is an established therapy for treating patients with movement disorders such as Parkinson's disease. Patient-specific computational modelling and visualisation have been shown to play a key role in surgical and therapeutic decisions for DBS. The computational models use brain imaging, such as magnetic resonance (MR) and computed tomography (CT), to determine the DBS electrode positions within the patient's head. The finite resolution of brain imaging, however, introduces uncertainty in electrode positions. The DBS stimulation settings for optimal patient response are sensitive to the relative positioning of DBS electrodes to a specific neural substrate (white/grey matter). In our contribution, we study positional uncertainty in the DBS electrodes for imaging with finite resolution. In a three-step approach, we first derive a closed-form mathematical model characterising the geometry of the DBS electrodes. Second, we devise a statistical framework for quantifying the uncertainty in the positional attributes of the DBS electrodes, namely the direction of longitudinal axis and the contact-centre positions at subvoxel levels. The statistical framework leverages the analytical model derived in step one and a Bayesian probabilistic model for uncertainty quantification. Finally, the uncertainty in contact-centre positions is interactively visualised through volume rendering and isosurfacing techniques. We demonstrate the efficacy of our contribution through experiments on synthetic and real datasets. We show that the spatial variations in true electrode positions are significant for finite resolution imaging, and interactive visualisation can be instrumental in exploring probabilistic positional variations in the DBS lead.



Exploration of periodic flow fields
A. Sanderson, X. Tricoche. In 18th International Symposium on Flow Visualization, 2018.

One of the difficulties researchers face when exploring flow fields is understanding the respective strengths and limitations of the visualization and analysis techniques that can be applied to their particular problem. We consider in this paper the visualization of doubly periodic flow fields. Specifically, we compare and contrast two traditional visualization techniques, the Poincaré plot and the finite-time Lyapunov exponent (FTLE) plot with a technique recently proposed by the authors, which enhances the Poincaré plot with analytical results that reveal the topology. As is often the case, no single technique achieves a holistic visualization of the flow field that would address all the needs of the analysis. Instead, we show that additional insight can be gained from applying them in combination.



Association Rules-Based Multivariate Analysis and Visualization of Spatiotemporal Climate Data
F. Wang, W. Li, S. Wang, C.R. Johnson. In ISPRS International Journal of Geo-Information, Vol. 7, No. 7, MDPI AG, pp. 266. July, 2018.
DOI: 10.3390/ijgi7070266

Understanding atmospheric phenomena involves analysis of large-scale spatiotemporal multivariate data. The complexity and heterogeneity of such data pose a significant challenge in discovering and understanding the association between multiple climate variables. To tackle this challenge, we present an interactive heuristic visualization system that supports climate scientists and the public in their exploration and analysis of atmospheric phenomena of interest. Three techniques are introduced: (1) web-based spatiotemporal climate data visualization; (2) multiview and multivariate scientific data analysis; and (3) data mining-enabled visual analytics. The Arctic System Reanalysis (ASR) data are used to demonstrate and validate the effectiveness and usefulness of our method through a case study of "The Great Arctic Cyclone of 2012". The results show that different variables have strong associations near the polar cyclone area. This work also provides techniques for identifying multivariate correlation and for better understanding the driving factors of climate phenomena.



Juniper: A Tree+ Table Approach to Multivariate Graph Visualization
C. Nobre, M. Streit, A. Lex. In CoRR, 2018.

Analyzing large, multivariate graphs is an important problem in many domains, yet such graphs are challenging to visualize. In this paper, we introduce a novel, scalable, tree+table multivariate graph visualization technique, which makes many tasks related to multivariate graph analysis easier to achieve. The core principle we follow is to selectively query for nodes or subgraphs of interest and visualize these subgraphs as a spanning tree of the graph. The tree is laid out in a linear layout, which enables us to juxtapose the nodes with a table visualization where diverse attributes can be shown. We also use this table as an adjacency matrix, so that the resulting technique is a hybrid node-link/adjacency matrix technique. We implement this concept in Juniper, and complement it with a set of interaction techniques that enable analysts to dynamically grow, re-structure, and aggregate the tree, as well as change the layout or show paths between nodes. We demonstrate the utility of our tool in usage scenarios for different multivariate networks: a bipartite network of scholars, papers, and citation metrics, and a multitype network of story characters, places, books, etc.



Discrete Stratified Morse Theory: A User's Guide
K Knudson, B Wang. In CoRR, 2018.

Inspired by the works of Forman on discrete Morse theory, which is a combinatorial adaptation to cell complexes of classical Morse theory on manifolds, we introduce a discrete analogue of the stratified Morse theory of Goresky and MacPherson (1988). We describe the basics of this theory and prove fundamental theorems relating the topology of a general simplicial complex with the critical simplices of a discrete stratified Morse function on the complex. We also provide an algorithm that constructs a discrete stratified Morse function out of an arbitrary function defined on a finite simplicial complex; this is different from simply constructing a discrete Morse function on such a complex. We borrow Forman's idea of a "user's guide," where we give simple examples to convey the utility of our theory.



MOG: Mapper on Graphs for Relationship Preserving Clustering
M. Hajij, B. Wang, P. Rosen. In CoRR, 2018.

The interconnected nature of graphs often results in difficult to interpret clutter. Typically techniques focus on either decluttering by clustering nodes with similar properties or grouping edges with similar relationship. We propose using mapper, a powerful topological data analysis tool, to summarize the structure of a graph in a way that both clusters data with similar properties and preserves relationships. Typically, mapper operates on a given data by utilizing a scalar function defined on every point in the data and a cover for scalar function codomain. The output of mapper is a graph that summarize the shape of the space. In this paper, we outline how to use this mapper construction on an input graphs, outline three filter functions that capture important structures of the input graph, and provide an interface for interactively modifying the cover. To validate our approach, we conduct several case studies on synthetic and real world data sets and demonstrate how our method can give meaningful summaries for graphs with various complexities



Visual Exploration of Semantic Relationships in Neural Word Embeddings
S. Liu, P.T. Bremer, J.J. Thiagarajan, V. Srikumar, B. Wang, Y. Livnat, V. Pascucci. In IEEE Transactions on Visualization and Computer Graphics, Vol. 24, No. 1, IEEE, pp. 553--562. Jan, 2018.
DOI: 10.1109/tvcg.2017.2745141

Constructing distributed representations for words through neural language models and using the resulting vector spaces for analysis has become a crucial component of natural language processing (NLP). However, despite their widespread application, little is known about the structure and properties of these spaces. To gain insights into the relationship between words, the NLP community has begun to adapt high-dimensional visualization techniques. In particular, researchers commonly use t-distributed stochastic neighbor embeddings (t-SNE) and principal component analysis (PCA) to create two-dimensional embeddings for assessing the overall structure and exploring linear relationships (e.g., word analogies), respectively. Unfortunately, these techniques often produce mediocre or even misleading results and cannot address domain-specific visualization challenges that are crucial for understanding semantic relationships in word embeddings. Here, we introduce new embedding techniques for visualizing semantic and syntactic analogies, and the corresponding tests to determine whether the resulting views capture salient structures. Additionally, we introduce two novel views for a comprehensive study of analogy relationships. Finally, we augment t-SNE embeddings to convey uncertainty information in order to allow a reliable interpretation. Combined, the different views address a number of domain-specific tasks difficult to solve with existing tools.



A virtual reality visualization tool for neuron tracing
W Usher, P Klacansky, F Federer, PT Bremer, A Knoll, J. Yarch, A. Angelucci, V. Pascucci . In IEEE Transactions on Visualization and Computer Graphics, Vol. 24, No. 1, IEEE, pp. 994--1003. Jan, 2018.
DOI: 10.1109/tvcg.2017.2744079

racing neurons in large-scale microscopy data is crucial to establishing a wiring diagram of the brain, which is needed to understand how neural circuits in the brain process information and generate behavior. Automatic techniques often fail for large and complex datasets, and connectomics researchers may spend weeks or months manually tracing neurons using 2D image stacks. We present a design study of a new virtual reality (VR) system, developed in collaboration with trained neuroanatomists, to trace neurons in microscope scans of the visual cortex of primates. We hypothesize that using consumer-grade VR technology to interact with neurons directly in 3D will help neuroscientists better resolve complex cases and enable them to trace neurons faster and with less physical and mental strain. We discuss both the design process and technical challenges in developing an interactive system to navigate and manipulate terabyte-sized image volumes in VR. Using a number of different datasets, we demonstrate that, compared to widely used commercial software, consumer-grade VR presents a promising alternative for scientists.



Visual Detection of Structural Changes in Time-Varying Graphs Using Persistent Homology
M. Hajij, B. Wang, C. Scheidegger, P. Rosen. In 2018 IEEE Pacific Visualization Symposium (PacificVis), IEEE, April, 2018.
DOI: 10.1109/pacificvis.2018.00024

Topological data analysis is an emerging area in exploratory data analysis and data mining. Its main tool, persistent homology, has become a popular technique to study the structure of complex, high-dimensional data. In this paper, we propose a novel method using persistent homology to quantify structural changes in time-varying graphs. Specifically, we transform each instance of the time-varying graph into a metric space, extract topological features using persistent homology, and compare those features over time. We provide a visualization that assists in time-varying graph exploration and helps to identify patterns of behavior within the data. To validate our approach, we conduct several case studies on real-world datasets and show how our method can find cyclic patterns, deviations from those patterns, and one-time events in time-varying graphs. We also examine whether a persistence-based similarity measure satisfies a set of well-established, desirable properties for graph metrics.



OpenSpace: Changing the Narrative of Public Dissemination in Astronomical Visualization from What to How
A. Bock, E. Axelsson, C. Emmart, M. Kuznetsova, C. Hansen, A. Ynnerman. In IEEE Computer Graphics and Applications, Vol. 38, No. 3, IEEE, pp. 44--57. May, 2018.
DOI: 10.1109/mcg.2018.032421653

We present the development of an open-source software called OpenSpace that bridges the gap between scientific discoveries and public dissemination and thus paves the way for the next generation of science communication and data exploration. We describe how the platform enables interactive presentations of dynamic and time-varying processes by domain experts to the general public. The concepts are demonstrated through four cases: Image acquisitions of the New Horizons and Rosetta spacecraft, the dissemination of space weather phenomena, and the display of high-resolution planetary images. Each case has been presented at public events with great success. These cases highlight the details of data acquisition, rather than presenting the final results, showing the audience the value of supporting the efforts of the scientific discovery.



Outcomes of an electronic social network intervention with neuro-oncology patient family caregivers
M. Reblin, D. Ketcher, P. Forsyth, E. Mendivil, L. Kane, J. Pok, M. Meyer, Y.Wu, J. Agutter. In Journal of Neuro-Oncology, Springer Nature, pp. 1--7. May, 2018.
DOI: 10.1007/s11060-018-2909-2

Introduction

Informal family caregivers (FCG) are an integral and crucial human component in the cancer care continuum. However, research and interventions to help alleviate documented anxiety and burden on this group is lacking. To address the absence of effective interventions, we developed the electronic Support Network Assessment Program (eSNAP) which aims to automate the capture and visualization of social support, an important target for overall FCG support. This study seeks to describe the preliminary efficacy and outcomes of the eSNAP intervention.

Methods

Forty FCGs were enrolled into a longitudinal, two-group randomized design to compare the eSNAP intervention in caregivers of patients with primary brain tumors against controls who did not receive the intervention. Participants were followed for six weeks with questionnaires to assess demographics, caregiver burden, anxiety, depression, and social support. Questionnaires given at baseline (T1) and then 3-weeks (T2), and 6-weeks (T3) post baseline questionnaire.

Results

FCGs reported high caregiver burden and distress at baseline, with burden remaining stable over the course of the study. The intervention group was significantly less depressed, but anxiety remained stable across groups.

Conclusions

With the lessons learned and feedback obtained from FCGs, this study is the first step to developing an effective social support intervention to support FCGs and healthcare providers in improving cancer care.



TopoMS: Comprehensive topological exploration for molecular and condensed‐matter systems
H. Bhatia, A.G. Gyulassy, V. Lordi, J.E. Pask, V. Pascucci, P.T. Bremer. In Journal of Computational Chemistry, Vol. 39, No. 16, Wiley, pp. 936--952. March, 2018.
DOI: 10.1002/jcc.25181

We introduce TopoMS, a computational tool enabling detailed topological analysis of molecular and condensed‐matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molecular graph. With roots in techniques from computational topology, and using a shared‐memory parallel approach, TopoMS provides scalable, numerically robust, and topologically consistent analysis. TopoMS can be used as a command‐line tool or with a GUI (graphical user interface), where the latter also enables an interactive exploration of the molecular graph. This paper presents algorithmic details of TopoMS and compares it with state‐of‐the‐art tools: Bader charge analysis v1.0 (Arnaldsson et al., 01/11/17) and molecular graph extraction using Critic2 (Otero‐de‐la‐Roza et al., Comput. Phys. Commun. 2014, 185, 1007). TopoMS not only combines the functionality of these individual codes but also demonstrates up to 4× performance gain on a standard laptop, faster convergence to fine‐grid solution, robustness against lattice bias, and topological consistency. TopoMS is released publicly under BSD License. © 2018 Wiley Periodicals, Inc.



Research and Education in Computational Science and Engineering
U. Ruede, K. Willcox, L. C. McInnes, H. De Sterck, G. Biros, H. Bungartz, J. Corones, E. Cramer, J. Crowley, O. Ghattas, M. Gunzburger, M. Hanke, R. Harrison, M. Heroux, J. Hesthaven, P. Jimack, C. Johnson, K. E. Jordan, D. E. Keyes, R. Krause, V. Kumar, S. Mayer, J. Meza, K. M. Mrken, J. T. Oden, L. Petzold, P. Raghavan, S. M. Shontz, A. Trefethen, P. Turner, V. Voevodin, B. Wohlmuth,, C. S. Woodward. In SIAM Review, Vol. 60, No. 3, SIAM, pp. 707--754. Jan, 2018.
DOI: 10.1137/16m1096840

This report presents challenges, opportunities and directions for computational science and engineering (CSE) research and education for the next decade. Over the past two decades the field of CSE has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers with algorithmic inventions and software systems that transcend disciplines and scales. CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments—including the architectural complexity of extreme-scale computing, the data revolution and increased attention to data-driven discovery, and the specialization required to follow the applications to new frontiers—is redefining the scope and reach of the CSE endeavor. With these many current and expanding opportunities for the CSE field, there is a growing demand for CSE graduates and a need to expand CSE educational offerings. This need includes CSE programs at both the undergraduate and graduate levels, as well as continuing education and professional development programs, exploiting the synergy between computational science and data science. Yet, as institutions consider new and evolving educational programs, it is essential to consider the broader research challenges and opportunities that provide the context for CSE education and workforce development.



Revisiting Abnormalities in Brain Network Architecture Underlying Autism Using Topology-Inspired Statistical Inference,
S. Palande, V. Jose, B. Zielinski, J. Anderson, P.T. Fletcher, B. Wang. In Connectomics in NeuroImaging, Springer International Publishing, pp. 98--107. 2017.
DOI: 10.1007/978-3-319-67159-8_12

A large body of evidence relates autism with abnormal structural and functional brain connectivity. Structural covariance MRI (scMRI) is a technique that maps brain regions with covarying gray matter density across subjects. It provides a way to probe the anatomical structures underlying intrinsic connectivity networks (ICNs) through the analysis of the gray matter signal covariance. In this paper, we apply topological data analysis in conjunction with scMRI to explore network-specific differences in the gray matter structure in subjects with autism versus age-, gender- and IQ-matched controls. Specifically, we investigate topological differences in gray matter structures captured by structural covariance networks (SCNs) derived from three ICNs strongly implicated in autism, namely, the salience network (SN), the default mode network (DMN) and the executive control network (ECN). By combining topological data analysis with statistical inference, our results provide evidence of statistically significant network-specific structural abnormalities in autism, from SCNs derived from SN and ECN. These differences in brain architecture are consistent with direct structural analysis using scMRI (Zielinski et al. 2012).



Worksheets for Guiding Novices through the Visualization Design Process
S. McKenna, A. Lex, M. Meyer. In CoRR, 2017.

For visualization pedagogy, an important but challenging notion to teach is design, from making to evaluating visualization encodings, user interactions, or data visualization systems. In our previous work, we introduced the design activity framework to codify the high-level activities of the visualization design process. This framework has helped structure experts' design processes to create visualization systems, but the framework's four activities lack a breakdown into steps with a concrete example to help novices utilizing this framework in their own real-world design process. To provide students with such concrete guidelines, we created worksheets for each design activity: understand, ideate, make, and deploy. Each worksheet presents a high-level summary of the activity with actionable, guided steps for a novice designer to follow. We validated the use of this framework and the worksheets in a graduate-level visualization course taught at our university. For this evaluation, we surveyed the class and conducted 13 student interviews to garner qualitative, open-ended feedback and suggestions on the worksheets. We conclude this work with a discussion and highlight various areas for future work on improving visualization design pedagogy.



Exploration of Heterogeneous Data Using Robust Similarity
M. Mirzargar, R.T. Whitaker, R.M. Kirby. In CoRR, 2017.

Heterogeneous data pose serious challenges to data analysis tasks, including exploration and visualization. Current techniques often utilize dimensionality reductions, aggregation, or conversion to numerical values to analyze heterogeneous data. However, the effectiveness of such techniques to find subtle structures such as the presence of multiple modes or detection of outliers is hindered by the challenge to find the proper subspaces or prior knowledge to reveal the structures. In this paper, we propose a generic similarity-based exploration technique that is applicable to a wide variety of datatypes and their combinations, including heterogeneous ensembles. The proposed concept of similarity has a close connection to statistical analysis and can be deployed for summarization, revealing fine structures such as the presence of multiple modes, and detection of anomalies or outliers. We then propose a visual encoding framework that enables the exploration of a heterogeneous dataset in different levels of detail and provides insightful information about both global and local structures. We demonstrate the utility of the proposed technique using various real datasets, including ensemble data.



Visualizing Sensor Network Coverage with Location Uncertainty
T. Sodergren, J. Hair, J.M. Phillips, B. Wang. In CoRR, Vol. abs/1710.06925, 2017.

We present an interactive visualization system for exploring the coverage in sensor networks with uncertain sensor locations. We consider a simple case of uncertainty where the location of each sensor is confined to a discrete number of points sampled uniformly at random from a region with a fixed radius. Employing techniques from topological data analysis, we model and visualize network coverage by quantifying the uncertainty defined on its simplicial complex representations. We demonstrate the capabilities and effectiveness of our tool via the exploration of randomly distributed sensor networks.



Visualization in Meteorology---A Survey of Techniques and Tools for Data Analysis Tasks
M. Rautenhaus, M. Böttinger, S. Siemen, R. Hoffman, R.M. Kirby, M. Mirzargar, N. Rober, R. Westermann. In IEEE Transactions on Visualization and Computer Graphics, IEEE, pp. 1--1. 2017.
DOI: 10.1109/tvcg.2017.2779501

This article surveys the history and current state of the art of visualization in meteorology, focusing on visualization techniques and tools used for meteorological data analysis. We examine characteristics of meteorological data and analysis tasks, describe the development of computer graphics methods for visualization in meteorology from the 1960s to today, and visit the state of the art of visualization techniques and tools in operational weather forecasting and atmospheric research. We approach the topic from both the visualization and the meteorological side, showing visualization techniques commonly used in meteorological practice, and surveying recent studies in visualization research aimed at meteorological applications. Our overview covers visualization techniques from the fields of display design, 3D visualization, flow dynamics, feature-based visualization, comparative visualization and data fusion, uncertainty and ensemble visualization, interactive visual analysis, efficient rendering, and scalability and reproducibility. We discuss demands and challenges for visualization research targeting meteorological data analysis, highlighting aspects in demonstration of benefit, interactive visual analysis, seamless visualization, ensemble visualization, 3D visualization, and technical issues.



Taggle: Scalable Visualization of Tabular Data through Aggregation
K. Furmanova, S. Gratzl, H. Stitz, T. Zichner, M. Jaresova, M. Ennemoser, A. Lex, M. Streit. In CoRR, 2017.

Visualization of tabular data---for both presentation and exploration purposes---is a well-researched area. Although effective visual presentations of complex tables are supported by various plotting libraries, creating such tables is a tedious process and requires scripting skills. In contrast, interactive table visualizations that are designed for exploration purposes either operate at the level of individual rows, where large parts of the table are accessible only via scrolling, or provide a high-level overview that often lacks context-preserving drill-down capabilities. In this work we present Taggle, a novel visualization technique for exploring and presenting large and complex tables that are composed of individual columns of categorical or numerical data and homogeneous matrices. The key contribution of Taggle is the hierarchical aggregation of data subsets, for which the user can also choose suitable visual representations.The aggregation strategy is complemented by the ability to sort hierarchically such that groups of items can be flexibly defined by combining categorical stratifications and by rich data selection and filtering capabilities. We demonstrate the usefulness of Taggle for interactive analysis and presentation of complex genomics data for the purpose of drug discovery.



Reducing network congestion and synchronization overhead during aggregation of hierarchical data,
S. Kumar, D. Hoang, S. Petruzza, J. Edwards, V. Pascucci. In 2017 IEEE 24th International Conference on High Performance Computing (HiPC), IEEE, Dec, 2017.
DOI: 10.1109/hipc.2017.00034

Hierarchical data representations have been shown to be effective tools for coping with large-scale scientific data. Writing hierarchical data on supercomputers, however, is challenging as it often involves all-to-one communication during aggregation of low-resolution data which tends to span the entire network domain, resulting in several bottlenecks. We introduce the concept of indexing templates, which succinctly describe data organization and can be used to alter movement of data in beneficial ways. We present two techniques, domain partitioning and localized aggregation, that leverage indexing templates to alleviate congestion and synchronization overheads during data aggregation. We report experimental results that show significant I/O speedup using our proposed schemes on two of today's fastest supercomputers, Mira and Shaheen II, using the Uintah and S3D simulation frameworks.