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

2006


 C.R. Johnson, D.M. Weinstein. “Biomedical Computing and Visualization,” In Proceedings of the Twenty-Ninth Australasian Computer Science Conference (ACSC2006): Conferences in Research and Practice in Information Technology (CRPIT), Hobart, Australia, Vol. 48, Edited by Vladimir Estivill-Castro and Gill Dobbie, pp. 3-10. 2006.


C.R. Johnson, R. Moorhead, T. Munzner, H. Pfister, P. Rheingans, T. S. Yoo. “NIH-NSF Visualization Research Challenges Report,” Note: http://tab.computer.org/vgtc/vrc/index.html, IEEE Press, 2006.
ISBN: 0-7695-2733-7


J.T. Johnson III, M.S. Hansen, I. Wu, L.J. Healy, C.R. Johnson, G.M. Jones, M.R. Capecchi, C. Keller. “Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping,” In PLoS Genetics, Vol. 2, No. 1, pp. 471--477. April, 2006.


C.R. Johnson. “Computational Methods and Software for Bioelectric Field Problems,” In Biomedical Engineering Handbook, 2nd Edition, Vol. 1, Ch. 23, Edited by J.D. Bronzino, CRC Press, Boca Raton, pp. 1--23. 2006.


C.R. Johnson, S.G. Parker. “Problem Solving Environments for DDDAS,” In Proceedings of the Ninth Copper Mountain Conference on Iterative Methods, Copper Mountain, CO, Note: Minisymposium: Actually Doing Dynamic Data-driven Application Simulations, April, 2006.


J.T. Johnson III, M.S. Hansen, I.Q Wu, L.J. Healy, C.R. Johnson, G.M. Jones, M.R. Capecchi, C.Keller. “Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping,” In Proceedings of the Teratology 46th Annual Meeting, Tucson, AZ, 2006.


C.R. Johnson, R. Moorhead, T. Munzner, H. Pfister, P. Rheingans, T.S. Yoo, (Eds.). “NIH/NSF Visualization Research Challenges Report,” Note: IEEE Press, 2006.
ISBN: 0-7695-2733-7


M. Jolley, J. Triedman, C.-F. Westin, D.M. Weinstein, R.S. MacLeod, D.H. Brooks. “Image Based Modeling of Defibrillation in Children,” In Proceedings of the 26th Annual International Conference of the IEEE EMBS, New York, NY, USA August, 2006.


E. Jurrus, T. Tasdizen, P. Koshevoy, P.T. Fletcher, M. Hardy, C-B. Chien, W. Denk, R.T. Whitaker. “Axon Tracking in Serial Block-Face Scanning Electron Microscopy,” In Workshop on Microscopic Image Analysis with Applications in Biology, MICCAI, October, 2006.


G. Kindlmann, X. Tricoche, C.-F. Westin. “Anisotropy Creases Delineate White Matter Structure in Diffusion Tensor MRI,” In Proceedings of the Ninth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'06), Copenhagen, Denmark, Springer Lecture Notes in Computer Science 4190, pp. 126--133. October, 2006.


N.D. Kirkpatrick, J.B. Hoying, S.K. Botting, J.A. Weiss, U. Utzinger. “In Vitro Model for Endogenous Optical Signatures of Collagen,” In Journal of Biomedical Optics, Vol. 11, No. 5, September/October, 2006.


R.M. Kirby, C.R. Johnson, M. Berzins. “Involving Undergraduates in Computational Science and Engineering Research: Successes and Challenges,” In Proceedings of Computational Science - ICCS 2006: 6th International Conference, Reading, UK, Lecture Notes in Computer Science, Vol. 3992, May 28-31, 2006.


R.M. Kirby, S.J. Sherwin. “Stabilisation of Spectral/hp Element Methods Through Spectral Vanishing Viscosity: Application to Fluid Mechanics Modelling,” In Computer Methods in Applied Mechanics and Engineering, Vol. 195, pp. 3128--3144. 2006.


R.M. Kirby, S.J. Sherwin. “Aliasing Errors Due to Quadratic Non-Linearities On Triangular Spectral/hp Element Discretisations,” In Journal of Engineering Mathematics, Vol. 56, No. 3, pp. 273--288. 2006.


R.M. Kirby, Z. Yosibash, G.E. Karniadakis. “Towards Stable Coupling Methods for High-Order Discretizations of Fluid-Structure Interaction: Algorithms and Observations,” In Journal of Computational Physics, Vol. 223, No. 2, pp. 489--518. 2006.


R.M. Kirby, S.J. Sherwin. “Aliasing Errors Due to Quadratic Non-Linearities On Triangular Spectral/hp Element Discretisations,” In Journal of Engineering Mathematics, Vol. 56, pp. 273--288. 2006.


A. Knoll, I. Wald, S.G. Parker, C.D. Hansen. “Interactive Isosurface Ray Tracing of Large Octree Volumes,” SCI Institute Technical Report, No. UUSCI-2006-026, University of Utah, 2006.


P.A. Koshevoy, T. Tasdizen, R.T. Whitaker. “Implementation of an Automatic Slice-to-Slice Registration Tool,” SCI Institute Technical Report, No. UUSCI-2006-018, University of Utah, 2006.


P.A. Koshevoy, T. Tasdizen, R.T. Whitaker. “Implementation of an Automatic Image Registration Tool,” SCI Institute Technical Report, No. UUSCI-2006-020, University of Utah, 2006.


P. Koshevoy, T. Tasdizen, R.T. Whitaker, B. Jones, R. Marc. “Assembly of Large Three-Dimensional Volumes from Serial-Section Transmission Electron Microscopy,” In Proceedings of 2006 MICCAI Workshop on Microscopic Image Analysis with Applications in Biology, October, 2006.