SCIENTIFIC COMPUTING AND IMAGING INSTITUTE
at the University of Utah

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

SCI Publications

2010


C.E. Scheidegger, T. Etiene, L.G. Nonato, C.T. Silva. “Edge Flows: Stratified Morse Theory for Simple, Correct Isosurface Extraction,” SCI Technical Report, No. UUSCI-2010-002, SCI Institute, University of Utah, 2010.


M. Schott, P. Grosset, T. Martin, V. Pegoraro, C.D. Hansen. “Depth of Field Effects for Interactive Direct Volume Rendering,” SCI Technical Report, No. UUSCI-2010-005, SCI Institute, University of Utah, 2010.


C. Schlimper, O. Nemitz, U. Dorenbeck, J. Scorzin, R.T. Whitaker, T. Tasdizen, M. Rumpf, K. Schaller. “Restoring three-dimensional magnetic resonance angiography images with mean curvature motion,” In Neurological Research, Vol. 32, No. 1, Note: Epub 2009 Nov 26, pp. 87--93. February, 2010.
DOI: 10.1179/016164110X12556180206077
PubMed ID: 19941735


N.M. Segerson, M. Daccarett, T.J. Badger, A. Shabaan, N. Akoum, E.N. Fish, S. Rao, N.S. Burgon, Y. Adjei-Poku, E. Kholmovski, S. Vijayakumar, E.V. DiBella, R.S. MacLeod, N.F. Marrouche. “Magnetic resonance imaging-confirmed ablative debulking of the left atrial posterior wall and septum for treatment of persistent atrial fibrillation: rationale and initial experience,” In Journal of Cardiovascular Electrophysiology, Vol. 21, No. 2, pp. 126--132. 2010.
PubMed ID: 19804549


M. Seyedhosseini, A.R.C. Paiva, T. Tasdizen. “Image Parsing with a Three-State Series Neural Network Classifier,” In Proc. IEEE Intl. Conference on Pattern Recognition, Istanbul, Turkey, pp. 4508--4511. 2010.
DOI: 10.1109/ICPR.2010.1095


C. Silva, E. Anderson, E. Santos, J. Freire. “Using VisTrails and Provenance for Teaching Scientific Visualization,” In EUROGRAPHICS 2010 Educator Program, Note: Awarded Best Paper!, 2010.


N.P. Singh, P.T. Fletcher, J.S. Preston, L. Ha, R. King, J.S. Marron, M. Wiener, S. Joshi. “Multivariate Statistical Analysis of Deformation Momenta Relating Anatomical Shape to Neuropsychological Measures,” In Medical Image Computing and Computer-Assisted Intervention – MICCAI 2010, Lecture Notes in Computer Science (LCNS), Vol. 6363/2010, pp. 529-537. 2010.
DOI: 10.1007/978-3-642-15711-0_66
PubMed ID: 20879441


M. Steffen, R.M. Kirby, M. Berzins. “Decoupling and Balancing of Space and Time Errors in the Material Point Method (MPM),” In International Journal for Numerical Methods in Engineering, Vol. 82, No. 10, pp. 1207--1243. 2010.


J.G. Stinstra, R.S. MacLeod, C.S. Henriquez. “Incorporating Histology into a 3D Microscopic Computer Model of Myocardium to Study Propagation at a Cellular Level,” In Annals of Biomedical Engineering (ABME), Vol. 38, No. 4, pp. 3399--1414. 2010.
DOI: 10.1007/s10439-009-9883-y


D. Swenson, J.A. Levine, Z. Fu, J.D. Tate, R.S. MacLeod. “The Effect of Non-Conformal Finite Element Boundaries on Electrical Monodomain and Bidomain Simulations,” In Computing in Cardiology, Vol. 37, IEEE, pp. 97--100. 2010.
ISSN: 0276-6547


T. Tasdizen, P. Koshevoy, B.C. Grimm, J.R. Anderson, B.W. Jones, C.B. Watt, R.T. Whitaker, R.E. Marc. “Automatic mosaicking and volume assembly for high-throughput serial-section transmission electron microscopy,” In Journal of Neuroscience Methods, Vol. 193, No. 1, pp. 132--144. 2010.
PubMed ID: 20713087


J.D. Tate, J.G. Stinstra, T.A. Pilcher, R.S. MacLeod. “Implantable Cardioverter Defibrillator Predictive Simulation Validation,” In Computing in Cardiology, pp. 853-–856. September, 2010.

ABSTRACT

Despite the growing use of implantable cardioverter defibrillators (ICDs) in adults and children, there has been little progress in optimizing device and electrode placement. To facilitate effective placement of ICDs, especially in unique cases of children with congenital heart defects, we have developed a predictive model that evaluates the efficacy of a delivered shock. Most recently, we have also developed and carried out an experimental validation approach based on measurements from clinical cases. We have developed a method to obtain body surface potential maps of ICD discharges during implantation surgery and compared these measured potentials with simulated surface potentials to determine simulation accuracy.

Each study began with an full torso MRI or CT scan of the subject, from which we created patient specific geometric models. Using a customized limited leadset applied to the anterior surface of the torso away from the sterile field, we recorded body surface potentials during ICD testing. Subsequent X-ray images documented the actual location of ICD and electrodes for placement of the device in the geometric model. We then computed the defibrillation field, including body surface potentials, and compared them to the measured values.

Comparison of the simulated and measured potentials yielded very similar patterns and a typical correlation between 0.8 and 0.9 and a percentage error between 0.2 and 0.35. The high correlation of the potential maps suggest that the predictive simulation generates realistic potential values. Ongoing sensi- tivity studies will determine the robustness of the results and pave the way for use of this approach for predictive computational optimization studies before device implantation.


R. Tchoua, S. Klasky, N. Podhorszki, B. Grimm, A. Khan, E. Santos, C.T. Silva, P. Mouallem, M. Vouk. “Collaborative Monitoring and Analysis for Simulation Scientists,” In Proceedings of The 2010 International Symposium on Collaborative Technologies and Systems (CTS 2010), pp. 235--244. 2010.
DOI: 10.1109/CTS.2010.5478506

ABSTRACT

Collaboratively monitoring and analyzing large scale simulations from petascale computers is an important area of research and development within the scientific community. This paper addresses these issues when teams of colleagues from different research areas work together to help understand the complex data generated from these simulations. In particular, we address the issues when geographically diverse teams of disparate researchers work together to understand the complex science being simulated on high performance computers. Most application scientists want to focus on the sciences and spend a minimum amount of time learning new tools or adopting new techniques to monitor and analyze their simulation data. The challenge of eSimMon, our web-based system is to decrease or eliminate some of the hurdles on the scientists' path to scientific discovery, and allow these collaborations to flourish.

Keywords: collaboration, simulation


J. Tierny, J. Daniels II, L.G. Nonato, V. Pascucci, C.T. Silva. “Interactive Quadrangulation with Reeb Atlases and Connectivity Textures,” SCI Technical Report, No. UUSCI-2010-006, SCI Institute, University of Utah, 2010.


N.J. Tustison, S.P. Awate, J. Cai, T.A. Altes, G.W. Miller, E.E. de Lange, J.P. Mugler 3rd, J.C. Gee. “Pulmonary kinematics from tagged hyperpolarized helium-3 MRI,” In Journal of Magnetic Resonance Imaging, JMRI, Vol. 31, No. 5, pp. 1236--1241. 2010.
PubMed ID: 20432362


C. Tuttle, L.G. Nonato, C.T. Silva. “PedVis: A Structured, Space-Efficient Technique for Pedigree Visualization,” In IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 16, No. 6, pp. 1063--1072. Nov, 2010.
DOI: 10.1109/TVCG.2010.185

ABSTRACT

Public genealogical databases are becoming increasingly populated with historical data and records of the current population's ancestors. As this increasing amount of available information is used to link individuals to their ancestors, the resulting trees become deeper and more dense, which justifies the need for using organized, space-efficient layouts to display the data. Existing layouts are often only able to show a small subset of the data at a time. As a result, it is easy to become lost when navigating through the data or to lose sight of the overall tree structure. On the contrary, leaving space for unknown ancestors allows one to better understand the tree's structure, but leaving this space becomes expensive and allows fewer generations to be displayed at a time. In this work, we propose that the H-tree based layout be used in genealogical software to display ancestral trees. We will show that this layout presents an increase in the number of displayable generations, provides a nicely arranged, symmetrical, intuitive and organized fractal structure, increases the user's ability to understand and navigate through the data, and accounts for the visualization requirements necessary for displaying such trees. Finally, user-study results indicate potential for user acceptance of the new layout.


A. van Dam, J. Foley, J. Guttag, P. Hanrahan, C.R. Johnson, R. Katz, H. Kelly, P. Lee, D.E. Shaw. “CRA-E White Paper: Creating Environments for Computational Researcher Education,” Note: Computing Research Association (CRA), August, 2010.


H.T. Vo, D.K. Osmari, B. Summa, J.L.D. Comba, V. Pascucci, C.T. Silva. “Streaming-Enabled Parallel Dataflow Architecture for Multicore Systems,” In Computer Graphics Forum, Vol. 29, No. 3, pp. 1073--1082. 2010.


H.T. Vo, D.K. Osmari, B. Summa, J.L.D. Comba, V. Pascucci, C.T. Silva. “Streaming-Enabled Parallel Dataflow Architecture for Multicore Systems,” In Computer Graphics Forum, Vol. 29, No. 3, Wiley-Blackwell, pp. 1073--1082. Aug, 2010.
DOI: 10.1111/j.1467-8659.2009.01704.x

ABSTRACT

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We propose a new framework design for exploiting multi-core architectures in the context of visualization dataflow systems. Recent hardware advancements have greatly increased the levels of parallelism available with all indications showing this trend will continue in the future. Existing visualization dataflow systems have attempted to take advantage of these new resources, though they still have a number of limitations when deployed on shared memory multi-core architectures. Ideally, visualization systems should be built on top of a parallel dataflow scheme that can optimally utilize CPUs and assign resources adaptively to pipeline elements. We propose the design of a flexible dataflow architecture aimed at addressing many of the shortcomings of existing systems including a unified execution model for both demand-driven and event-driven models; a resource scheduler that can automatically make decisions on how to allocate computing resources; and support for more general streaming data structures which include unstructured elements. We have implemented our system on top of VTK with backward compatibility. In this paper, we provide evidence of performance improvements on a number of applications.


P.E.J. Vos, S.J. Sherwin, R.M. Kirby. “h-p Efficiently: Implementing Finite and Spectral/hp Element Methods to Achieve Optimal Performance for Low- and High-Order Discretisations,” In Journal of Computational Physics, Vol. 229, No. 13, pp. 5161--5181. 2010.