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


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

P.P.J. Sloan, M.F. Cohen, S.J. Gortler. “Time Critical Lumigraph Rendering,” In 1997 Symposium on Interactive 3D Graphics, Apr, 1997.

W. Speares, M. Berzins. “A 3D Unstructured Mesh Adaptation Algorithm for Time Dependent Shock Dominated Problems,” In Int. Jour Numerical Methods in Fluids, Vol. 25, pp. 81--104. 1997.

A. Tomlin, M. Berzins, J.M. Ware, J. Smith, M. Pilling. “On the use of adaptive gridding methods for modelling chemical transport from multi-scale sources,” In Atmospheric Env., Vol. 31, No. 18, pp. 2945--2959. 1997.

D.M. Weinstein, C.R. Johnson. “Effects of Geometric Uncertainty on the Inverse EEG Problem,” In Computational, Experimental, and Numerical Methods for Solving Ill-Posed Inverse Imaging Problems:Medical and Nonmedical Applications, SPIE '97, Vol. 3171, Edited by R.L. Barbour and M.J. Carvlin and M.A. Fiddy, SPIE, pp. 138--145. 1997.

D.M. Weinstein, C.R. Johnson. “Cache-rings for Memory Efficient Isosurface Construction,” School of Computing Technical Report, No. UUCS-97-016, University of Utah, Salt Lake City, UT 1997.

F. Yu, Y. Livnat, C.R. Johnson. “An Automatic Adaptive Refinement and Derefinement Method for 3D Elliptic Problems,” In Applied Numerical Mathematics, 1997.


O. Alter, Y. Yamamoto. “Protective Measurement of the Wave Function of a Single Squeezed Harmonic Oscillator State,” In Physical Review A, Vol. 53, No. 5, pp. R2911--R2914. May, 1996.
DOI: 10.1103/PhysRevA.53.R2911

O. Alter, Y. Yamamoto. “Inhibition of the Measurement of the Wavefunction of a Single Quantum System and the Projection Postulate,” In Quantum Physics, Chaos Theory and Cosmology, Edited by M. Namiki and I. Ohba and K. Maeda and Y. Aizawa, American Institute of Physics, pp. 151--172. 1996.
DOI: 10.1103/PhysRevLett.74.4106

O. Alter, Y. Yamamoto. “The Quantum Zeno Effect of a Single System is Equivalent to the Indetermination of the Quantum State of a Single System,” In Quantum Interferometry, Edited by F. De Martini and G. Denardo and Y. Shih, VCH, pp. 539--544. 1996.
DOI: 10.1103/PhysRevA.55.R2499

O. Alter, Y. Yamamoto. “The Unknown Wavefunction of a Single System Cannot Be Inferred Using Repeated Quantum Measurements,” In Quantum Coherence and Decoherence, Edited by K. Fujikawa and Y. A. Ono, Elsevier Science, Amsterdam, Netherlands, pp. 31--34. 1996.

C.L. Bajaj, V. Pascucci, D.R. Schikore. “Fast Isocontouring for Improved Interactivity,” In 1996 Volume Visualization Symposium, IEEE Computer Society, pp. 39--46. October, 1996.
ISBN: 0-89791-741-3

C.L. Bajaj, V. Pascucci. “Splitting a Complex of Convex Polytopes in any Dimension,” In Proceedings of the Twelfth Annual Symposium On Computational Geometry (ISG '96), ACM Press, New York pp. 88--97. May, 1996.
ISBN: 0-89791-832-0

C.L. Bajaj, F. Bernardini, V. Pascucci, D.R. Schikore. “Interrogative Visualization of the Visible Human Datasets,” In Proceedings of the The Visible Human Project Conference, 1996.