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


S. Joshi, M.I. Miller. “Landmark Matching Via Large Deformation Diffeomorphisms,” In IEEE Transactions on Image Processing, Vol. 9, No. 8, pp. 1357--1370. August, 2000.

G.L. Kindlmann, D.M. Weinstein, D. Hart. “Strategies for Direct Volume Rendering of Diffusion Tensor Fields,” In IEEE Trans. Vis & Comp. Graph., Vol. 6, No. 2, pp. 124--138. April-June, 2000.

Y. Livnat, S.G. Parker, C.R. Johnson. “Fast Isosurface Extraction Methods for Large Image Data Sets,” In Handbook of Medical Imaging, Edited by A.N. Bankman, Academic Press, San Diego, CA pp. 731--745. Nov, 2000.

S.G. Parker, M. Miller, C.D. Hansen, C.R. Johnson. “Computational Steering and the SCIRun Integrated Problem Solving Environment,” In Proceedings of Dagstuhl 1997 Workshop on Scientific Visualization, Note: Invited and peer reviewed, Edited by Hans Hagen and Greg Nielson and Frits Post, pp. 257--266. 2000.

V. Pascucci, C.L. Bajaj. “Time Critical Isosurface Refinement and Smoothing,” In Proceedings of the ACM/IEEE Volume Visualization and Graphics Symposium 2000, Salt lake City, Utah, Note: UCRL-JC-139628, pp. 33--42. October, 2000.

E. Reinhard, B. Smits, C.D. Hansen. “Dynamic Acceleration Structures for Interactive Ray Tracing,” In Proceedings Eurographics Workshop on Rendering, Brno, Czech Republic, pp. 299--306. June, 2000.

E. Reinhard, C.D. Hansen. “A Comparison of Parallel Compositing Techniques on Shared Memory Architectures,” In Proceedings of The 2nd Eurographics Workshop on Parallel Graphics and Visualization, Spain, pp. 115--124. September, 2000.

G. Scheuermann, W. Kollmann, X. Tricoche, T. Wischgoll. “Evolution of Topology in Axi-Symmetric and 3D Viscous Flows,” In Numerical Simulations of Incompressible Flows, World Scientific Publishing, New Jersey, pp. 622--643. 2000.

A. Shamir, V. Pascucci, C.L. Bajaj. “Multi-Resolution Dynamic Meshes with Arbitrary Deformations,” In Proceedings of IEEE Conference on Visualization (VIS-00), Salt lake City, Utah, Note: UCRL-JC-139680, pp. 423--430. 2000.

P. Sutton, C.D. Hansen. “Accelerated Isosurface Extraction in Time-varying Fields,” In IEEE Trans. Vis & Comp. Graph., Vol. 6, No. 2, pp. 98--107. 2000.

P.M. Sutton, C.D. Hansen, H.W. Shen, D. Schikore. “A Case Study of Isosurface Extraction Algorithm Performance,” In Proceeding of The Joint Eurographics - IEEE TCVG Symposium on Visualization 2000, Amsterdam, pp. 259--268. May, 2000.

T. Tasdizen, J.-P. Tarel, D.B. Cooper. “Improving the Stability of Algebraic Curves for Applications,” In IEEE Transactions on Image Processing, Vol. 9, No. 3, pp. 405--416. March, 2000.

T. Tasdizen, D.B. Cooper. “Boundary Estimation from Intensity/Color Images with Algebraic Curve Models,” In Proceedings 15th International Conference on Pattern Recognition. ICPR-2000, IEEE, 2000.
DOI: 10.1109/icpr.2000.905308


A concept and algorithm are presented for non-iterative robust estimation of piecewise smooth curves of maximal edge strength in small image windows-typically 8/spl times/8 to 32/spl times/32. This boundary-estimation algorithm has the nice properties that it uses all the data in the window and thus can find locally weak boundaries embedded in noise or texture and boundaries when there are more than two regions to be segmented in a window; it does not require step edges-but handles ramp edges well. The curve-estimates found are among the level sets of a dth degree polynomial fit to "suitable" weightings of the image gradient vector at each pixel in the image window. Since the polynomial fitting is linear least squares, the computation to this point is very fast. Level sets then chosen to be appropriate boundary curves are those having the highest differences in average gray level in regions to either side. This computation is also fast. The boundary curves and segmented regions found are suitable for all purposes but especially for indexing using algebraic curve invariants in this form.

A.S. Tomlin, S. Ghorai, G. Hart, M. Berzins. “3-D Adaptive Unstructured Meshes in Air Pollution Modelling,” In Environmental Modeling and Software, Vol. 15, No. 4, pp. 681--692. 2000.

N. Touheed, P. Selwood, P.K. Jimack, M. Berzins. “A Comparison of Some Dynamic Load Balancing Algorithms for a Parallel Adaptive Flow Solver,” In Parallel Computing, Vol. 26, No. 12, pp. 1535--1554. 2000.

X. Tricoche, G. Scheuermann, H. Hagen. “Higher Order Singularities in Piecewise Linear Vector Fields,” In The Mathematics of Surfaces IX, Springer, London, pp. 99--113. 2000.

X. Tricoche, G. Scheuermann, H. Hagen. “A Topology Simplification Method for 2D Vector Fields,” In Proceedings of IEEE Visualization 2000, pp. 359--366. 2000.

D.C. Van Essen, H.A. Drury, S. Joshi, M. Miller. “Functional and Structural Mapping of Human Cerebral Cortex: Solutions are in the Surfaces,” In Adv Neurol, Vol. 84, pp. 23--34. 2000.

D.M. Weinstein, L. Zhukov, G. Potts. “Localization of Multiple Deep Epileptic Sources in a Realistic Head Model via Independent Component Analysis,” School of Computing Technical Report, No. UUCS-2000-004, University of Utah, February, 2000.

D.M. Weinstein, L. Zhukov, C.R. Johnson. “Lead-Field Bases for EEG Source Imaging,” In Annal. Biomed. Eng., Vol. 28, No. 9, pp. 1059--1065. Sep, 2000.