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

2001


B. Taccardi, B.B. Punske, R.S. MacLeod, Q. Ni. “Extracardiac Effects of Myocardial Electrical Anisotropy,” In Biomed. Technik, Vol. 46(suppl 2), pp. 216--218. 2001.



X. Tricoche, G. Scheuermann, H. Hagen. “Tensor Topology Tracking: A Visualization Method for Time-Dependent 2D Symmetric Tensor Fields,” In Computer Graphics Forum, Vol. 20, No. 3, Wiley-Blackwell, pp. 461-470. Sep, 2001.
DOI: 10.1111/1467-8659.00539



X. Tricoche, G. Scheuermann, H. Hagen. “Vector and Tensor Topology Simplification on Irregular Grids,” In Proceedings of the Joint Eurographics-IEEE TCVG Symposium on Visualization: Data Visualization 2001, pp. 101--116. 2001.



X. Tricoche, G. Scheuermann, H. Hagen. “Topology-based Visualization of Time-Dependent 2D Vector Fields,” In Proceedings of the Joint Eurographics-IEEE TCVG Symposium on Visualization: Data Visualization 2001, pp. 117--126. 2001.



X. Tricoche, G. Scheuermann, H. Hagen. “Continuous Topology Simplification of Planar Vector Fields,” In Proceedings of IEEE Visualization 2001, pp. 159--166. 2001.



R. Van Uitert, D. Weinstein, C.R. Johnson, L. Zhukov. “Finite Element EEG and MEG Simulations for Realistic Head Models: Quadratic vs. Linear Approximations,” In Biomed. Technik, Vol. 46, pp. 32--34. 2001.



M. Walkley, P.K. Jimack, M. Berzins. “Mesh Quality for Three-dimensional Finite Element Solutions on Anisotropic Meshes,” In Proceedings of FEM3D, GUKUTO International Series, Mathematical Sciences and Applications, Vol. 15, pp. 310--321. 2001.



M. Walkley, P.K. Jimack, M. Berzins. “Anisotropic Adaptivity for Finite Element Solutions of 3-D Convection-Dominated Problems,” In Numerical Methods for Fluid Dynamics VII, Edited by M.J. Baines, ICFD, Oxford, pp. 525--531. 2001.
ISBN: 0 9524929 2 X



M. Walkley, P.K. Jimack, M. Berzins. “Mesh Quality and Anisotropic Adaptivity for Finite Element Solutions of 3-D Convection-Dominated Problems,” In Proceedings of ECCOMAS Computational Fluid Dynamics Conference 2001, Swansea, UK, 2001.
ISBN: 0 905 091 12 4



L. Wang, S.C. Joshi, M.I. Miller, J. Csernansky. “Statistical Analysis of Hippocampal Asymmetry in Schizophrenia,” In Neuroimage, Vol. 14, No. 3, pp. 531--545. September, 2001.



D. Weinstein, O. Portniaguine, L. Zhukov. “A Comparison of Dipolar and Focused Inversion for EEG Source Localization,” In Biomed. Technik, Vol. 46 (special issue), pp. 121--123. Sep, 2001.



J.A. Weiss, J.C. Gardiner. “Computational Modeling of Ligament Mechanics,” In Critical Reviews in Biomedical Engineering, Vol. 29, No. 3, pp. 1--70. 2001.



R. Westermann, C.R. Johnson, T. Ertl. “Topology Preserving Smoothing of Vector Fields,” In IEEE Trans. Vis & Comp. Graph., Vol. 7, No. 3, pp. 222--229. 2001.
DOI: 10.1109/2945.942690

ABSTRACT

Proposes a technique for topology-preserving smoothing of sampled vector fields. The vector field data is first converted into a scalar representation in which time surfaces implicitly exist as level sets. We then locally analyze the dynamic behavior of the level sets by placing geometric primitives in the scalar field and by subsequently distorting these primitives with respect to local variations in this field. From the distorted primitives, we calculate the curvature normal and we use the normal magnitude and its direction to separate distinct flow features. Geometrical and topological considerations are then combined to successively smooth dense flow fields, at the same time retaining their topological structure.

Keywords: vector field methods, ip image processing signal processing, surface processing, ncrr



R.T. Whitaker. “Reconstructing Terrain Maps from Dense Range Data,” In IEEE International Conference on Image Processing, pp. 165--168. October, 2001.



R.T. Whitaker, X. Xue. “Variable-Conductance, Level-Set Curvature for Image Denoising,” In IEEE International Conference on Image Processing, pp. 142--145. October, 2001.



D. Xiu, G.E. Karniadakis. “A Semi-Lagrangian High-Order Method for Navier-Stokes Equations,” In Journal of Computational Physics, Vol. 172, No. 2, pp. 658--684. 2001.
DOI: 10.1006/jcph.2001.6847

ABSTRACT

We present a semi-Lagrangian method for advection–diffusion and incompressible Navier–Stokes equations. The focus is on constructing stable schemes of secondorder temporal accuracy, as this is a crucial element for the successful application of semi-Lagrangian methods to turbulence simulations. We implement the method in the context of unstructured spectral/hp element discretization, which allows for efficient search-interpolation procedures as well as for illumination of the nonmonotonic behavior of the temporal (advection) error of the form: (see pdf for formula) We present numerical results that validate this error estimate for the advection–diffusion equation, and we document that such estimate is also valid for the Navier–Stokes equations at moderate or high Reynolds number. Two- and three-dimensional laminar and transitional flow simulations suggest that semi-Lagrangian schemes are more efficient than their Eulerian counterparts for high-order discretizations on nonuniform grids.



P. Yushkevich, S.M. Pizer, S. Joshi, J.S. Marron. “Intuitive, Localized Analysis of Shape Variability,” In Information Processing in Medical Imaging (IPMI), pp. 402--408. June, 2001.



L. Zhukov, D.M. Weinstein, C.R. Johnson, R.S. Macleod. “Spatio-temporal Multi-dipole Source Localization Using ICA and Lead-Fields in FEM Head Models,” In Proceedings of the IEEE Engineering in Medicine and Biology Society 23rd Annual International Conference, Istanbul, Turkey Oct, 2001.


2000


O. Alter, P.O. Brown, D. Botstein. “Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling,” In Proceedings of the National Academy of Sciences, Vol. 97, No. 18, Proceedings of the National Academy of Sciences, pp. 10101--10106. August, 2000.
DOI: 10.1073/pnas.97.18.10101



Th. Apel, M. Berzins, P.K. Jimack, G. Kunert, A. Plaks, I. Tsukerman, M. Walkley. “Mesh Shape and Anistropic Elements: Theory and Practice,” In The Mathematics of Finite Elements and Applications X, Edited by J.R. Whiteman, Elsevier, pp. 367--376. 2000.