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

1998


G. Kindlmann, J. Durkin. “Semi-Automatic Generation of Transfer Functions for Direct Volume Rendering,” In IEEE Symposium on Volume Visualization, IEEE Press, pp. 79--86. Oct, 1998.



Y. Livnat, C.D. Hansen. “View Dependent Isosurface Extraction,” In IEEE Visualization '98, pp. 175--180. Oct, 1998.



M. Miller, C.D. Hansen, C.R. Johnson. “Simulation Steering with SCIRun in a Distributed Memory Environment,” In Lecture Notes in Computer Science, Springer-Verlag, In Applied Parallel Computing, 4th International Workshop, PARA'98, Lecture Notes in Computer Science, Vol. 1541, Edited by B. Kagstrom and J. Dongarra and E. Elmroth and J. Wasniewski, Springer-Verlag, Berlin pp. 366--376. 1998.



M. Miller, C.D. Hansen, S.G. Parker, C.R. Johnson. “Simulation Steering with SCIRun in a Distributed Memory Environment,” In Seventh IEEE International Symposium on High Performance Distributed Computing (HPDC-7), Jul, 1998.



J. Pan, C.G.W. Sheppard, A. Tindall, M. Berzins, S.V. Pennington, J.M. Ware. “End Gas Inhomogeneity, Autoignition and Knock,” SAE meeting technical report, San Fransisco, CA, No. 982616, SAE, 1998.



S.G. Parker, P. Shirley, Y. Livnat, C.D. Hansen, P.-P. Sloan. “Interactive Ray Tracing for Isosurface Extraction,” In IEEE Visualization '98, pp. 233--238. October, 1998.



S.G. Parker, P. Shirley, B. Smits. “Single Sample Soft Shadows,” School of Computing Technical Report, No. UUCS-98-019, University of Utah, October, 1998.



S.G. Parker, M. Miller, C.D. Hansen, C.R. Johnson, P.-P. Sloan. “An Integrated Problem Solving Environment: The SCIRun Computational Steering System,” In 31st Hawaii International Conference on System Sciences (HICSS-31), Vol. VII, Edited by H. El-Rewini, pub-IEEE, pp. 147--156. January, 1998.



G.F. Potts, D.M. Weinstein, B.F. O'Donnell M.E., C.R. Johnson, R.W. McCarley. “Bioelectric Modeling of the P300 in Schizophrenia,” In Biological Psychiatry (suppl.), pp. 396. 1998.



G.F. Potts, C.G. Wible, M.E. Shenton, D.M. Weinstein, I.A. Fisher, M.E. Levention, L.D. Gugino, R.W. McCarley. “Localization of Visual Cortex with Coregistered Functional Magnetic Resonance Imaging, Bioelectrically Modeled Cortical Visual Evoked Potential, and Transcranial Magnetic Stimulation Induced Visual Suppression,” In Journal of Cognitive Neuroscience (suppl.), pp. 42. 1998.



M.A. Puso, J.A. Weiss. “Finite Element Implementation of Anisotropic Quasilinear Viscoelasticity Using a Discrete Spectrum Approximation,” In Journal of Biomechanical Engineering, Vol. 120, pp. 62--70. 1998.



K.M. Quapp, J.A. Weiss. “Material Characterization of Human Medial Collateral Ligament,” In Journal of Biomechanical Engineering, Vol. 120, pp. 757--763. 1998.



M. Richards, J.A. Goulet, J.A. Weiss, N.A. Waanders, M.B. Schaffler, S.A. Goldstein. “Bone Regeneration and Fracture Healing: Experience with Distraction Osteogenesis Model,” In Clinical Orthopaedics and Related Research, Vol. 355S, pp. 191--204. 1998.



P.Selwood, M.Berzins, J. Nash, P.M. Dew. “Portable Parallel Adaptation of Unstructured Tetrahedral Meshes,” In Proceedings of Irregular 98 Conference, Lecture Notes in Computer Science (LNCS), Vol. 1457, Edited by A. Ferreira et al., Springer, pp. 56--67. 1998.



P.A. Sleigh, M. Berzins, P.H. Gaskell, N.G. Wright. “An Unstructured Finite Volume Algorithm for Predicting Flow in Rivers and Estuaries,” In Computers and Fluids, Vol. 27, No. 4, pp. 479--508. 1998.



P.P.J. Sloan, D.M. Weinstein, J.D. Brederson. “Importance Driven Texture Coordinate Optimization,” In Eurographics 98, Sep, 1998.



M. Sosonkina, L.T. Watson, R.K. Kapania, H.F. Walker. “A new adaptive GMRES algorithm for achieving high accuracy,” In Numerical Linear Algebra and Applications, Vol. 5, No. 4, pp. 275--297. 1998.
DOI: 10.1002/(SICI)1099-1506(199807/08)5:43.0.CO;2-B

ABSTRACT

GMRES(k) is widely used for solving non-symmetric linear systems. However, it is inadequate either when it converges only for k close to the problem size or when numerical error in the modified Gram–Schmidt process used in the GMRES orthogonalization phase dramatically affects the algorithm performance. An adaptive version of GMRES(k) which tunes the restart value k based on criteria estimating the GMRES convergence rate for the given problem is proposed here. This adaptive GMRES(k) procedure outperforms standard GMRES(k), several other GMRES-like methods, and QMR on actual large scale sparse structural mechanics postbuckling and analog circuit simulation problems. There are some applications, such as homotopy methods for high Reynolds number viscous flows, solid mechanics postbuckling analysis, and analog circuit simulation, where very high accuracy in the linear system solutions is essential. In this context, the modified Gram–Schmidt process in GMRES, can fail causing the entire GMRES iteration to fail. It is shown that the adaptive GMRES(k) with the orthogonalization performed by Householder transformations succeeds whenever GMRES(k) with the orthogonalization performed by the modified Gram–Schmidt process fails, and the extra cost of computing Householder transformations is justified for these applications.



R. Stevens, H. Fuchs, A. van Dam, P. Hanrahan, C.R. Johnson, C. McMillan, P. Heermann, S. Louis, T. Defanti, D. Reed, E. Cohen. “Data and Visualization Corridors: Report on the 1998 DVC Workshop Series,” Note: DOE Report, September, 1998.

ABSTRACT

The Department of Energy and the National Science Foundation sponsored a series of workshops on data manipulation and visualization of large-scale scientific datasets. Three workshops were held in 1998, bringing together experts in high-performance computing, scientific visualization, emerging computer technologies, physics, chemistry, materials science, and engineering. These workshops were followed by two writing and review sessions, as well as numerous electronic collaborations, to synthesize the results. The results of these efforts are reported here. Across the government, mission agencies are charged with understanding scientific and engineering problems of unprecedented complexity. The DOE Accelerated Strategic Computing Initiative, for example, will soon be faced with the problem of understanding the enormous datasets created by teraops simulations, while NASA already has a severe problem in coping with the flood of data captured by earth observation satellites. Unfortunately, scientific visualization algorithms, and high-performance display hardware and software on which they depend, have not kept pace with the sheer size of emerging datasets, which threaten to overwhelm our ability to conduct research. Our capability to manipulate and explore large datasets is growing only slowly, while human cognitive and visual perception are an absolutely fixed resource. Thus, there is a pressing need for new methods of handling truly massive datasets, of exploring and visualizing them, and of communicating them over geographic distances. This report, written by representatives from academia, industry, national laboratories, and the government, is intended as a first step toward the timely creation of a comprehensive federal program in data manipulation and scientific visualization. There is, at this time, an exciting confluence of ideas on data handling, compression, telepresence, and scientific visualization. The combination of these new ideas, which we refer to as Da ta and Visualization Corridors (DVC), can raise scientific data understanding to new levels and will improve the way science is practiced



T. Tasdizen, L. Akarun, C. Ersoy. “Color Quantization with Genetic Algorithms,” In Signal Processing: Image Communication, Vol. 12, pp. 49--57. 1998.



M.D. Tocci, C.T. Kelley, C.T. Miller, C.E. Kees. “Inexact Newton Methods and the Method of Lines for Solving Richards' Equation in Two Space Dimensions,” In Computational Geosciences, Vol. 2, No. 4, pp. 291--309. 1998.
DOI: 10.1023/A:1011562522244

ABSTRACT

Richards' equation (RE) is often used to model flow in unsaturated porous media. This model captures physical effects, such as sharp fronts in fluid pressures and saturations, which are present in more complex models of multiphase flow. The numerical solution of RE is difficult not only because of these physical effects but also because of the mathematical problems that arise in dealing with the nonlinearities. The method of lines has been shown to be very effective for solving RE in one space dimension. When solving RE in two space dimensions, direct methods for solving the linearized problem for the Newton step are impractical. In this work, we show how the method of lines and Newton-iterative methods, which solve linear equations with iterative methods, can be applied to RE in two space dimensions. We present theoretical results on convergence and use that theory to design an adaptive method for computation of the linear tolerance. Numerical results show the method to be effective and robust compared with an existing approach.