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.R. Johnson, M. Berzins, L. Zhukov, R. Coffey. “SCIRun: Applications to Atmospheric Diffusion Using Unstructured Meshes,” In Numerical Methods for Fluid Dynamics VI, Edited by M.J. Baines, Oxford University Press, pp. 111--122. 1998.

G. Kindlmann, J. Durkin. “Semi-Automatic Generation of Transfer Functions for Direct Volume Rendering,” In IEEE Symposium on Volume Visualization, IEEE Press, pp. 79--86. Oct, 1998.

Y. Livnat, C.D. Hansen. “View Dependent Isosurface Extraction,” In IEEE Visualization '98, pp. 175--180. Oct, 1998.

M. Miller, C.D. Hansen, C.R. Johnson. “Simulation Steering with SCIRun in a Distributed Memory Environment,” In Lecture Notes in Computer Science, Springer-Verlag, In Applied Parallel Computing, 4th International Workshop, PARA'98, Lecture Notes in Computer Science, Vol. 1541, Edited by B. Kagstrom and J. Dongarra and E. Elmroth and J. Wasniewski, Springer-Verlag, Berlin pp. 366--376. 1998.

M. Miller, C.D. Hansen, S.G. Parker, C.R. Johnson. “Simulation Steering with SCIRun in a Distributed Memory Environment,” In Seventh IEEE International Symposium on High Performance Distributed Computing (HPDC-7), Jul, 1998.

J. Pan, C.G.W. Sheppard, A. Tindall, M. Berzins, S.V. Pennington, J.M. Ware. “End Gas Inhomogeneity, Autoignition and Knock,” SAE meeting technical report, San Fransisco, CA, No. 982616, SAE, 1998.

S.G. Parker, P. Shirley, Y. Livnat, C.D. Hansen, P.-P. Sloan. “Interactive Ray Tracing for Isosurface Extraction,” In IEEE Visualization '98, pp. 233--238. October, 1998.

S.G. Parker, P. Shirley, B. Smits. “Single Sample Soft Shadows,” School of Computing Technical Report, No. UUCS-98-019, University of Utah, October, 1998.

S.G. Parker, M. Miller, C.D. Hansen, C.R. Johnson, P.-P. Sloan. “An Integrated Problem Solving Environment: The SCIRun Computational Steering System,” In 31st Hawaii International Conference on System Sciences (HICSS-31), Vol. VII, Edited by H. El-Rewini, pub-IEEE, pp. 147--156. January, 1998.

G.F. Potts, D.M. Weinstein, B.F. O'Donnell M.E., C.R. Johnson, R.W. McCarley. “Bioelectric Modeling of the P300 in Schizophrenia,” In Biological Psychiatry (suppl.), pp. 396. 1998.

G.F. Potts, C.G. Wible, M.E. Shenton, D.M. Weinstein, I.A. Fisher, M.E. Levention, L.D. Gugino, R.W. McCarley. “Localization of Visual Cortex with Coregistered Functional Magnetic Resonance Imaging, Bioelectrically Modeled Cortical Visual Evoked Potential, and Transcranial Magnetic Stimulation Induced Visual Suppression,” In Journal of Cognitive Neuroscience (suppl.), pp. 42. 1998.

M.A. Puso, J.A. Weiss. “Finite Element Implementation of Anisotropic Quasilinear Viscoelasticity Using a Discrete Spectrum Approximation,” In Journal of Biomechanical Engineering, Vol. 120, pp. 62--70. 1998.

K.M. Quapp, J.A. Weiss. “Material Characterization of Human Medial Collateral Ligament,” In Journal of Biomechanical Engineering, Vol. 120, pp. 757--763. 1998.

M. Richards, J.A. Goulet, J.A. Weiss, N.A. Waanders, M.B. Schaffler, S.A. Goldstein. “Bone Regeneration and Fracture Healing: Experience with Distraction Osteogenesis Model,” In Clinical Orthopaedics and Related Research, Vol. 355S, pp. 191--204. 1998.

P.Selwood, M.Berzins, J. Nash, P.M. Dew. “Portable Parallel Adaptation of Unstructured Tetrahedral Meshes,” In Proceedings of Irregular 98 Conference, Lecture Notes in Computer Science (LNCS), Vol. 1457, Edited by A. Ferreira et al., Springer, pp. 56--67. 1998.

P.A. Sleigh, M. Berzins, P.H. Gaskell, N.G. Wright. “An Unstructured Finite Volume Algorithm for Predicting Flow in Rivers and Estuaries,” In Computers and Fluids, Vol. 27, No. 4, pp. 479--508. 1998.

P.P.J. Sloan, D.M. Weinstein, J.D. Brederson. “Importance Driven Texture Coordinate Optimization,” In Eurographics 98, Sep, 1998.

R. Stevens, H. Fuchs, A. van Dam, P. Hanrahan, C.R. Johnson, C. McMillan, P. Heermann, S. Louis, T. Defanti, D. Reed, E. Cohen. “Data and Visualization Corridors: Report on the 1998 DVC Workshop Series,” Note: DOE Report, September, 1998.


The Department of Energy and the National Science Foundation sponsored a series of workshops on data manipulation and visualization of large-scale scientific datasets. Three workshops were held in 1998, bringing together experts in high-performance computing, scientific visualization, emerging computer technologies, physics, chemistry, materials science, and engineering. These workshops were followed by two writing and review sessions, as well as numerous electronic collaborations, to synthesize the results. The results of these efforts are reported here. Across the government, mission agencies are charged with understanding scientific and engineering problems of unprecedented complexity. The DOE Accelerated Strategic Computing Initiative, for example, will soon be faced with the problem of understanding the enormous datasets created by teraops simulations, while NASA already has a severe problem in coping with the flood of data captured by earth observation satellites. Unfortunately, scientific visualization algorithms, and high-performance display hardware and software on which they depend, have not kept pace with the sheer size of emerging datasets, which threaten to overwhelm our ability to conduct research. Our capability to manipulate and explore large datasets is growing only slowly, while human cognitive and visual perception are an absolutely fixed resource. Thus, there is a pressing need for new methods of handling truly massive datasets, of exploring and visualizing them, and of communicating them over geographic distances. This report, written by representatives from academia, industry, national laboratories, and the government, is intended as a first step toward the timely creation of a comprehensive federal program in data manipulation and scientific visualization. There is, at this time, an exciting confluence of ideas on data handling, compression, telepresence, and scientific visualization. The combination of these new ideas, which we refer to as Da ta and Visualization Corridors (DVC), can raise scientific data understanding to new levels and will improve the way science is practiced

T. Tasdizen, L. Akarun, C. Ersoy. “Color Quantization with Genetic Algorithms,” In Signal Processing: Image Communication, Vol. 12, pp. 49--57. 1998.

N. Touheed, P. Selwood, P.K. Jimack, M. Berzins. “Parallel Dynamic Load-Balancing for the Solution of Transient CFD Problems Using Adaptive Tetrahedral Meshes,” In Parallel Computational Fluid Dynamics - Recent Developments and Advances Using Parallel Computers, Edited by D.R. Emerson and A. Ecer and J. Periaux and N. Satufoka and P. Fox, Elsevier Science, pp. 81--88. 1998.