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


 H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci. “Local and Global Comparison of Continuous Functions,” In Proceedings of the IEEE Conference on Visualization (VIS-04), Note: UCRL-PROC-208677, pp. 275--280. October, 2004.


H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci. “Time-Varying Reeb Graphs for Continuous Space-Time Data,” In SCG '04: Proceedings of the Twentieth Annual Symposium on Computational Geometry, Brooklyn, New York, USA, Note: UCRL-PROC-208697, ACM Press, pp. 366--372. 2004.
ISBN: 1-58113-885-7


P.T. Fletcher, C. Lu, S.M. Pizer, S. Joshi. “Principal Geodesic Analysis for the Study of Nonlinear Statistics of Shape,” In IEEE Trans Med Imaging, Vol. 23, No. 8, pp. 995--1005. August, 2004.


P.T. Fletcher, S. Joshi. “Principal Geodesic Analysis on Symmetric Spaces: Statistics of Diffusion Tensors,” In Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis, Springer-Verlag, Lecture Notes In Computer Science, Vol. 3117, pp. 87--98. 2004.
DOI: 10.1109/TMI.2004.831793


P.T. Fletcher. “Statistical Variability in Nonlinear Spaces: Application to Shape Analysis and DT-MRI,” Note: Ph.D. Thesis, University of North Carolina Department of Computer Science, August, 2004.


J. Freire, M. Benedikt. “Managing XML Data: An Abridged Overview,” In Computing in Science and Engineering, Vol. 6, No. 4, IEEE Computer Society, pp. 12--19. 2004.
ISSN: 1521-9615


J. Freire, M. Ramanath, L. Zhang. “A Flexible Infrastructure for Gathering XML Statistics and Estimating Query Cardinality,” In Proceedings of the 20th International Conference on Data Engineering, pp. 857. 2004.
ISBN: 0-7695-2065-0


C. Garth, X. Tricoche, G. Scheuermann. “Tracking of Vector Field Singularities in Unstructured 3D Time-Dependent Datasets,” In Proceeding of IEEE Visualization 2004, pp. 329--336. 2004.


C. Garth, X. Tricoche, T. Salzbrunn, T. Bobach, G. Scheuermann. “Surface Techniques for Vortex Visualization,” In Proceedings of Joint Eurographics - IEEE TCVG Symposium on Visualization, pp. 155--164. May, 2004.


A. Ghodrati, D.H. Brooks, R.S. MacLeod. “On Selecting and Using Reduced Sets of Leads for Electrocardiographic Imaging Using Reconstruction-Quality Criteria,” In Proceedings of The SIAM Conference on Imaging Science 2004, Salt Lake City, UT, Note: abstract., May, 2004.


A. Ghodrati, F. Calderero, D.H. Brooks, G. Tadmor, R.S. MacLeod. “A Level Sets Algorithm for the Inverse Problem of Electrocardiography,” In Proceedings of the Asilomar Conf. on Sig. and Sys., Vol. 2, pp. 1590--1594. November, 2004.


C.E. Goodyer, R. Fairlie, D.E. Hart, M. Berzins, L.E. Scales. “Calculation of Friction in Steady-State and Transient EHL Simulations Transient Processes in Tribology,” In Transient Processes in Tribology: Proceeding of the 31st Leeds-Lyon Symposium on Tribology, Edited by A.A. Lubrecht and G. Dalmaz, Elsevier, pp. 579--590. 2004.


C. Gribble, S.G. Parker, C.D. Hansen. “Interactive Volume Rendering of Large Datasets Using the Silicon Graphics Onyx4 Visualization System,” No. UUCS-04-003, University of Utah School of Computing, January 27th, 2004.


J.E. Guilkey, Y. Zhang, J.B. Hoying, J.A. Weiss. “Mechanical Simulation of Multicellular Structures with the Material Point Method,” In Proc 6th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering, Madrid, Spain, Note: Winner of the Taylor and Francis Prize for Outstanding Innovation in Computer Methods in Biomechanics and Biomedical Engineering, March, 2004.


Y. Guo, J.A. Nairn. “Calculation of J-Integral and Stress Intensity Factors using the Material Point Method,” In Computer Modeling in Engineering and Sciences, Vol. 6, No. 3, pp. 295--308. 2004.

ABSTRACT

The Material Point Method (MPM), which is a particle-based, meshless method that discretizes material bodies into a collection of material points (the particles), is a new method for numerical analysis of dynamic solid mechanics problems. Recently, MPM has been generalized to include dynamic stress analysis of structures with explicit cracks. This paper considers evaluation of crack-tip parameters, such as J-integral and stress intensity factors, from MPM calculations involving explicit cracks. Examples for both static and dynamic problems for pure modes I and II or mixed mode loading show that MPM works well for calculation of fracture parameters. The MPM results agree well with results obtained by other numerical methods and with analytical solutions.


 Q. Han, C. Lu, G. Liu, S.M. Pizer, S. Joshi, A. Thall. “Representing Multi-Figure Anatomical Objects,” In Proceedings of the International Symposium on Biomedical Imaging (ISBI), Piscataway, NJ, pp. 1251--1254. 2004.


Y. He, T.R. Lutz, M.D. Ediger, C. Ayyagari, D. Bedrov, G.D. Smith. “NMR Experiments and Molecular Dynamics Simulations of the Segmental Dynamics of Polystyrene,” In Macromolecules, Vol. 37, No. 13, pp. 5032--5039. May, 2004.
DOI: 10.1021/ma049843r

ABSTRACT

We have performed NMR spin-lattice relaxation experiments and molecular dynamics (MD) computer simulations on atactic polystyrene (a-PS). The segmental correlation times of three different molecular weight a-PS (Mn = 1600, 2100, 10 900 g/mol) were extracted from NMR by measuring the 2H spin-lattice relaxation times (T1) over a broad temperature range (390-510 K). MD simulations of an a-PS melt of molecular weight 2200 g/mol were carried out at 475, 500, and 535 K. Comparisons between experiments and simulations show that the MD simulations reproduce both the shape of the P2(t) orientation autocorrelation function and its temperature dependence, while the simulated segmental correlation times are slower than experimental results by a factor of 1.8. If the simulations are rescaled by this factor, they reproduce both the experimental T1 values and the slight difference in dynamics between the backbone and side group of PS.


 C.S. Henriquez, J.V. Tranquillo, D.M. Weinstein, E.W. Hsu, C.R. Johnson. “Three-dimensional Propagation in Mathematic Models: Integrative Model of the Mouse Heart,” In Cardiac Electrophysiology: From Cell to Bedside, 4th edition, Ch. 30, Edited by D.P. Zipes and J. Jalife, Saunders, pp. 273--281. 2004.


B. Hopenfeld, J.G. Stinstra, R.S. MacLeod. “Mechanism for ST Depression Associated with Contiguous Subendocardial Ischemia,” In J. Cardiovasc. Electrophysiol., Vol. 15, No. 10, pp. 1200--1206. 2004.


M. Ikits, J.M. Kniss, A.E. Lefohn, C.D. Hansen. “Volume Rendering Techniques,” In GPU Gems: Programming Techniques, Tipsand Tricks for Real-Time Graphics, Edited by Randima Fernando, Addison Wesley, pp. 667--692. 2004.