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


 R.S. MacLeod, S. Shome, J.G. Stinstra, B.P. Punske, B. Hopenfeld. “Mechanisms of Ischemia-Induced ST-Segment Changes,” In J. Electrocardiol., Vol. 38(4 Suppl), pp. 8--13. November, 2005.


R.S. MacLeod. “Mechanisms of ischemia-induced ST-segment changes,” In Journal of Electrocardiology, Vol. 38, No. 4 , Elsevier, pp. 8--13. Oct, 2005.
DOI: 10.1016/j.jelectrocard.2005.06.095


R.S. MacLeod, F. Kornreich, A. van Oosterom, P. Rautaharju, R. Selvester, G. Wagner, C. Zywietz. “Report of the First Virtual Visualization of the Reconstructed Electrocardiographic Display Symposium,” In Journal of Electrocardiology, Vol. 38, pp. 385--399. 2005.


R. McDermott, A. Kerstein, R. Schmidt, P.J. Smith. “The Ensemble Mean Limit of the One-Dimensional Turbulence Model and Application to Residual Stress Closure in Finite-Volume Large-Eddy Simulation,” In Journal of Turbulence, Vol. 6, 2005.
DOI: 10.1080/14685240500293894

ABSTRACT

In order to gain insight into the one-dimensional turbulence (ODT) model of Kerstein [1] as it pertains to residual stress closure in large-eddy simulation (LES), we develop ensemble mean closure (EMC), an algebraic stress closure based on the mappings and time scale physics employed in ODT. To allow analytic determination of the stress the ODT model is simplified, conceptually, such that eddy events act upon a velocity field linearized by the local resolved scale strain. EMC can account for viscous effects, addressing the laminar flow finite eddy viscosity problem without implementation of the dynamic procedure [2]. The algebraic form of the model lends itself to analysis [3] and we are able to derive a theoretical value for the eddy rate constant. This value is a bound on the rate constant for full ODT subgrid closure and yields good results in LES of decaying isotropic turbulence with EMC.


 M.D. Meyer, H. Pfister, C.D. Hansen, C.R. Johnson. “Image-Based Volume Rendering with Opacity Light Fields,” SCI Institute Technical Report, No. UUSCI-2005-002, University of Utah, 2005.


M.D. Meyer, P. Georgel, R.T. Whitaker. “Robust Particle Systems for Curvature Dependent Sampling of Implicit Surfaces,” In In Proceedings of the International Conference on Shape Modeling and Applications (SMI), pp. 124--133. June, 2005.


S.M. Moore, R.E. Debski, B. Ellis, P.J. McMahon, J.A. Weiss. “All Three Regions of the Inferior Glenohumeral Ligament Contribute to Anterior Stability,” In Proceedings, 51st Annual Orthopaedic Research Society Meeting, Vol. 30, pp. 804. 2005.


J.A. Nairn. “Simulation of Crack Growth in Ductile Materials,” In Engineering Fracture Mechanics, Vol. 72, No. 6, pp. 961--979. April, 2005.
DOI: 10.1016/j.engfracmech.2004.08.006

ABSTRACT

During crack growth of real materials, the total energy released can be partitioned into elastic and dissipative terms. By analyzing material models with mechanisms for dissipating energy and tracking all energy terms during crack growth, it is proposed that computer simulations of fracture can model crack growth by a total energy balance condition. One approach for developing fracture simulations is illustrated by analysis of elastic–plastic fracture. General equations were derived to predict crack growth and crack stability in terms of global energy release rate and irreversible energy effects. To distinguish plastic fracture from non-linear elastic fracture, it was necessary to imply an extra irreversible energy term. A key component of fracture simulations is to model this extra work. A model used here was to assume that the extra irreversible energy is proportional to the plastic work in a plastic-flow analysis. This idea was used to develop a virtual material based on Dugdale yield zones at the crack tips. A Dugdale virtual material was subjected to computer fracture experiments that showed it has many fracture properties in common with real ductile materials. A Dugdale material can serve as a model material for new simulations with the goal of studying the role of structure in the fracture properties of composites. One sample calculation showed that the toughness of a Dugdale material in an adhesive joint mimics the effect of joint thickness on the toughness of real adhesives. It is expected, however, that better virtual materials will be required before fracture simulations will be a viable approach to studying composite fracture. The approach of this paper is extensible to more advanced plasticity models and therefore to the development of better virtual materials.


 V. Natarajan, V. Pascucci. “Volumetric Data Analysis Using Morse-Smale Complexes,” In Proceedings of the International Conference Shape Modeling and Applications, Edited by A.G. Belyaev and A.A. Pasko and M. Spagnuolo, IEEE Computer Society, pp. 320--325. June, 2005.


R. Palmer, S. Barrus, Y. Yang, G. Gopalakrishnan, R.M. Kirby. “Gauss: A Framework for Verifying Scientific Computing Software,” In Proceeding of the Software Model Checking Workshop, Edinburgh, Scotland, July, 2005.


S.M. Pizer, P.T. Fletcher, S. Joshi, A.G. Gash, J. Stough, A. Thall, G. Tracton, E. Chaney. “A Method and Software for Segmentation of Anatomic Object Ensembles by Deformable M-Reps,” In Med Phys, Vol. 32, No. 5, pp. 1335--1345. May, 2005.


S.M. Pizer, J.Y. Jeong, C. Lu, K. Muller, S. Joshi. “Estimating the Statistics of Multi-Object Anatomic Geometry Using Inter-Object Relationships,” In Proceedings of International Workshop on Deep Structure, Singularities and Computer Vision (DSSCV), Edited by O.F. Olsen and L. Florack and A Kuijper, pp. 60--71. June, 2005.


M. Ramanath, L. Zhang, J. Freire, J. Haritsa. “IMAX: Incremental Maintenance of Schema-Based XML Statistics,” In International Conference on Data Engineering (ICDE), IEEE Computer Society, Los Alamitos, CA, USA pp. 273--284. 2005.
ISSN: 1084-4627


D. Reed, R. Bajcsy, J.M. Griffiths, J. Dongarra, C.R. Johnson. “Computational Science: Ensuring America's Competitiveness,” Note: President's Information Technology Advisory Committee (PITAC), June, 2005.


F. Sachse, M. Cole, R.M. Kirby, X. Tricoche, C.R. Johnson. “Advanced Modeling and Visualization of Cardiothoracic Electrical Fields,” In Proceedings of 13th Medicine Meets Virtual Reality (MMVR13), 2005.


A.A. Samsonov, E.V.R. DiBella, P. Kellman, E.G. Kholmovski, C.R. Johnson. “Adaptive k-t BLAST/k-t SENSE for Accelerating Cardiac Perfusion MRI,” In Proceedings of the Society for Cardiovascular Magnetic Resonance (SCMR) 8th Annual Scientific Sessions, pp. 277--278. 2005.


A.A. Samsonov, E.G. Khölmovski, C.R. Johnson. “POCS-Enhanced Parallel MRI Correction of MR Image Artifacts,” In Proc. Intl. Soc. Mag. Reson., Note: Abstract, pp. 690. 2005.


G. Scheuermann, X. Tricoche. “Topological Methods for Flow Visualization,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 341--356. 2005.
ISBN: 0-12-387582-X


C. Scheidegger, S. Fleishman, C.T. Silva.. “Triangulating Point-Set Surfaces With Bounded Error,” In Proceedings of the Third Eurographics/ACM Symposium on Geometry Processing, Eurographics Association, pp. 63--72. 2005.
ISBN: 3-905673-24-X


C. Scheidegger, J. Comba, R. Cunha.. “Practical CFD Simulations on the GPU Using SMAC,” In Computer Graphics Forum, Vol. 24, No. 4, pp. 715--728. 2005.