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


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.

M. van Kreveld, R. van Oostrum, C. Bajaj, V. Pascucci, D.R. Schikore. “Contour Trees and Small Seed Sets for Isosurface Traversal,” In Proceedings of the 13th International Annual Symposium on Computational Geometry (SCG-97), ACM Press, New York pp. 212--220. June, 1997.
ISBN: 0-89791-878-9

M. Krogh, J. Painter, C.D. Hansen. “Parallel Sphere Rendering,” In Parallel Computing, Vol. 23, No. 7, pp. 961--974. 1997.

Z. Lei, T. Tasdizen, D.B. Cooper. “PIMS and Invariant Parts for Shape Recognition,” In Sixth International Conference on Computer Vision, Narosa Publishing House, 1997.
DOI: 10.1109/iccv.1998.710813

A.L. Levy, T.J. Schaewe, M.I. Miller, K.R. Smith, A.M. Hammoud, J.M. Henderson, S. Joshi, K.E. Mark, C.D. Sturm, L.L. McDurmont Jr, R. Bucholz. “An Internet-Connected, Patient-Specific, Deformable Brain Atlas Integrated into a Surgical Navigation System,” In J Digit Imaging, Vol. 10, No. 3 (Suppl. 1), pp. 231--237. August, 1997.

M. Miller, A. Banerjee, G. Christensen, S. Joshi, N. Khaneja, U. Grenander, L. Matejic. “Statistical Methods in Computational Anatomy,” In Stat Methods Med Res, Vol. 6, No. 3, pp. 267--299. September, 1997.

M.I. Miller, S. Joshi. “Discussion of Mathematics for Object Recognition Shape, Invariance and Deformations,” In Proceedings of the Workshop on Mathematics for Object Recognition Shape, Invariance and Deformations, Edited by L. Younes, November, 1997.

S.G. Parker, D.M. Weinstein, C.R. Johnson. “The SCIRun Computational Steering Software System,” In Modern Software Tools in Scientific Computing, Edited by E. Arge and A.M. Bruaset and H.P. Langtangen, Birkhauser Press, Boston pp. 1--40. 1997.


We present the design, implementation and application of SCIRun, a scientific programming environment that allows the interactive construction, debugging, and steering of large-scale scientific computations. Using this "computational workbench," a scientist can design and modify simulations interactively via a dataflow programming model. SCIRun enables scientists to design and modify model geometry, interactively change simulation parameters and boundary conditions, and interactively visualize geometric models and simulation results. We discuss the ubiquitous roles SCIRun plays as a computational tool (e.g. resource manager, thread scheduler, development environment), and how we have applied an object oriented design (implemented in C++) to the scientific computing process. Finally, we demonstrate the application of SCIRun to large scale problems in computational medicine. 1.1 Introduction 1.1.1 Visual Computing and Interactive Steering In recent years, the scientific computing commu...

Keywords: scirun, problem solving environments, ncrr, scientific visualization, pse pses problem solving envoronment, bioelectric fields

S.G. Parker, D.M. Beazley, C.R. Johnson. “Computational Steering Software Systems and Strategies,” In IEEE Computational Science and Engineering, Vol. 4, No. 4, pp. 50--59. 1997.

P. Selwood, N.A. Verhoeven, J.M. Nash, M. Berzins, N.P. Weatherill, P.M. Dew, K. Morgan. “Parallel Mesh Generation and Adaptivity : Partitioning and Analysis,” In Parallel C.F.D.- Proc. of Parallel CFD 96 Conference, Capri, Italy, Edited by A.Ecer and J.Periaux and N.Satufoka and P.Schiano, Elesvier Science BV, May, 1997.
ISBN: 0-444 823271

P. Selwood, M. Berzins, P.M. Dew. “3D Parallel Mesh Adaptivity: Data Structures and Algorithms,” In Proc. of SIAM Conf. on Parallel Processing for Scientific Computing, Minneapolis, MN, USA, pp. (CD-Rom). March, 1997.
ISBN: 0-89871-395-1