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


C.L. Bajaj, V. Pascucci, G. Zhuang. “Progressive Compression and Transmission of Arbitrary Triangular Meshes,” In Proceedings of the 10th Annual IEEE Conference on Visualization (VIS-99), San Francisco, CA, pp. 307--316. October 24-29, 1999.

C.L. Bajaj, V. Pascucci, D. Thompson, X.Y. Zhang. “Parallel Accelerated Isocontouring for Out-Of-Core Visualization,” In Proceedings of First Parallel Visualization and Graphics Symposium 1999, San Francisco, CA, IEEE Computer Society, October, 1999.

C.L. Bajaj, V. Pascucci, G. Zhuang. “Single Resolution Compression of Arbitrary Triangular Meshes with Properties,” In Proceedings of DCC: Data Compression Conference 1999, IEEE Computer Society, Snowbird, Utah March, 1999.

C.L. Bajaj, S. Cutchin, V. Pascucci, A. Paoluzzi, C. Morgia. “Web Based Collaborative CAAD,” In Proceedings of the 5th Symposium on Solid Modeling and Applications, 1999.

C. Bajaj, V. Pascucci, E. Petajan, G. Zhuang. “Polygonal Model Coding Evaluation for Low bit-rate Communication,” In Proceedings of the International Workshop on Synthetic - Natural Hybrid Coding and Three Dimensional Imaging, September, 1999.

M. Berzins, L.J.K. Durbeck. “Unstructured Mesh Methods Applied to Hyperbolic PDEs with Source Terms: Error Estimates and Mesh Quality,” In Godunov Methods: Theory and Applications Conference and Short Course, Oxford. numeritek Ltd.URL, October, 1999.

M. Berzins, J. Nash, P. Selwood. “Parallel Solution of Reacting Flow Problems using Unstructured Tetrahedral Meshes,” In Proceedings of 9th SIAM Parallel Processing for Scientific Computing, Philadelphia, PA, 1999.
ISBN: 0-89871-435-4

M. Berzins. “A Solution Based H1 Norm Triangular Mesh Quality Indicator,” In Grid Generation and Adaptive Algorithms, Edited by Marshal W. Bern, Joseph E. Flaherty, Mitchell Luskin, Springer, pp. 77-88. 1999.


The issue of mesh quality measures for triangular (and tetrahedral) meshes is considered. A new mesh quality measure is based both on geometrical and solution information and is derived by considering the error in the H 1 norm when linear triangular elements are used to approximate a quadratic function. The new measure is then compared with the recent mesh quality measure based on the L 2 norm. Simple examples are used to show that the choice of norm is critical in deciding what is a good triangulation

M. Berzins. “Mesh Quality - Geometry, Error Estimates or Both?,” In Engineering and Computers, Vol. 15, pp. 236--247. 1999.

D. Botstein, L. Smarr, D. Agard, M. Levitt, D. Lippman, D. Herrington, C.R. Johnson, G Rose, G. Rubin, A. Levison, M. Spence, H. Smith, C. Peskin, G. Jacobs. “NIH Biomedical Information Science and Technology Initiative (BISTI),” Note: Prepared by the Working Group on Biomedical Computing Advisory Committee to the Director, National Institutes of Health, July, 1999.


The biomedical community is increasingly taking advantage of the power of computing, both to manage and analyze data, and to model biological processes. The working group should investigate the needs of NIH-supported investigators for computing resources, including hardware, software, networking, algorithms, and training. It should take into account efforts to create a national information infrastructure, and look at working with other agencies (particularly NSF and DOE) to ensure that the research needs of the NIH-funded community are met.

It should also investigate the impediments biologists face in utilizing high-end computing, such as a paucity of researchers with cross-disciplinary skills. The panel should consider both today's unmet needs and the growing requirements over the next five years (a reasonable horizon for extrapolating the advances in the rapidly changing fields of computing and computational biology).

The result of deliberations should be a report to the NIH Director, which will be presented to the Advisory Committee to the Director. The report should include recommendations for NIH actions to support the growing needs of NIH-funded investigators for biomedical computing.

J.D. Brederson. “The I3Stick: An Inexpensive, Immersive, Interaction Device,” School of Computing Technical Report, No. UUCS-99-014, University of Utah, November, 1999.

D.H. Brooks, G.F. Ahmad, R.S. MacLeod, G.M. Maratos. “Inverse Electrocardiography by Simultaneous Imposition of Multiple Constraints,” In IEEE Trans Biomed. Eng., Vol. 46, No. 1, pp. 3--18. 1999.

T.H.C. Childs, M. Berzins, G.R. Ryder, A. Towtoni. “Selective Laser Sintering of an Amorphous Polymer-Simulations and Experiments,” In Proceedings of the Institution of Mechanical Engineers Part B: Journal of Engineering Manufacture, Vol. 213, No. B4, pp. 333--349. 1999.


L. Durbeck. “Evaporation: A Technique for Visualizing Mesh Quality,” In 8th International Meshing Roundtable, Sandia National Laboratories, pp. 259--265. Oct, 1999.

C. Guerra, V. Pascucci. “On Matching Sets of 3D Segments,” In Proceedings of SPIE Vision Geometry VIII, Denver, USA pp. 157-167. 1999.

C. Guerra, V. Pascucci. “3D Segment Matching Using the Hausdorff Distance,” In Proceedings of the IEEE Conference on Image Processing and its Applications, IPA99, pp. 18--22. 1999.

C. Guerra, V. Pascucci. “Segment Matching for Protein Secondary Structure Comparison,” In Proceedings of the Third International Conference on Computational Molecular Biology, RECOMB'99, ACM, Lyon, France pp. 30. 1999.

C.D. Hansen, T. Udeshi, S.G. Parker, P. Shirley. “Parallel Methods for Isosurface Visualization,” In Ninth SIAM Conference on Parallel Processing for Scientific Computing, Note: extended abstract, 1999.

R.E. Hogan, K.E. Mark, L. Wang, S.C. Joshi, M.I. Miller, R.D. Bucholz. “MR Imaging Deformation-Based Segmentation of the Hippocampus in Patients with Mesial Temporal Sclerosis and Temporal Lobe Epilepsy,” In Epilepsia, Vol. 40, No. 7, 1999.

C.R. Johnson, S.G. Parker. “The SCIRun Parallel Scientific Computing Problem Solving Environment,” In Ninth SIAM Conference on Parallel Processing for Scientific Computing, 1999.