Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
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, 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.


Charles Hansen

Volume Rendering
Ray Tracing

Valerio Pascucci

Topological Methods
Data Streaming
Big Data

Chris Johnson

Scalar, Vector, and
Tensor Field Visualization,
Uncertainty Visualization

Mike Kirby

Uncertainty Visualization

Ross Whitaker

Topological Methods
Uncertainty Visualization
alex lex

Alex Lex

Information Visualization

Bei Wang

Information Visualization
Scientific Visualization
Topological Data Analysis

Centers and Labs:

Funded Research Projects:

Publications in Visualization:

Multi-Resolution-Display System for Virtual Reality Setups
J. Grueninger, H. Hoffman, U. Kloos, J. Krüger. In Proceedings of the 14th International Conference on Human-Computer Interaction, HCI International, Lecture Notes in Computer Science, Vol. 6779/2011, pp. 180--189. 2011.
DOI: 10.1007/978-3-642-21716-6_19

Most large-area video projection systems offer only limited spacial resolution. Consequently, images of detailed scenery cannot be displayed at full fidelity. A possible but significantly more costly strategy is a tiled projection display. If this solution is not feasible then either aliasing occurs or some anti-aliasing method is used at the cost of reduced scene quality.

In this paper we describe a novel cost effective multi-resolution display system. It allows users to select any part of a stereoscopic projection and view it in significantly higher resolution than possible with the standard projection alone. To achieve this, a pair of video projectors, which can be moved by stepper motors, project a high-resolution inset into a small portion of the low-resolution image. To avoid crosstalk between the low and high resolution projections, a mask is rendered into the low resolution scene to black out the area on the screen that is covered by the inlay.

To demonstrate the effectiveness of our multi-resolution display setup it has been integrated into a number of real life scenarios: a virtual factory, an airplane cabin simulation, and a focus and context volume visualization application (see Figure 1).

Visualization of Discrete Gradient Construction (Multimedia submission)
Attila Gyulassy, J.A. Levine, V. Pascucci. In Proceedings of the 27th Symposium on Computational Geometry, Paris, France, ACM, pp. 289--290. June, 2011.
DOI: 10.1145/1998196.1998241

This video presents a visualization of a recent algorithm to compute discrete gradient fields on regular cell complexes [3]. Discrete gradient fields are used in practical methods that robustly translate smooth Morse theory to combinatorial domains. We describe the stages of the algorithm, highlighting both its simplicity and generality.

GPU-Based Interactive Cut-Surface Extraction From High-0rder Finite Element Fields
B. Nelson, R. Haimes, R.M. Kirby. In IEEE Transactions on Visualization and Computer Graphics (IEEE Visualization Issue), Vol. 17, No. 12, pp. 1803--1811. 2011.

We present a GPU-based ray-tracing system for the accurate and interactive visualization of cut-surfaces through 3D simulations of physical processes created from spectral/hp high-order finite element methods. When used by the numerical analyst to debug the solver, the ability for the imagery to precisely reflect the data is critical. In practice, the investigator interactively selects from a palette of visualization tools to construct a scene that can answer a query of the data. This is effective as long as the implicit contract of image quality between the individual and the visualization system is upheld. OpenGL rendering of scientific visualizations has worked remarkably well for exploratory visualization for most solver results. This is due to the consistency between the use of first-order representations in the simulation and the linear assumptions inherent in OpenGL (planar fragments and color-space interpolation). Unfortunately, the contract is broken when the solver discretization is of higher-order. There have been attempts to mitigate this through the use of spatial adaptation and/or texture mapping. These methods do a better job of approximating what the imagery should be but are not exact and tend to be view-dependent. This paper introduces new rendering mechanisms that specifically deal with the kinds of native data generated by high-order finite element solvers. The exploratory visualization tools are reassessed and cast in this system with the focus on image accuracy. This is accomplished in a GPU setting to ensure interactivity.

Flow Visualization with Quantified Spatial and Temporal Errors using Edge Maps
H. Bhatia, S. Jadhav, P.-T. Bremer, G. Chen, J.A. Levine, L.G. Nonato, V. Pascucci. In IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 18, No. 9, IEEE Society, pp. 1383--1396. 2011.
DOI: 10.1109/TVCG.2011.265

Asymmetric Tensor Field Visualization for Surfaces
G. Chen, D. Palke, Z. Lin, H. Yeh, P. Vincent, R.S. Laramee, E. Zhang. In IEEE Transactions on Visualization and Computer Graphics, Vol. 17, No. 12, IEEE, pp. 1979-1988. Dec, 2011.
DOI: 10.1109/tvcg.2011.170

Combinatorial Vector Field Topology in 3 Dimensions
W. Reich, Dominic Schneider, Christian Heine, Alexander Wiebel, Guoning Chen, Gerik Scheuermann. In Mathematical Methods in Biomedical Image Analysis (MMBIA) Proceedings IEEE MMBIA 2012, pp. 47--59. November, 2011.
DOI: 10.1007/978-3-642-23175-9_4

In this paper, we present two combinatorial methods to process 3-D steady vector fields, which both use graph algorithms to extract features from the underlying vector field. Combinatorial approaches are known to be less sensitive to noise than extracting individual trajectories. Both of the methods are a straightforward extension of an existing 2-D technique to 3-D fields. We observed that the first technique can generate overly coarse results and therefore we present a second method that works using the same concepts but produces more detailed results. We evaluate our method on a CFD-simulation of a gas furnace chamber. Finally, we discuss several possibilities for categorizing the invariant sets with respect to the flow.

Automatic Stream Surface Seeding
M. Edmunds, T. McLoughlin, R.S. Laramee, G. Chen, E. Zhang, N. Max. In EUROGRAPHICS 2011 Short Papers, pp. 53--56. 2011.

A wildland fire modeling and visualization environment,
J. Mandel, J.D. Beezley, A. Kochanski, V.Y. Kondratenko, L. Zhang, E. Anderson, J. Daniels II, C.T. Silva, C.R. Johnson. In Proceedings of the Ninth Symposium on Fire and Forest Meteorology, pp. (published online). 2011.

Simple and Efficient Mesh Layout with Space-Filling Curves
H.T. Vo, C.T. Silva, L.F. Scheidegger, V. Pascucci. In Journal of Graphics, GPU, and Game Tools, pp. 25--39. 2011.
ISSN: 2151-237X

Feature-Based Statistical Analysis of Combustion Simulation Data
J.C. Bennett, V. Krishnamoorthy, S. Liu, R.W. Grout, E.R. Hawkes, J.H. Chen, J. Shepherd, V. Pascucci, P.-T. Bremer. In IEEE Transactions on Visualization and Computer Graphics, Proceedings of the 2011 IEEE Visualization Conference, Vol. 17, No. 12, pp. 1822--1831. 2011.

Branching and Circular Features in High Dimensional Data
Bei Wang, B. Summa, V. Pascucci, M. Vejdemo-Johansson. In IEEE Transactions of Visualization and Computer Graphics (TVCG), Vol. 17, No. 12, pp. 1902--1911. 2011.
DOI: 10.1109/TVCG.2011.177
PubMed ID: 22034307

Large observations and simulations in scientific research give rise to high-dimensional data sets that present many challenges and opportunities in data analysis and visualization. Researchers in application domains such as engineering, computational biology, climate study, imaging and motion capture are faced with the problem of how to discover compact representations of high dimensional data while preserving their intrinsic structure. In many applications, the original data is projected onto low-dimensional space via dimensionality reduction techniques prior to modeling. One problem with this approach is that the projection step in the process can fail to preserve structure in the data that is only apparent in high dimensions. Conversely, such techniques may create structural illusions in the projection, implying structure not present in the original high-dimensional data. Our solution is to utilize topological techniques to recover important structures in high-dimensional data that contains non-trivial topology. Specifically, we are interested in high-dimensional branching structures. We construct local circle-valued coordinate functions to represent such features. Subsequently, we perform dimensionality reduction on the data while ensuring such structures are visually preserved. Additionally, we study the effects of global circular structures on visualizations. Our results reveal never-before-seen structures on real-world data sets from a variety of applications.

Keywords: Dimensionality reduction, circular coordinates, visualization, topological analysis

Combinatorial Laplacian Image Cloning
A. Cuadros-Vargas, L.G. Nonato, V. Pascucci. In Proceedings of XXIV Sibgrapi – Conference on Graphics, Patterns and Images, pp. 236--241. 2011.
DOI: 10.1109/SIBGRAPI.2011.7

Seamless image cloning has become one of the most important editing operation for photomontage. Recent coordinate-based methods have lessened considerably the computational cost of image cloning, thus enabling interactive applications. However, those techniques still bear severe limitations as to concavities and dynamic shape deformation. In this paper we present novel methodology for image cloning that turns out to be highly efficient in terms of computational times while still being more flexible than existing techniques. Our approach builds on combinatorial Laplacian and fast Cholesky factorization to ensure interactive image manipulation, handling holes, concavities, and dynamic deformations during the cloning process. The provided experimental results show that the proposed technique outperforms existing methods in requisites such as accuracy and flexibility.

Experiences in Disseminating Educational Visualizations
N. Andrysco, P. Rosen, V. Popescu, B. Benes, K.R. Gurney. In Lecture Notes in Computer Science (7th International Symposium on Visual Computing), Vol. 2, pp. 239--248. September, 2011.
DOI: 10.1007/978-3-642-24031-7_24

Most visualizations produced in academia or industry have a specific niche audience that is well versed in either the often complicated visualization methods or the scientific domain of the data. Sometimes it is useful to produce visualizations that can communicate results to a broad audience that will not have the domain specific knowledge often needed to understand the results. In this work, we present our experiences in disseminating the results of two studies to national audience. The resulting visualizations and press releases allowed the studies’ researchers to educate a national, if not global, audience.

An Evaluation of 3-D Scene Exploration Using a Multiperspective Image Framework
P. Rosen, V. Popescu. In The Visual Computer, Vol. 27, No. 6-8, Springer-Verlag New York, Inc., pp. 623--632. 2011.
DOI: 10.1007/s00371-011-0599-2
PubMed ID: 22661796
PubMed Central ID: PMC3364594

Multiperspective images (MPIs) show more than what is visible from a single viewpoint and are a promising approach for alleviating the problem of occlusions. We present a comprehensive user study that investigates the effectiveness of MPIs for 3-D scene exploration. A total of 47 subjects performed searching, counting, and spatial orientation tasks using both conventional and multiperspective images. We use a flexible MPI framework that allows trading off disocclusion power for image simplicity. The framework also allows rendering MPI images at interactive rates, which enables investigating interactive navigation and dynamic 3-D scenes. The results of our experiments show that MPIs can greatly outperform conventional images. For searching, subjects performed on average 28% faster using an MPI. For counting, accuracy was on average 91% using MPIs as compared to 42% for conventional images.

Keywords: Interactive 3-D scene exploration, Navigation, Occlusions, User study, Visual interfaces

A User Study of Visualization Effectiveness Using EEG and Cognitive Load
E.W. Anderson, K.C. Potter, L.E. Matzen, J.F. Shepherd, G.A. Preston, C.T. Silva. In Computer Graphics Forum, Vol. 30, No. 3, Note: Awarded 2nd Best Paper!, Edited by H. Hauser and H. Pfister and J.J. van Wijk, pp. 791--800. June, 2011.
DOI: 10.1111/j.1467-8659.2011.01928.x

Effectively evaluating visualization techniques is a difficult task often assessed through feedback from user studies and expert evaluations. This work presents an alternative approach to visualization evaluation in which brain activity is passively recorded using electroencephalography (EEG). These measurements are used to compare different visualization techniques in terms of the burden they place on a viewer's cognitive resources. In this paper, EEG signals and response times are recorded while users interpret different representations of data distributions. This information is processed to provide insight into the cognitive load imposed on the viewer. This paper describes the design of the user study performed, the extraction of cognitive load measures from EEG data, and how those measures are used to quantitatively evaluate the effectiveness of visualizations.

Branching and Circular Features in High Dimensional Data
SCI Technical Report, Bei Wang, B. Summa, V. Pascucci, M. Vejdemo-Johansson. No. UUSCI-2011-005, SCI Institute, University of Utah, 2011.

Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications (Mathematics and Visualization),
Valerio Pascucci, Xavier Tricoche, Hans Hagen, Julien Tierny. Springer, 2011.
ISBN: 978-3642150135

An End-to-End Framework for Evaluating Surface Reconstruction
SCI Technical Report, M. Berger, J.A. Levine, L.G. Nonato, G. Taubin, C.T. Silva. No. UUSCI-2011-001, SCI Institute, University of Utah, 2011.

Non-Pinhole Approximations for Interactive Rendering
P. Rosen, V. Popescu, K. Hayward, C. Wyman. In IEEE Computer Graphics and Applications, Vol. 99, 2011.

Edge Maps: Representing Flow with Bounded Error
H. Bhatia, S. Jadhav, P.-T. Bremer, G. Chen, J.A. Levine, L.G. Nonato, V. Pascucci. In Proceedings of IEEE Pacific Visualization Symposium 2011, Hong Kong, China, Note: Won Best Paper Award!, pp. 75--82. March, 2011.
DOI: 10.1109/PACIFICVIS.2011.5742375