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.S. Henriquez, C.R. Johnson, K.A. Henneberg L.J., A.E. Pollard. “Large Scale Biomedical Modeling and Simulation: From Concepts to Results,” SCI Institute Technical Report, No. UUSCI-1995-001, University of Utah, 1995.

D.C. Hodgson, P.K. Jimack, P. Selwood, M. Berzins. “Scalable, Parallel Generation of Partitioned Unstructured Meshes,” In Parallel C.F.D. -- Implementations and Results using Parallel Computers, Parallel CFD Conference 1995, pasadena, California, Edited by A. Ecer and J. Periaux and N. Satufoka and S. Taylor, pp. 665-672. June, 1995.
ISBN: 0-444 823220

C.R. Johnson, R.S. MacLeod, J.A. Schmidt. “Software Tools for Modeling, Computation, and Visualization in Medicine,” In CompMed 94 Proceedings, World Scientific, 1995.

C.R. Johnson, S.G. Parker. “Applications in Computational Medicine using SCIRun: A Computational Steering Programming Environment,” In Supercomputer `95, Edited by H.W. Meuer, Springer-Verlag, pp. 2--19. 1995.

C.R. Johnson. “Direct and Inverse Bioelectric Field Problems,” In Computational Science Education Project, Edited by E. Oliver and M. Strayer and V. Meiser and D. Zachmann and R. Giles, DOE, Washington, D.C. 1995.

C.R. Johnson. “Numerical Methods for Bioelectric Field Problems,” In The Biomedical Engineering Handbook, Edited by J.D. Bronzino, CRC Press, Boca Ratan pp. 161--188. 1995.

S.C. Joshi, M.I. Miller, G.E. Christensen, A. Banerjee, T.A. Coogan, U. Grenander. “Hierarchical brain mapping via a generalized Dirichlet solution for mapping brain manifolds,” In Proc. of the SPIE International Symposium on Optical Science, Engineering, and Instrumentation, pp. 278--289. August, 1995.

S.C. Joshi, J. Wang, M.I. Miller, D.V. Essen, U. Grenander. “On the Differential Geometry of the Cortical Surface,” In Proceedings of SPIE 1995 International Symposium: Vision Geometry IV, San Diego, CA, pp. 304--311. August, 1995.

R.N. Klepfer, C.R. Johnson, R.S. MacLeod. “The Effects of Inhomogeneities and Anisotropies on Electrocardiographic Fields: A Three-Dimensional Finite Element Study,” In IEEE Engineering in Medicine and Biology Society 17th Annual International Conference, IEEE Press, pp. 233--234. 1995.

J. Painter, P. McCormick, M. Krogh, C.D. Hansen, G.C. de Verdiere. “ACLMPL: Portable and Efficient Message Passing for MPPs,” In First European T3D User's Group Workshop, Lausanne Switzerland, pp. 4--10. November, 1995.

A. Paoluzzi, V. Pascucci, M. Vicentino. “Geometric Programming: A Programming Approach to Geometric Design,” In ACM Transactions on Graphics, Vol. 14, No. 3, pp. 266--306. July, 1995.

A. Paoluzzi, V. Pascucci. “Building Design Programming with a Functional Language,” In Proceedings of 6th Conference on Computing in Civil and Building Engineering, Berlin, Germany, AA Balkema, Rotterdam, July, 1995.

A. Paoluzzi, V. Pascucci, C. Sansoni. “Prototype Shape Modeling with a Design Language,” In Proceedings of the Sixth Int. Conf. on Computer-Aided Architectural Design Futures, The Global Design Studio, Edited by Milton Tan and Robert Teh, Centre for Advanced Studies in Architecture, National University of Singapore pp. 59--78. 1995.

S.G. Parker, C.R. Johnson. “SCIRun: A Scientific Programming Environment for Computational Steering,” In Proceedings of the 1995 ACM/IEEE Conference on Supercomputing, San Diego, California, USA, Supercomputing '95, No. 52, ACM, New York, NY, USA 1995.
ISBN: 0-89791-816-9
DOI: 10.1145/224170.224354

V. Pascucci, V. Ferrucci, A. Paoluzzi. “Dimension-independent convex-cell based HPC: representation scheme and implementation issues,” In SMA '95: Proceedings of the Third Symposium on Solid Modeling and Applications, Note: held May 17-19, 1995 in Salt Lake City, Utah, ACM, pp. 163--174. May, 1995.

R.D. Rabbitt, J.A. Weiss, G.E. Christensen, M.I. Miller. “Mapping of Hyperelastic Deformable Templates Using the Finite Element Method,” In Proc SPIE (Vision Geometry IV), Vol. 2573, pp. 252--265. 1995.

J.A. Schmidt, C.R. Johnson, J.C. Eason, R.S. MacLeod. “Applications of Automatic Mesh Generation and Adaptive Methods in Computational Medicine,” In Modeling, Mesh Generation, and AdaptiveMethodsforPartial Differential Equations, Edited by I. Babuska and J.E. Flaherty and W.D. Henshaw and J.E. Hopcroft and J.E. Oliger and T. Tezduyar, Springer-Verlag, pp. 367--390. 1995.

J.A. Schmidt, C.R. Johnson. “Defibsim: An Interactive Defibrillation Device Design Tool,” In IEEE Engineering in Medicine and Biology Society 17th Annual International Conference, IEEE Press, pp. 305--306. 1995.

J.A. Schmidt, C.R. Johnson, R.S. MacLeod. “An Interactive Computer Model for Defibrillation Device Design,” In International Congress on Electrocardiology, ICE, pp. 160--161. 1995.

H.W. Shen, C.R. Johnson. “Sweeping Simplices: A Fast Iso-surface Extraction Algorithm for Unstructured Grids,” In IEEE Visualization `95, IEEE Press, pp. 143--150. 1995.