SCI Publications

2007


C.P. Gribble, C. Brownlee, S.G. Parker. “Practical Global Illumination for Interactive Particle Visualization,” In Computers and Graphics, Vol. 32, No. 1, pp. 14--24. February, 2007.


A. Gyulassy, V. Natarajan, B. Hamann, V. Pascucci. “Efficient Computation of Morse-Smale Complexes for Three-dimensional Scalar Functions,” In IEEE Transactions on Visualization and Computer Graphics, Note: (presented at IEEE VIS 2007), 2007.


A. Gyulassy, V. Natarajan, B. Hamann, M. Duchaineau, V. Pascucci, E. Bringa, A. Higginbotham. “Topologically Clean Distance Fields,” In IEEE Transactions on Visualization and Computer Graphics, Note: (presented at IEEE VIS 2007), 2007.


C.W. Hamman, R.M. Kirby, M. Berzins. “Parallelization and Scalability of a Spectral Element Channel Flow Solver for Incompressible Navier-Stokes Equations,” In Concurrency and Computation: Practice and Experience, Vol. 14, No. 10, pp. 1403--1422. 2007.


C.R. Hamman, R.M. Kirby, M. Berzins. “Parallel Direct Simulation of Incompressible Navier Stokes Equations,” In Concurrency and Computation, Vol. 19, No. 10, pp. 1403-1427. 2007.


H.B. Henninger, C.J. Underwood, S.A. Maas, R.T. Whitaker, J.A. Weiss. “Spatial Distribution and Orientation of Dermatan Sulfate in Human Medial Collateral Ligament,” In Journal of Structural Biology, Vol. 158, No. 1, pp. 33--45. April, 2007.
DOI: 10.1016/j.jsb.2006.10.008

ABSTRACT

The proteoglycan decorin and its associated glycosaminoglycan (GAG), dermatan sulfate (DS), regulate collagen fibril formation, control fibril diameter, and have been suggested to contribute to the mechanical stability and material properties of connective tissues. The spatial distribution and orientation of DS within the tissue are relevant to these mechanical roles, but measurements of length and orientation from 2D transmission electron microscopy (TEM) are prone to errors from projection. The objectives of this study were to construct a 3D geometric model of DS GAGs and collagen fibrils, and to use the model to interpret TEM measurements of the spatial orientation and length of DS GAGs in the medial collateral ligament of the human knee. DS was distinguished from other sulfated GAGs by treating tissue with chondroitinase B, an enzyme that selectively degrades DS. An image processing pipeline was developed to analyze the TEM micrographs. The 3D model of collagen and GAGs quantified the projection error in the 2D TEM measurements. Model predictions of 3D GAG orientation were highly sensitive to the assumed GAG length distribution, with the baseline input distribution of 69 ± 23 nm providing the best predictions of the angle measurements from TEM micrographs. The corresponding orientation distribution for DS GAGs was maximal at orientations orthogonal to the collagen fibrils, tapering to near zero with axial alignment. Sulfated GAGs that remained after chondroitinase B treatment were preferentially aligned along the collagen fibril. DS therefore appears more likely to bridge the interfibrillar gap than non-DS GAGs. In addition to providing quantitative data for DS GAG length and orientation in the human MCL, this study demonstrates how a 3D geometric model can be used to provide a priori information for interpretation of geometric measurements from 2D micrographs.

Keywords: computational biomechanics, mrl


X. Huang, Y.Z. Lee, M. McKeown, G. Gerig, H. Gu, W. Lin, M.M. Lewis, S. Ford, A.I. Troster, D.R. Weinberger, Styner. “Asymmetrical ventricular enlargement in Parkinson's Disease,” In Movement Disorders, Vol. 22, No. 11, pp. 1657--1660. August 15, 2007.


M. Ikits. “Interactive Exploration of Volumetric Data Sets With a Combined Visual and Haptic Interface,” Note: Ph.D. Thesis, University of Utah School of Computing, 2007.


T. Ize, I. Wald, S.G. Parker. “Asynchronous BVH Construction for Ray Tracing Dynamic Scenes on Parallel Multi-Core Architectures,” In Proceedings of the 2007 Eurographics Symposium on Parallel Graphics and Visualization, pp. 101--108. 2007.


T. Ize, P. Shirley, S.G. Parker. “Grid Creation Strategies for Efficient Ray Tracing,” In Proceedings of the 2007 IEEE/Eurographics Symposium on Interactive Ray Tracing, pp. 27--32. 2007.


W.-K. Jeong, P.T. Fletcher, R. Tao, R.T. Whitaker. “Interactive Visualization of Volumetric White Matter Connectivity in DT-MRI Using a Parallel-Hardware Hamilton-Jacobi Solver,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 6, pp. 1480--1487. 2007.
PubMed ID: 17968100


C.R. Johnson, R. Ross, S. Ahern, J. Ahrens, W. Bethel, K.L. Ma, M. Papka, J. van Rosendale, H.W. Shen, J. Thomas. “DOE Visualization and Knowledge Discovery,” Note: Report from the DOE/ASCR Workshop on Visual Analysis and Data Exploration at Extreme Scale, October, 2007.


M. Jolley, J.G. Stinstra, D.M. Weinstein, S. Pieper, R.S.J. Estepar, G. Kindlmann, R.S. MacLeod, D.H. Brooks, J.K. Triedman. “Open-Source Environment for Interactive Finite Element Modeling of Optimal ICD Electrode Placement,” In Functional Imaging and Modeling of the Heart, Lecture Notes in Computer Science (LCNS), Vol. 4466/2007, pp. 373--382. 2007.
ISBN: 978-3-540-72906-8


B.W. Jones, R.E. Marc, C.B. Watt, K. Kinardi, D. DeMill, J.H. Yang, T. Tasdizen, P. Koshevoy, E. Jurrus, R.T. Whitaker. “Structure and Function of Microneuromas in Retinal Remodeling,” In The Association for Research in Vision and Ophthalmology (ARVO) Conference, Note: (abstract), 2007.


C. Jones, K.-L. Ma, A.R. Sanderson, L. Myers. “Visual Interrogation of Gyrokinetic Particle Simulations,” In Journal of Physics, Conference Series, Vol. 78, pp. 012033 (6pp). 2007.


G. Kindlmann, D.B. Ennis, R.T. Whitaker, C.-F. Westin. “Diffusion Tensor Analysis With Invariant Gradients and Rotation Tangents,” In IEEE Transactions on Medical Imaging, Vol. 26, No. 11, pp. 1483--1499. 2007.


R.M. Kirby, Z. Yosibash, G.E. Karniadakis. “Towards Stable Coupling Methods for High-Order Discretizations of Fluid-Structure Interaction: Algorithms and Observations,” In Journal of Computational Physics, Vol. 223, No. 2, pp. 489--518. 2007.


J.M. Kniss, W. Hunt, K. Potter, P. Sen. “IStar: A Raster Representation for Scalable Image and Volume Data,” In IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 13, No. 6, pp. 1424--1431. Nov, 2007.
DOI: 10.1109/TVCG.2007.70572

ABSTRACT

Topology has been an important tool for analyzing scalar data and flow fields in visualization. In this work, we analyze the topology of multivariate image and volume data sets with discontinuities in order to create an efficient, raster-based representation we call IStar. Specifically, the topology information is used to create a dual structure that contains nodes and connectivity information for every segmentable region in the original data set. This graph structure, along with a sampled representation of the segmented data set, is embedded into a standard raster image which can then be substantially downsampled and compressed. During rendering, the raster image is upsampled and the dual graph is used to reconstruct the original function. Unlike traditional raster approaches, our representation can preserve sharp discontinuities at any level of magnification, much like scalable vector graphics. However, because our representation is raster-based, it is well suited to the real-time rendering pipeline. We demonstrate this by reconstructing our data sets on graphics hardware at real-time rates.


A. Knoll, C.D. Hansen, I. Wald. “Coherent Multiresolution Isosurface Ray Tracing,” SCI Institute Technical Report, No. UUSCI-2007-001, University of Utah, 2007.


A. Knoll, Y. Hijazi, C.D. Hansen, I. Wald, H. Hagen. “Interactive Ray Tracing of Arbitrary Implicit Functions,” SCI Institute Technical Report, No. UUSCI-2007-002, University of Utah, 2007.