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

2004


 Won-Ki Jeong, Tolga Tasdizen, Ross Whitaker. “Anisotropic Diffusion of Height Field Data using Multigrid Solver on GPU,” In Proceedings ACM Workshop on General Purpose Computing on Graphics Processors, 2004, 2004.


C.R. Johnson. “Top Scientific Visualization Research Problems,” In IEEE Computer Graphics and Applications: Visualization Viewpoints, Vol. 24, No. 4, pp. 13--17. July/August, 2004.


C.R. Johnson, R.S. MacLeod, S.G. Parker, D.M. Weinstein. “Biomedical Computing and Visualization Software Environments,” In Comm. ACM, Vol. 47, No. 11, pp. 64--71. 2004.


S. Joshi, B. Davis, M Jomier, G. Gerig. “Unbiased Diffeomorphic Atlas Construction for Computational Anatomy,” In Neuroimage, Vol. 23 Suppl. 1, pp. S151--S160. 2004.


A. Kadlag, A.V. Wanjari, J. Freire, J. Haritsa. “Supporting Exploratory Queries in Databases,” In Database Systems for Advanced Applications, Lecture Notes in Computer Science (LNCS), Vol. 2973/2004, pp. 25-26. 2004.


G Kindlmann. “Superquadric Tensor Glyphs,” In Proceeding of The Joint Eurographics - IEEE TCVG Symposium on Visualization 2004, pp. 147--154. May, 2004.


G.L. Kindlmann, D.M. Weinstein, A.D. Lee, A.W. Toga, P.M. Thompson. “Visualization of Anatomic Covariance Tensor Fields,” In Proceedings of the IEEE Engineering in Medicine and Biology Society 26th Annual International Conference, 2004.


G. Kindlmann, A. L. Alexander, M. Lazar, J. Lee, T. Tasdizen, R.T. Whitaker. “An Algorithm for Moment-Based Global Registration of Echo Planar Diffusion-Weighted Images,” In Proceedings of 12th Annual ISMRM, pp. 2200. 2004.


G. Kindlmann. “Visualization and Analysis of Diffusion Tensor Fields,” Technical Report, No. UUCS-04-014, Note: PhD Thesis, School of Computing, University of Utah, 2004.


R.M. Kirby, Z. Yosibash. “Solution of Von-Karman Dynamic Non-linear Plate Equations Using a Pseudo-spectral Method,” In Comp. Meth. Appl. Mech. & Eng., Vol. 193, No. 6-8, pp. 575-599. 2004.


R.M. Kirby, G.E. Karniadakis. “Spectral Element and hp Methods,” In Encyclopedia of Computational Mechanics, Vol. 3, Ch. 3, Edited by E. Stein and R. de Borst and T.J.R. Hughes, John Wiley and Sons, NY, pp. 61--88. 2004.


R.M. Kirby, Z. Yosibash. “Solution of von-Karman Dynamic Non-Linear Plate Equations Using a Pseudo-Spectral Method,” In Computer Methods in Applied Mechanics and Engineering, Vol. 193, No. 6-8, pp. 575--599. 2004.


J.M. Kniss, J.P. Schulze, U. Wössner, P. Winkler, U. Lang, C.D. Hansen. “Medical Applications of Multi-field Volume Rendering and VR Techniques,” In Proceeding of The Joint Eurographics - IEEE TCVG Symposium on Visualization 2004, pp. 249--254. 2004.


L. Krishnan, J.A. Weiss, M.D. Wessman MD, J.B. Hoying. “Design and Application of a Test System for Viscoelastic Characterization of Collagen Gels,” In Tiss. Eng., Vol. 10, No. (1-2), pp. 241--252. 2004.


G. Krishnamoorthy, R. Rawat, P.J. Smith. “Parallel Computations of Radiative Heat Transfer Using the Discrete Ordinates Method,” In Numerical Heat Transfer, Part B: Fundamentals, Vol. 47, No. 1, pp. 19--38. 2004.
DOI: 10.1080/10407790490487451

ABSTRACT

The discrete ordinates method is spatially decomposed to solve the radiative transport equation on parallel computers. Mathematical libraries developed by third parties are used to solve the matrices that result during the solution procedure. The radiation component is verified by comparing computed values against a benchmark. Fixed and scaled problem size efficiencies are examined. Contrary to most previous studies, the parallel efficiencies did not depend strongly on the optical thickness of the medium for our model problem. Timing studies show that GMRES, BiCGSTAB iterative methods with block Jacobi preconditioning perform the best for solving these matrix systems.


 D. Laney, V. Pascucci. “Progressive Compression of Volumetric Subdivision Meshes,” In Proceedings of the International Symposium on 3D Data Processing, Visualization, and Transmission (3DPVT), Note: UCRL-CONF-203679, pp. 293--300. September, 2004.


A.E. Lefohn, J.M. Kniss, C.D. Hansen, R.T. Whitaker. “A Streaming Narrow-Band Algorithm: Interactive Deformation and Visualization of Level Sets,” In IEEE Trans. Vis & Comp. Graph., pp. 422--433. 2004.


L. Linsen, V. Pascucci, M.A. Duchaineau, B. Hamann, K.I. Joy. “Wavelet-Based Multiresolution with N-th-Root-of-2,” In Geometric Modeling, Dagstuhl 2002. Proceedings of the Dagstuhl Seminar on Geometric Modeling, Note: UCRL-PROC-208699, Dagstuhl, Germany May, 2004.


L. Linsen, J.T. Gray, V. Pascucci, M.A. Duchaineau, B. Hamann, K.I. Joy. “Hierarchical Large-scale Volume Representation with 3rd-root-of-2 Subdivision and Trivariate B-spline Wavelets,” In Geometric Modeling for Scientific Visualization, Edited by G. Brunnett and B. Hamann and H. Mueller, Springer-Verlag, pp. 359--377. 2004.
DOI: 10.1007/978-3-662-07443-5_22


L. Linsen, V. Pascucci, M.A. Duchaineau, B. Hamann, K.I. Joy. “Wavelet-Based Multiresolution with n-th-root-of-2,” In Proceedings of Geometric Modeling, Dagstuhl 2002, Dagstuhl, Germany, Note: UCRL-PROC-208699, May, 2004.