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

2005


 Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod. “Bayesian Solutions and Performance Analysis in Bioelectric Inverse Problems,” In IEEE Trans Biomed. Eng., Vol. 52, No. 6, pp. 1009--1020. June, 2005.


Y.T. Shiu, J.A. Weiss, J.B. Hoying, M.N. Iwamoto, I.S. Joung, C.T. Quam. “The Role of Mechanical Stresses in Angiogenesis,” In CRC Crit. Rev. Biomed. Eng., Vol. 33, No. 5, pp. 431--510. 2005.


C.T. Silva, J.L.D. Comba, S.P. Callahan, F.F. Bernardon. “A Survey of GPU-Based Volume Rendering of Unstructured Grids,” In Revista de Informatica Teorica e Aplicada, Vol. 12, No. 2, pp. 9--29. 2005.
ISSN: 01034308


S. Sirisup, G.E. Karniadakis, D. Xiu, I.G. Kevrekidis. “Equation-free/Galerkin-free POD-assisted Computation of Incompressible Flows,” In Journal of Computational Physics, Vol. 207, No. 2, pp. 568--587. 2005.
DOI: 10.1016/j.jcp.2005.01.024

ABSTRACT

We present a Galerkin-free, proper orthogonal decomposition (POD)-assisted computational methodology for numerical simulations of the long-term dynamics of the incompressible Navier–Stokes equations. The approach is based on the \"equation-free\" framework: we use short, appropriate initialized bursts of full direct numerical simulations (DNS) of the Navier–Stokes equations to observe, estimate, and accelerate, through \"projective integration\", the evolution of the flow dynamics. The main assumption is that the long-term dynamics of the flow lie on a low-dimensional, attracting, and invariant manifold, which can be parametrized, not necessarily spanned, by a few POD basis functions. We start with a discussion of the consistency and accuracy of the approach, and then illustrate it through numerical examples: two-dimensional periodic and quasi-periodic flows past a circular cylinder. We demonstrate that the approach can successfully resolve complex flow dynamics at a reduced computational cost and that it can capture the long-term asymptotic state of the flow in cases where traditional Galerkin-POD models fail. The approach trades the overhead involved in developing POD-Galerkin and POD-nonlinear Galerkin codes, for the repeated (yet short, and on demand) use of an existing full DNS simulator. Moreover, since in this approach the POD modes are used to observe rather than span the true system dynamics, the computation is much less sensitive than POD-Galerkin to values of the system parameters (e.g., the Reynolds number) and the particular simulation data ensemble used to obtain the POD basis functions.


 J.G. Stinstra, D.M. Weinstein, B. Hopenfeld, C.S. Henriquez, R.S. MacLeod. “Software Challenges in the New Field of Integrated Cardiac Models,” In Proceedings of The Joint Meeting of The 5th International Conference on Bioelectromagnetism and The 5th International Symposium on Noninvasive Functional Source Imaging within the Human Brain and Heart, Vol. 7, pp. 195--198. 2005.


J.G. Stinstra, B. Hopenfeld, R.S. MacLeod. “On the Passive Cardiac Conductivity,” In Annal. Biomed. Eng., Vol. 33, No. 12, pp. 1743--1751. 2005.


J.G. Stinstra, S. Shome, B. Hopenfeld, R.S. MacLeod. “Modelling Passive Cardiac Conductivity During Ischaemia,” In Med. Biol. Eng. Comput., Vol. 43, No. 6, pp. 776--782. 2005.


Q. Sun, R.T. Burks, P.E. Greis, N.S. Phatak, J.A. Weiss. “Noninvasive Measurement of Meniscus Strain Using Hyperelastic Warping,” In 51st Annual Orthopaedic Research Society Meeting, Vol. 30, pp. 478. 2005.


T. Suzuki, S. Takahashi, J. Shepherd. “An Interior Surface Generation Method for All-Hexahedral Meshing,” In Proceedings of The 14th International Meshing Roundtable, Springer-Verlag, pp. 377--398. September, 2005.


B. Taccardi, B.B. Punske, F. Sachse, X. Tricoche, P. Colli-Franzone, L.F. Pavarino, C. Zabawa. “Intramural Activation and Repolarization Sequences in Canine Ventricles. Experimental and Simulation Studies,” In J. Electrocardiol., Vol. 38, No. 4, pp. 131-137. 2005.


T. Tasdizen, S.P. Awate, R.T. Whitaker, N. Foster. “MRI Tissue Classification with Neighborhood Statistics: A Nonparametric, Entropy-Minimizing Approach,” In Proceedings of The 8th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pp. 517--525. 2005.
PubMed ID: 16685999


T. Tasdizen, R.T. Whitaker, R. Marc, B. Jones. “Enhancement of Cell Boundaries in Transmission Micropscopy Images,” In IEEE International Conference on Image Processing, Vol. 2, pp. 129--132. 2005.


T. Tasdizen, R.T. Whitaker, R. Marc, B. Jones. “Automatic Correction of Non-uniform Illumination in Transmission Electron Microscopy Images,” SCI Institute Technical Report, No. UUSCI-2005-008, University of Utah, 2005.


T. Tasdizen, R.T. Whitaker, R. Marc, B. Jones. “Automatic Correction of Non-uniform Illumination in Transmission Electron Microscopy Images,” SCI Institute Technical Report, No. UUSCI-2005-007, University of Utah, 2005.


T. Terriberry, S. Joshi, G. Gerig. “Hypothesis Testing with Nonlinear Shape Models,” In Information Processing in Medical Imaging (IPMI), Edited by G Christensen and M Sonka, pp. 15--26. July, 2005.


X. Tricoche, C. Garth, G. Scheuermann. “Fast and Robust Extraction of Separation Line Features,” In Scientific Visualization: The Visual Extraction of Knowledge from Data, Edited by G.-P. Bonneau and T. Ertl and G.M. Nielson, Springer, pp. 249--264. 2005.


D. Uesu, L. Bavoil, S. Fleishman, J. Shepherd, C.T. Silva. “Simplication of Unstructured Tetrahedral Meshes by Point Sampling,” In Proceedings of the 2005 International Workshop on Volume Graphics, pp. 157--238. 2005.


A.I. Veress, G.T. Gullberg, J.A. Weiss. “Measurement of Strain in the Left Ventricle with Cine-MRI and Deformable Image Registration,” In ASME J. Biom. Eng., Vol. 127, No. 7, pp. 1195--1207. July 21, 2005.


A. Violi, G.A. Voth. “A Multi-scale Computational Approach for Nanoparticle Growth in Combustion Environments,” In High Performance Computing and Communications: Lecture Notes in Computer Science (LNCS), Vol. 3726, pp. 938--947. 2005.

ABSTRACT

In this paper a new and powerful computer simulation capability for the characterization of carbonaceous nanoparticle assemblies across multiple, connected scales, starting from the molecular scale is presented. The goal is to provide a computational infrastructure that can reveal through multi-scale computer simulation how chemistry can influence the structure and function of carbonaceous assemblies at significantly larger length and time scales. Atomistic simulation methodologies, such as Molecular Dynamics and Kinetic Monte Carlo, are used to describe the particle growth and the different spatial and temporal scales are connected in a multi-scale fashion so that key information is passed upward in scale. The modeling of the multiple scales are allowed to be dynamically coupled within a single computer simulation using the latest generation MPI protocol within a grid-based computing scheme.


 I. Wald, C. Benthin, A. Efremov, T. Dahmen, J. Gunther, A. Dietrich, V. Havran, H. Seidel, P. Slusallek. “A Ray Tracing based Virtual Reality Framework for Industrial Design,” SCI Institute Technical Report, No. UUSCI-2005-009, University of Utah, 2005.