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


M. Berzins, J.M. Ware. “Positive Cell Centered Finite Volume Discretisation Methods for Hyperbolic Equations on Irregular Meshes,” In Applied Numerical Mathematics, Vol. 16, pp. 417--438. 1995.


The conditions sufficient to ensure positivity and linearity preservation for a cell-centered finite volume schemefor time-dependent hyperbolic equations using irregular one-dimensional and triangular two-dimensional meshes arederived. The conditions require standard flux limiters to be modified and also involve possible constraints on themeshes. The accuracy of this finite volume scheme is considered and is illustrated by two simple numerical examples.

M. Berzins, P. Gaskell, A. Sleigh, A.S. Tomlin, J. Ware. “An adaptive CFD solver for time-dependent environmental flow problems,” In Proceedings of the Institute of Computational Fluid Dynamics Conference, Edited by K.W. Morton, M.J. Baines, Oxford University Press, pp. 311-317. 1995.

M. Berzins, T.H.C. Childs, K.W. Dalgarno, G.R. Ryder, G. Stein. “Densification and Distortion in Selective Laser Sintering of Polycarbonate,” In Proc 6th Symposium on Solid Free Form Fabrication, University of Texas at Austin, Edited by J.W. Barlow et al., pp. 196--203. 1995.

M. Berzins. “Temporal Error Control in the Method of Lines for Convection Dominated Equations,” In SIAM Journal on Scientific Computing, Vol. 16, pp. 558--580. 1995.

G.E. Christensen, R.D. Rabbitt, M.I. Miller, S.C. Joshi, U. Grenander, T.A. Coogan. “Topological Properties of Smooth Anatomic Maps,” In Information Processing in Medical Imaging, pp. 101--112. 1995.

P. Gharpure, C.R. Johnson. “A Cellular Automaton Model of Electrical Activation in Canine Ventricles: A Validation Study,” SCI Institute Technical Report, No. UUSCI-1995-002, University of Utah, 1995.

J.W. Haller, M.I. Miller, G.E. Christensen, S. Joshi, M. Gado, J. Csernansky, M.W. Vannier. “A Comparison of Automated and Manual Segmentation of Hippocampus MR Images,” In Proceedings of SPIE Medical Imaging, pp. 206--215. March, 1995.

J.W. Haller, G.E. Christensen, S. Joshi, M.I. Miller, M.W. Vannier. “Digital Atlas-Based Segmentation of the Hippocampus,” In Computer Assisted Radiology: Proceedings of the International Symposium on Computer and Communications Systems for Image Guided Diagnosis and Therapy, Edited by C.C. Jaffe and H.U. Lemke and K. Inamura and M.W. Vannier, pp. 152--157. June, 1995.

C.D. Hansen, G.C. de Verdiere, M. Krogh, J. Painter, R. Troutman. “Binary-Swap Volumetric Rendering on the T3D,” In Cray Users Group Conference, Denver, Co., pp. 61--69. March, 1995.

C.D. Hansen, M. Krogh, W. White. “Massively Parallel Visualization: Parallel Rendering,” In SIAM Parallel Computation Conference, San Francisco, Ca., pp. 790--795. February, 1995.

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.