SCIENTIFIC COMPUTING AND IMAGING INSTITUTE
at the University of Utah

An internationally recognized leader in visualization, scientific computing, and image analysis

SCI Publications

2011


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


Bei Wang, B. Summa, V. Pascucci, M. Vejdemo-Johansson. “Branching and Circular Features in High Dimensional Data,” 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

ABSTRACT

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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


D. Wang, R.M. Kirby, R.S. Macleod, C.R. Johnson. “An optimization framework for inversely estimating myocardial transmembrane potentials and localizing ischemia,” In Proceedings of the International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS), pp. 1680--1683. 2011.
DOI: 10.1109/IEMBS.2011.6090483
PubMed ID: 22254648
PubMed Central ID: PMC3336368

ABSTRACT

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By combining a static bidomain heart model with a torso conduction model, we studied the inverse electrocardiographic problem of computing the transmembrane potentials (TMPs) throughout the myocardium from a body-surface potential map, and then used the recovered potentials to localize myocardial ischemia. Our main contribution is solving the inverse problem within a constrained optimization framework, which is a generalization of previous methods for calculating transmembrane potentials. The framework offers ample flexibility for users to apply various physiologically-based constraints, and is well supported by mature algorithms and solvers developed by the optimization community. By avoiding the traditional inverse ECG approach of building the lead-field matrix, the framework greatly reduces computation cost and, by setting the associated forward problem as a constraint, the framework enables one to flexibly set individualized resolutions for each physical variable, a desirable feature for balancing model accuracy, ill-conditioning and computation tractability. Although the task of computing myocardial TMPs at an arbitrary time instance remains an open problem, we showed that it is possible to obtain TMPs with moderate accuracy during the ST segment by assuming all cardiac cells are at the plateau phase. Moreover, the calculated TMPs yielded a good estimate of ischemic regions, which was of more clinical interest than the voltage values themselves. We conducted finite element simulations of a phantom experiment over a 2D torso model with synthetic ischemic data. Preliminary results indicated that our approach is feasible and suitably accurate for the common case of transmural myocardial ischemia.


S. Williams, M. Petersen, P.-T. Bremer, M. Hecht, V. Pascucci, J. Ahrens, M. Hlawitschka, B. Hamann. “Adaptive Extraction and Quantification of Geophysical Vortices,” In IEEE Transactions on Visualization and Computer Graphics, Proceedings of the 2011 IEEE Visualization Conference, Vol. 17, No. 12, pp. 2088--2095. 2011.


C. Yang, D. Xiu, R.M. Kirby. “Visualization of Covariance and Cross-covariance Field,” In International Journal for Uncertainty Quantification, Vol. 3, No. 1, pp. 25--38. 2011.
DOI: 10.1615/Int.J.UncertaintyQuantification.2011003369

ABSTRACT

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We present a numerical technique to visualize covariance and cross-covariance fields of a stochastic simulation. The method is local in the sense that it demonstrates the covariance structure of the solution at a point with its neighboring locations. When coupled with an efficient stochastic simulation solver, our framework allows one to effectively concurrently visualize both the mean and (cross-)covariance information for two-dimensional (spatial) simulation results. Most importantly, the visualization provides the scientist a means to identify interesting correlation structure of the solution field. The mathematical setup is discussed, along with several examples to demonstrate the efficacy of this approach.

Keywords: netl


H. Zhu, L. Kong, R. Li, M.S. Styner, G. Gerig, W. Lin, J.H. Gilmore. “FADTTS: Functional Analysis of Diffusion Tensor Tract Statistics,” In NeuroImage, Vol. 56, No. 3, pp. 1412--1425. 2011.
DOI: 10.1016/j.neuroimage.2011.01.075
PubMed ID: 21335092

2010


G. Adluru, T. Tasdizen, M.C. Schabel, E.V.R. DiBella. “Reconstruction of 3D Dynamic Contrast-Enhanced Magnetic Resonance Imaging Using Nonlocal Means,” In Journal of Magnetic Resonance Imaging, Vol. 32, pp. 1217--1227. 2010.
DOI: 10.1002/jmri.22358


G. Adluru, T. Tasdizen, R. Whitaker, E. DiBella. “Improving Undersampled MRI Reconstruction Using Non-Local Means,” In Proceedings of the 2010 International Conference on Pattern Recognition, pp. 4000--4003. 2010.
DOI: 10.1109/ICPR.2010.973


A.E. Anderson, B.J. Ellis, S.A. Maas, J.A. Weiss. “Effects of idealized joint geometry on finite element predictions of cartilage contact stresses in the hip,” In Journal of Biomechanics, Vol. 43, No. 7, pp. 1351--1357. May, 2010.

ABSTRACT

Computational models may have the ability to quantify the relationship between hip morphology, cartilage mechanics and osteoarthritis. Most models have assumed the hip joint to be a perfect ball and socket joint and have neglected deformation at the bone-cartilage interface. The objective of this study was to analyze finite element (FE) models of hip cartilage mechanics with varying degrees of simplified geometry and a model with a rigid bone material assumption to elucidate the effects on predictions of cartilage stress. A previously validated subject-specific FE model of a cadaveric hip joint was used as the basis for the models. Geometry for the bone-cartilage interface was either: (1) subject-specific (i.e. irregular), (2) spherical, or (3) a rotational conchoid. Cartilage was assigned either a varying (irregular) or constant thickness (smoothed). Loading conditions simulated walking, stair-climbing and descending stairs. FE predictions of contact stress for the simplified models were compared with predictions from the subject-specific model. Both spheres and conchoids provided a good approximation of native hip joint geometry (average fitting error ∼0.5 mm). However, models with spherical/conchoid bone geometry and smoothed articulating cartilage surfaces grossly underestimated peak and average contact pressures (50% and 25% lower, respectively) and overestimated contact area when compared to the subject-specific FE model. Models incorporating subject-specific bone geometry with smoothed articulating cartilage also underestimated pressures and predicted evenly distributed patterns of contact. The model with rigid bones predicted much higher pressures than the subject-specific model with deformable bones. The results demonstrate that simplifications to the geometry of the bone-cartilage interface, cartilage surface and bone material properties can have a dramatic effect on the predicted magnitude and distribution of cartilage contact pressures in the hip joint.

Keywords: mrl


E.W. Anderson, G.A. Preston, C.T. Silva. “Using Python for Signal Processing and Visualization,” In IEEE Computing in Science and Engineering, Vol. 12, No. 4, pp. 90--95. 2010.


J.R. Anderson, B.C. Grimm, S. Mohammed, B.W. Jones, T. Tasdizen, J. Spaltenstein, P. Koshevoy, R.T. Whitaker, R.E. Marc. “The Viking Viewer: Scalable Multiuser Annotation and Summarization of Large Volume Datasets,” In Journal of Microscopy, Vol. 241, No. 1, pp. 13--28. 2010.
DOI: 10.1111/j.1365-2818.2010.03402.x


G.A. Ateshian, S.A. Maas, J.A. Weiss. “Finite element algorithm for frictionless contact of porous permeable media under finite deformation and sliding,” In Journal of Biomechanical Engineering, Vol. 132, No. 6, Note: Cover article, 2010.


S.P. Awate, P.A. Yushkevich, Z. Song, D.J. Licht, J.C. Gee. “Cerebral cortical folding analysis with multivariate modeling and testing: Studies on gender differences and neonatal development,” In NeuroImage, Vol. 53, No. 2, pp. 450--459. 2010.
PubMed ID: 20630489


T.J. Badger, M. Daccarett, N.W. Akoum, Y.A. Adjei-Poku, N.S. Burgon, T.S. Haslam, S. Kalvaitis, S. Kuppahally, G. Vergara, L. McMullen, P.A. Anderson, E. Kholmovski, R.S. Macleod, N.F. Marrouche. “Evaluation of left atrial lesions after initial and repeat atrial fibrillation ablation: lessons learned from delayed-enhancement MRI in repeat ablation procedures,” In Circulation. Arrhythmia and Electrophysiology, Vol. 3, No. 3, pp. 249--259. 2010.
PubMed ID: 20335558


M. Berger, L.G. Nonato, V. Pascucci, C.T. Silva. “Fiedler Trees for Multiscale Surface Analysis,” In Computer & Graphics, Vol. 34, No. 3, Note: Special Issue of Sha, pp. 272--281. June, 2010.
DOI: 10.1016/j.cag.2010.03.009

ABSTRACT

In this work we introduce a new hierarchical surface decomposition method for multiscale analysis of surface meshes. In contrast to other multiresolution methods, our approach relies on spectral properties of the surface to build a binary hierarchical decomposition. Namely, we utilize the first nontrivial eigenfunction of the Laplace–Beltrami operator to recursively decompose the surface. For this reason we coin our surface decomposition the Fiedler tree. Using the Fiedler tree ensures a number of attractive properties, including: mesh-independent decomposition, well-formed and nearly equi-areal surface patches, and noise robustness. We show how the evenly distributed patches can be exploited for generating multiresolution high quality uniform meshes. Additionally, our decomposition permits a natural means for carrying out wavelet methods, resulting in an intuitive method for producing feature-sensitive meshes at multiple scales.


M. Berzins, J. Luitjens, Q. Meng, T. Harman, C.A. Wight, J.R. Peterson. “Uintah: A Scalable Framework for Hazard Analysis,” In Proceedings of the Teragrid 2010 Conference, TG 10, Note: Awarded Best Paper in the Science Track!, pp. (published online). July, 2010.
ISBN: 978-1-60558-818-6
DOI: 10.1145/1838574.1838577

ABSTRACT

The Uintah Software system was developed to provide an environment for solving a fluid-structure interaction problems on structured adaptive grids on large-scale, long-running, data-intensive problems. Uintah uses a novel asynchronous task-based approach with fully automated load balancing. The application of Uintah to a petascale problem in hazard analysis arising from "sympathetic" explosions in which the collective interactions of a large ensemble of explosives results in dramatically increased explosion violence, is considered. The advances in scalability and combustion modeling needed to begin to solve this problem are discussed and illustrated by prototypical computational results.

Keywords: Uintah, csafe


M. Berzins. “Nonlinear Data-Bounded Polynomial Approximations and their Applications in ENO Methods,” In Numerical Algorithms, Vol. 55, No. 2, pp. 171. 2010.


J.J.E. Blauer, J. Cates, C.J. McGann, E.G. Kholmovski, A. Alexander, M.W. Prastawa, S. Joshi, N.F. Marrouche, R.S. MacLeod. “MRI Based Injury Characterization Immediately Following Ablation of Atrial Fibrillation,” In Computing in Cardiology, Vol. 37, pp. 165--168. 2010.
ISSN: 0276−6574


C. Brownlee, V. Pegoraro, S. Shankar, P. McCormick, C.D. Hansen. “Physically-Based Interactive Schlieren Flow Visualization,” In Proceedings of IEEE Pacific Visualization 2010, Note: Won Best Paper Award!, 2010.


J.R. Bronson, J.A. Levine, R.T. Whitaker. “Particle Systems for Adaptive, Isotropic Meshing of CAD Models,” In Proceedings of the 19th International Meshing Roundtable, Note: Awarded Best Paper, Springer, pp. 279-296. 2010.
DOI: 10.1007/978-3-642-15414-0_17

ABSTRACT

We present a particle-based approach for generating adaptive triangular surface and tetrahedral volume meshes from CAD models. Input shapes are treated as a collection of smooth, parametric surface patches that can meet non-smoothly on boundaries. Our approach uses a hierarchical sampling scheme that places particles on features in order of increasing dimensionality. These particles reach a good distribution by minimizing an energy computed in 3D world space, with movements occurring in the parametric space of each surface patch.

Rather than using a pre-computed measure of feature size, our system automatically adapts to both curvature as well as a notion of topological separation. It also enforces a measure of smoothness on these constraints to construct a sizing field that acts as a proxy to piecewise-smooth feature size. We evaluate our technique with comparisons against other popular triangular meshing techniques for this domain.