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.E. Bowden, R.D. Rabbitt, J.A. Weiss. “Anatomical Registration and Segmentation by Warping Template Finite Element Models,” In Proc. SPIE (Laser-Tissue Interaction IX), Vol. 3254, pp. 469--476. 1998.

J.C. Csernansky, S. Joshi, L. Wang, M. Gado, J.P. Miller, U. Grenander, M.I. Miller. “Hippocampal Morphometry in Schizophrenia by High Dimensional Brain Mapping,” In Proceedings of the National Academy of Science, Vol. 95, pp. 11406--11411. September, 1998.

L.J.K Durbeck, N.J. Macias, D.M. Weinstein C.R., J.M. Hollerbach. “SCIRun/Haptic Display for Flow Fields,” In Proceedings of the Third PHANTOM Users Group Workshop, AI Lab Technical Report No. 1643 and RLE Technical Report No. 624, Edited by J.K. Salisbury and M.A. Srinivasan, pp. 71--75. Dec, 1998.

C.D. Hansen. “EUROGRAPHICS '97 Conference Report,” In Computer Graphics Quarterly, Vol. 32, No. 1, pp. 39. February, 1998.

C.D. Hansen. “EUROGRAPHICS '97: Budapest, Hungary, September 4-8, 1997: Meeting Report,” In Computer Graphics Forum, Vol. 16, No. 5, pp. 323--324. February, 1998.

G. Hart, A. Tomlin, J. Smith, M. Berzins. “Multi-scale Atmospheric Dispersion Modelling by the Use of Adaptive Grid Techniques,” In Environmental Monitoring and Assessment, Vol. 52, pp. 225--228. 1998.

C.R. Johnson, R.S. MacLeod. “Adaptive local regularization methods for the inverse ECG problem,” In Progress in Biophysics and Biochemistry, Vol. 69, No. 2/3, pp. 405. Dec, 1998.

C.R. Johnson. “Computer Visualization in Medicine,” In National Forum, Vol. Fall, pp. 17--21. 1998.

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.