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


R.T. Whitaker. “A Level-Set Approach to 3D Reconstruction From Range Data,” In International Journal of Computer Vision, Vol. 29, No. 3, pp. 203--231. 1998.


I. Ahmad, M. Berzins. “An Algorithm for ODEs from Atmospheric Dispersion Problems,” In Applied Numerical Mathematics, Vol. 25, pp. 137--149. 1997.

O. Alter, Y. Yamamoto. “Reply to the Comment on 'Protective Measurement of the Wave Function of a Single Squeezed Harmonic Oscillator State',” In Physical Review A, Vol. 56, No. 1, pp. 1057--1059. July, 1997.
DOI: 10.1103/PhysRevA.56.1057

O. Alter, Y. Yamamoto. “Quantum Zeno Effect and the Impossibility of Determining the Quantum State of a Single System,” In Physical Review A, Vol. 55, No. 4, pp. R2499--R2502. April, 1997.
DOI: 10.1103/PhysRevA.55.R2499

C.L. Bajaj, V. Pascucci, D.R. Schikore. “The Contour Spectrum,” In Proceedings of the 8th Annual IEEE Conference on Visualization (VIS-97), Edited by Roni Yagel and Hans Hagen, IEEE Computer Society, pp. 167--175. November, 1997.

C. Bajaj, H.Y. Lee, R. Merkert, V. Pascucci. “NURBS based B-rep Models for Macromolecules and their Properties,” In Proceedings of the 4th Symposium on Solid Modeling and Applications, Edited by Christoph Hoffmann and Wim Bronsvort, ACM Press, New York pp. 217--228. May, 1997.
ISBN: 0-89791-946-7

C.L. Bajaj, V. Pascucci, D.R. Schikore. “Fast Isocontouring for Structured and Unstructured Meshes in Any Dimension,” In Late Breaking Hot Topics Proceedings of the 8th Annual IEEE Conference on Visualization (VIS-97), Edited by Amitabj Varshney and David S. Ebert, IEEE Computer Society, pp. 25--28. November, 1997.

D.M. Beazley. “Using SWIG to control, prototype, and debug C program with Python,” In 4th International Python Conference, 1997.

M. Berzins, S.V. Pennington, P.R. Pratt, J.M. Ware. “SPRINT2D Software for Convection Dominated PDEs,” In Modern Software Tools in Scientific Computing, Edited by E. Arge and A.M. Bruaset and H.P. Langtangen, Birkhauser Press, 1997.


SPRINT2D is a set of software tools for solving time-dependent partial differential equations in two space variables. The software uses unstructured triangular meshes and adaptive error control in both space and time. This chapter describes the software and shows how the adaptive techniques may be used to increase the reliability of the solution procedure for a challenging combustion problem. The recent construction of a problem solving environment (PSE) has partially automated the use of SPRINT2D. This PSE consists of tools such as a visual domain specification tool, which helps ease the input of complex geometries, and a visual problem specification tool. After describing these components an evaluation will be made of SPRINT2D and its associated PSE.

M. Berzins, P.J. Capon, P.K. Jimack. “On Spatial Adaptivity and Interpolation when Using the Method of Lines,” In Applied Numerical Mathematics: Transactions of IMACS, Vol. 26, No. 1--2, pp. 117--133. 1997.

G.E. Christensen, S.C. Joshi, M. Miller. “Volumetric Transformation of Brain Anatomy,” In IEEE Trans Med Imaging, Vol. 16, No. 6, pp. 864--877. December, 1997.

G.E. Christensen, S.C. Joshi, M.I. Miller. “Volumetric Transformation of Brain Anatomy,” In IEEE Transactions on Medical Imaging, Vol. 16, No. 6, pp. 864--877. December, 1997.

D.J. Creasey, D.E. Heard, M. Pilling, B.J. Whitaker, M. Berzins, R. Fairlie. “Visualisation of a Supersonic Free-Jet Expansion Using Laser-Induced Fluorescence Spectroscopy: Application to the Measurement of Rate Constants at Ultralow Temperatures,” In Applied Physics B: Lasers and Optics, Vol. 65, pp. 375--391. 1997.

J.W. Haller, A. Banerjee, G.E. Christensen, M. Gado, S. Joshi, M.I. Miller, Y. Sheline, M.W. Vannier, J. Csernansky. “Three-Dimensional Hippocampal MR Morphometry with High-Dimensional Transformation of a Neuroanatomic Atlas,” In Radiology, Vol. 202, No. 2, pp. 504--510. February, 1997.

C.D. Hansen, M. Krogh, J. Painter. “Parallel Rendering Techniques for Massively Parallel Visualization,” In International Symposium on Parallel Algorithms/Architecture Synthesis, Aizu-Wakamatsu, Japan, pp. 276--281. March, 1997.

C.R. Johnson, D.M. Beazley, Y. Livnat, S.G. Parker, J.A. Schmidt, H.W. Shen, D.M. Weinstein. “Applications of Large-Scale Computing and Scientific Visualization in Medicine,” SCI Institute Technical Report, No. UUSCI-1997-001, University of Utah, 1997.

C.R. Johnson. “Computational and Numerical Methods for Bioelectric Field Problems,” In Critical Reviews in BioMedical Engineering, Vol. 25, No. 1, pp. 1--81. 1997.

S.C. Joshi, M.I. Miller, U. Grenander. “On the Geometry and Shape of Brain Sub-Manifolds,” In International Journal of Pattern Recognition and Artificial Intelligence, special issue on Magnetic Resonance Imaging, Vol. 11, No. 8, pp. 1317--1343. 1997.

S. Joshi, A. Banerjee, G.E. Christensan, J.G. Csernansky, J.W. Haller, M.I. Miller, L. Wang. “Gaussian Random Fields on Sub-Manifolds for Characterizing Brain Surfaces,” In Proceedings of the International Conference on Image Processing in Medical Imaging (IPMI), 1997.

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 Transactions on Biomedical Engineering, Vol. 44, No. 8, pp. 706--719. August, 1997.