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

2002


S.G. Parker. “A Component-Based Architecture for Parallel Multi-physics PDE Simulation,” In Proceedings of the International Conference on Computational Science (ICCS) 2002, Vol. 2331, pp. 719--734. 2002.



V. Pascucci, K. Cole-McLaughlin. “Efficient Computation of the Topology of Level Sets,” In Proceedings of IEEE Conference on Visualization (VIS-02), Boston, MA, Note: UCRL-JC-149277, pp. 187--194. October, 2002.



V. Pascucci. “Slow Growing Subdivision (SGS) in Any Dimension: Towards Removing the Curse Of Dimensionality,” In Proceedings of Eurographics 2002, Saabruken, Germany, Note: UCRL-ID-144257, pp. 451--460. September, 2002.



V. Pascucci. “Slow Growing Volumetric Subdivision for 3D Volumetric Data,” In SIGGRAPH 2002 Technical Sketches, 2002.



O. Portniaguine, M.S. Zhdanov. “3-D Magnetic Inversion with Data Compression and Image Focusing,” In Geophys., Vol. 67, No. 5, pp. 1532--1541. September - October, 2002.



H.W. Quartero, J.G. Stinstra, E.G. Golbach, E.J. Meijboom, M.J. Peters. “Clinical Implications of Fetal Magnetocardiography,” In Ultrasound Obstet Gynecol, Vol. 20, No. 2, pp. 142--153. 2002.



E. Reinhard, C.D. Hansen, S.G. Parker. “Interactive Ray Tracing of Time Varying Data,” In Proceedings of The 4th Eurographics Workshop on Parallel Graphics and Visualization, Germany, pp. 77--82. September, 2002.



A.A. Samsonov, R.T. Whitaker, C.R. Johnson. “Noise-Adaptive Nonlinear Filtering Technique for SENSE-Reconstructed Images,” In Proceedings of The 10th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Honolulu, pp. 74. 2002.



A.A. Samsonov, C.R. Johnson. “Noise-Adaptive Anisotropic Diffusion Filtering of MRI Images Reconstructed by SENSE (SENSitivity Encoding) Method,” In Proceedings of The 2002 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Washington DC, pp. 701--704. July, 2002.



A.A. Samsonov, R.T. Whitaker, E.G. Kholmovski, C.R. Johnson. “Parametric Method for Correction of Intensity Inhomogeneity in MRI Data,” In Proceedings of The 10th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Honolulu, pp. 154. 2002.



A.A. Samsonov, E.G. Kholmovski. “Method for Quality Improvement of Images Reconstructed From Sensitivity-Encoded Data,” In Proceedings of The 10th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Honolulu, pp. 2408. 2002.



Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod. “Including Sparse Noisy Epicardial Potential Measurements Into Bayesian Inverse Electrocardiography,” In Proceedings of EMBC 2002, 2002.



Y. Serinagaoglu, R.S. MacLeod, B. Yilmaz, D.H. Brooks. “Multielectrode Venous Catheter Mapping as a High Quality Constraint for Electrocardiographic Inverse Solution,” In J. Electrocardiol., Vol. 35 (supplement), 2002.



S. Shellman, K. Sikorski. “A Two Dimensional Bisection-Envelope Algorithm for Fixed Points,” In Journal of Complexity, Vol. 18, No. 2, pp. 641--659. June, 2002.
DOI: 10.1006/jcom.2001.0625

ABSTRACT

In this paper we present a new algorithm for the two-dimensional fixed point problem f(x)=x on the domain [0, 1]×[0, 1], where f is a Lipschitz continuous function with respect to the infinity norm, with constant 1. The computed approximation x satisfies ‖f(x)−xε for a specified tolerance ε0.5. The upper bound on the number of required function evaluations is given by 2⌈log2(1/ε)⌉+1. Similar bounds were derived for the case of the 2-norm by Z. Huang et al. (1999, J. Complexity15, 200–213), our bound is the first for the infinity norm case.



J. Simpson, A.R. Sanderson, E. Luke, K. Balling, R. Coffey. “Collaborative Remote Visualization,” In Proceedings of the IEEE/ACM SC2002 Conference, Baltimore, Maryland, November, 2002.



J. Simpson, A.R. Sanderson, E. Luke, K. Balling, R. Coffey. “Collaborative Remote Visualization,” In Presented before the Utah State Legislature, 2002.



G.D. Smith, O. Borodin, W. Paul. “A Molecular Dynamics Simulation Study of Dielectric Relaxation in a 1,4-Polybutadiene Melt,” In Journal of Chemical Physics, Vol. 117, No. 22, pp. 10350--10359. 2002.
DOI: 10.1063/1.1518684

ABSTRACT

We have carried out atomistic molecular dynamics simulations of a melt of 1,4-poly(butadiene) from temperatures well above the experimentally observed merging of the primary α process and secondary β process down to temperatures approaching the experimentally observed bifurcation temperature. The relaxation strength and maximum loss frequency and its temperature dependence for the combined α-β dielectric relaxation process from simulations were in good agreement with experiment. The maximum loss frequency, melt viscosity, chain normal-mode relaxation times and torsional autocorrelation times were found to exhibit nearly identical non-Arrhenius temperature dependencies well represented by a Vogel–Fulcher fit with parameters in good agreement with experimental values obtained from dielectric and viscosity measurements. The dielectric susceptibility showed increasing intensity at high frequency for the lower temperatures investigated, indicative of a breakdown in time-temperature superposition due to an emerging β process. Comparison of time scales for the chain normal-mode dynamics and dielectric relaxation revealed that the latter is associated with motions on the segmental length scale. The correspondence of time scales and temperature dependence for the dielectric relaxation and the torsional autocorrelation function further confirmed the localized nature of the dielectric relaxation and indicated that the combined α-β dielectric process is fundamentally tied to microscopic conformational dynamics of individual dihedrals. However, the mean conformational transition rates were found to exhibit Arrhenius temperature dependence, leading to a divergence of time scales between the torsional, dielectric, chain and mechanical relaxation processes and the rates of conformational transitions with decreasing temperature. This divergence was associated with the increasingly heterogeneous character of conformational dynamics in the melt with decreasing temperature. Hence, the time scale of the principal (α) relaxation in the melt is fundamentally correlated with the time scale for homogenization of conformational dynamics, and not to the time scale of the conformational transitions themselves.



J. Stinstra, M. Peters. “The Influence of Fetoabdominal Tissues on Fetal ECGs and MCGs,” In Arch Physiol Biochem, Vol. 110, No. 3, pp. 165--176. 2002.



B. Taccardi, B.B. Punske, R.S. MacLeod, Q. Ni. “Visualization, Analysis and Physiological Interpretation of Three-dimentional Cardiac Electric Fields,” In Proceedings of 24th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2002.



H. Tan, J.A. Nairn. “Hierarchical, Adaptive, Material Point Method in Dynamic Energy Release Rate Calculations,” In Computer Methods in Applied Mechanics and Engineering, Vol. 191, No. 19-20, pp. 2123--2137. March, 2002.
DOI: 10.1016/S0045-7825(01)00377-2

ABSTRACT

A crack-closure method was developed for use in material point method (MPM) calculations. The method can be used for calculation of the dynamic energy release rate in a variety of dynamic fracture mechanics problems. Most previous MPM analyses have used regular grids and a “lumped” mass matrix. For the most accurate energy release rate calculations, the regular grid had to be replaced by an adaptive grid that automatically refined the mesh around the crack tip and the lumped mass matrix had to be replaced by a full mass matrix. Using an adaptive mesh was more important to accuracy than was switching to a full mass matrix. Some sample calculations are given for energy release rate in a double cantilever beam specimen carried out by several different MPM methods.