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.

SCI Publications

2008


S. Gouttard, M. Styner, M.W. Prastawa, J. Piven, G. Gerig. “Assessment of Reliability of Multi-site Neuroimaging via Traveling Phantom Study,” In Proceedings of Medical Image Computing and Computer Assisted Intervention 2008, Lecture Notes in Computer Science LNCS, Vol. 5242, pp. 263--270. September, 2008.



C. 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, 2008.
DOI: 10.1016/j.cag.2007.11.001

ABSTRACT

Particle-based simulation methods are used to model a wide range of complex phenomena and to solve time-dependent problems of various scales. Effective visualizations of the resulting state will communicate subtle changes in the three-dimensional structure, spatial organization, and qualitative trends within a simulation as it evolves. We present two algorithms targeting upcoming, highly parallel multicore desktop systems to enable interactive navigation and exploration of large particle data sets with global illumination effects. Monte Carlo path tracing and texture mapping are used to capture computationally expensive illumination effects such as soft shadows and diffuse interreflection. The first approach is based on precomputation of luminance textures and removes expensive illumination calculations from the interactive rendering pipeline. The second approach is based on dynamic luminance texture generation and decouples interactive rendering from the computation of global illumination effects. These algorithms provide visual cues that enhance the ability to perform analysis and feature detection tasks while interrogating the data at interactive rates. We explore the performance of these algorithms and demonstrate their effectiveness using several large data sets.

Keywords: Interactive particle visualization, Global illumination, Ray tracing



C.W. Hamman, J.C. Klewicki, R.M. Kirby. “On the Lamb Vector Divergence in Navier-Stokes Flows,” In Journal of Fluid Mechanics, Vol. 610, pp. 261--284. 2008.



D.E. Hart. “Adjoint Error Estimation for Elastohydrodynamic Lubrication,” Note: Advisor: Martin Berzins, School of Computing, University of Leeds, January, 2008.

ABSTRACT

In this thesis, adjoint error estimation techniques are applied to complex elastohydrodynamic lubrication (EHL) problems. A functional is introduced, namely the friction, and justification is provided as to why this quantity, and hence its accuracy, is important. An iterative approach has been taken to develop understanding of the mechanisms at work. A series of successively complex cases are proposed, each with adjoint error estimation techniques applied to them. The first step is built up from a model free boundary problem, where the cavitation condition is captured correctly using a sliding mesh. The next problem tackled is a hydrodynamic problem, where non-linear viscosity and density are introduced. Finally, a full EHL line contact problem is introduced, where the surface deforms elastically under pressure. For each case presented, an estimate of a finer mesh friction, calculated from solutions obtained only on a coarse mesh, is corrected according to the adjoint error estimation technique. At each stage, care is taken to ensure that the error estimate is computed accurately when compared against the measured error in the friction.

Non-uniform meshes are introduced for the model free boundary problem. These nonuniform meshes are shown to give the same excellent predictions of the error as uniform meshes. Adaptive refinement is undertaken, with the mesh being refined using the adjoint error estimate. Results for this are presented for both the model free-boundary problem and the full EHL problem. This is shown to enable the accurate calculation of friction values using an order of magnitude fewer mesh points than with a uniform mesh.

Throughout this thesis, standard numerical techniques for calculating EHL solutions have been used. That is, regular mesh finite difference approximations have been used to discretise the problem, with multigrid used to efficiently solve the equations, and spatial adaptivity added through multigrid patches. The adjoint problems have been solved using standard linear algebra packages.



J.S. Hesthaven, R.M. Kirby. “Filtering in Legendre Spectral Methods,” In Mathematics of Computation, Vol. 77, No. 263, pp. 1425--1452. 2008.



Y. Hijazi, A. Knoll, M. Schott, A. Kensler, C.D. Hansen, H. Hagen. “CSG Operations of Arbitrary Primitives with Interval Arithmetic and Real-Time Ray Tracing,” SCI Technical Report, No. UUSCI-2008-008, University of Utah School of Computing, 2008.



B. Howe, P. Lawson, R. Bellinger, J. Freire, E. Anderson, E. Santos, C.E. Scheidegger, A. Baptista, C.T. Silva. “End-to-End eScience: Integrating Workflow, Query, Visualization, and Provenance at an Ocean Observatory,” In Proceedings of the 2008 Fourth IEEE International Conference on eScience, pp. 127--134. 2008.



T. Ize, I. Wald, S.G. Parker. “Ray Tracing with the BSP Tree,” In Proceedings of the IEEE Symposium on Interactive Ray Tracing, 2008, pp. 159--166. 2008.
DOI: 10.1109/RT.2008.4634637

ABSTRACT

One of the most fundamental concepts in computer graphics is binary space subdivision. In its purest form, this concept leads to binary space partitioning trees (BSP trees) with arbitrarily oriented space partitioning planes. In practice, however, most algorithms use kd-trees-a special case of BSP trees that restrict themselves to axis-aligned planes-since BSP trees are believed to be numerically unstable, costly to traverse, and intractable to build well. In this paper, we show that this is not true. Furthermore, after optimizing our general BSP traversal to also have a fast kd-tree style traversal path for axis-aligned splitting planes, we show it is indeed possible to build a general BSP based ray tracer that is highly competitive with state of the art BVH and kd-tree based systems. We demonstrate our ray tracer on a variety of scenes, and show that it is always competitive with-and often superior to-state of the art BVH and kd-tree based ray tracers.

Keywords: rt, ray tracing, bsp tree



W.-K. Jeong, R.T. Whitaker. “A Fast Iterative Method for Eikonal Equations,” In SIAM Journal on Scientific Computing, Vol. 30, No. 5, pp. 2512-2534. 2008.
DOI: 10.1137/060670298



C.R. Johnson, X. Tricoche. “Biomedical Visualization,” In Advances in Biomedical Engineering, Ch. 6, Edited by Pascal Verdonck, Elsvier Science, pp. 209--272. 2008.



M. Jolley, J.G. Stinstra, S. Pieper, R.S. MacLeod, D.H. Brooks, F. Cecchin, J.K. Triedman. “A Computer Modeling Tool for Comparing Novel ICD Electrode Orientations in Children and Adults,” In Heart Rhythm, Vol. 5, No. 4, pp. 565--572. April, 2008.
PubMed ID: 18362024



E. Jurrus, R.T. Whitaker, B. Jones, R. Marc, T. Tasdizen. “An Optimal-Path Approach for Neural Circuit Reconstruction,” In Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pp. 1609--1612. 2008.
PubMed ID: 19172170



R. Kashani, M. Hub, J.M. Balter, M.L. Kessler, L. Dong, L. Zhang, L. Xing, Y. Xie, D. Hawkes, J.A. Schnabel, J. McClelland, S. Joshi, Q. Chen, W. Lu. “Objective assessment of deformable image registration in radiotherapy: a multi-institution study,” In Medical Physics, Vol. 35, No. 12, pp. 5944--5953. 2008.
PubMed ID: 19175149



A. Kensler, A. Knoll, P. Shirley. “Better Gradient Noise,” SCI Institute Technical Report, No. UUSCI-2008-001, University of Utah, 2008.



A. Kensler. “Tree Rotations for Improving Bounding Volume Heirarchies,” In Proceedings of the 2008 IEEE Symposium on Interactive Ray Tracing, pp. 73--76. 2008.



R.M. Kirby, C.T. Silva. “The Need For Verifiable Visualization,” In IEEE Computer Graphics and Applications, Vol. 28, No. 5, pp. 78--83. 2008.
DOI: 10.1109/MCG.2008.103

ABSTRACT

Visualization is often employed as part of the simulation science pipeline, it's the window through which scientists examine their data for deriving new science, and the lens used to view modeling and discretization interactions within their simulations. We advocate that as a component of the simulation science pipeline, visualization must be explicitly considered as part of the validation and verification (V&V) process. In this article, the authors define V&V in the context of computational science, discuss the role of V&V in the scientific process, and present arguments for the need for verifiable visualization.



S. Klasky, M. Vouk, M. Parashar, A. Khan, N. Podhorszki, R. Barreto, D. Silver, S.G. Parker. “Collaborative Visualization Spaces for Petascale Simulations,” In Proceedings of 2008 International Symposium on Collaborative Technologies and Systems (CTS 2008), pp. 203--211. 2008.
DOI: 10.1109/CTS.2008.4543933



R.C. Knickmeyer, S. Gouttard, C. Kang, D. Evans, K. Wilber, K.J. Smith, R.M. Hamer, W. Lin, G. Gerig, J.H. Gilmore. “A Structural MRI Study of Human Brain Development from Birth to Two Years,” In The Journal of Neuroscience, Vol. 28, No. 47, pp. 12176--12182. Nov, 2008.
PubMed ID: 19020011



D. Koop, C.E. Scheidegger, S.P. Callahan, J. Freire, C.T. Silva. “VisComplete: Automating Suggestions for Visualization Systems,” In IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008), Vol. 14, No. 6, pp. 1691--1698. 2008.



L. Krishnan, C.J. Underwood, S.A. Maas, B.J. Ellis, T.C. Kode, J.B. Hoying, J.A. Weiss. “Effect of Mechanical Boundary Conditions on Orientation of Angiogenic Microvessels,” In Cardiovascular Research, Vol. 78, No. 2, pp. 324--332. 2008.