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

2007


 T.J. Lujan, M.S. Dalton, B.M. Thompson, B.J. Ellis, J.A. Weiss. “Effect of ACL Deficiency on MCL Strains and Joint Kinematics,” In Journal of Biomechanical Engineering, Vol. 129, No. 3, pp. 386--392. 2007.


T.J. Lujan, C.J. Underwood, H.B. Henninger, B.M. Thompson, J.A. Weiss. “Effect of Dermatan Sulfate Glycosaminoglycans on the Quasi-Static Material Properties of the Human Medial Collateral Ligament,” In Journal of Orthopaedic Research, Vol. 25, No. 7, pp. 894--903. 2007.


M. Malik, Y. Birnbaum, R.S. MacLeod, V. Shusterman. “Markers of impaired repolarization,” In Journal of Electrocardiology, Vol. 40, No. 1, pp. S54--S57. January, 2007.


M.D. Meyer, B. Nelson, R.M. Kirby, R.T. Whitaker. “Particle Systems for Efficient and Accurate Finite Element Visualization,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 5, pp. 1015--1026. 2007.


M.D. Meyer, R.M. Kirby, R.T. Whitaker. “Topology, Accuracy, and Quality of Isosurface Meshes Using Dynamic Particles,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 6, IEEE, pp. 1704--1711. Nov, 2007.


D. Nain, M. Styner, M. Niethammer, J.J. Levitt, M.E. Shenton, G. Gerig, A. Bobick, A. Tannenbaum. “Statistical Shape Analysis of Brain Structures Using Spherical Wavelets,” In Proceedings of the 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2007), IEEE Press, pp. 209--212. 2007.


O. Nemitz, T. Tasdizen, M. Rumpf, R.T. Whitaker. “Anisotropic Curvature Motion for Structure Enhancing Smoothing of 3D MR Angiography Data,” In Journal of Mathematical Imaging and Vision, Vol. 7, No. 3, pp. 217--229. 2007.
DOI: 10.1007/s10851-006-0645-2


E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby. “Unconditionally Stable Discretizations of the Immersed Boundary Equations,” In Journal of Computational Physics, Vol. 222, No. 2, pp. 702--719. 2007.


E.P. Newren, A.L. Fogelson, R.D. Guy, R.M. Kirby. “Unconditionally Stable Discretizations of the Immersed Boundary Equations,” In Journal of Computational Physics, Vol. 222, No. 2, pp. 702--719. March, 2007.


T. Ochotta, C.E. Scheidegger, J. Schreiner, Y. Lima, R.M. Kirby, C.T. Silva. “A Unified Projection Operator for Moving Least Squares Surfaces,” SCI Institute Technical Report, No. UUSCI-2007-006, University of Utah, 2007.


L. Omberg, G.H. Golub, O. Alter. “A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data From Different Studies,” In Proceedings of the National Academy of Sciences, Vol. 104, No. 47, Proceedings of the National Academy of Sciences, pp. 18371–-18376. November, 2007.
DOI: 10.1073/pnas.0709146104


R. Palmer, G. Gopalakrishnan, R.M. Kirby. “Semantics Driven Dynamic Partial-Order Reduction of MPI-based Parallel Programs,” In Proceedings of Parallel and Distributed Systems: Testing and Debugging (PADTAD), London, UK, Note: Awarded Best Paper, 2007.


S.G. Parker, S. Boulos, J. Bigler, A. Robison. “RTSL: a Ray Tracing Shading Language,” In In 2007 IEEE/Eurographics Symposium on Interactive Ray Tracing, pp. 149--160. 2007.


S.G. Parker, R. Armstrong, D. Bernholdt, T. Dahlgren, T. Epperly, J. Kenny, M. Krishnan, G. Kumfert, J. Larson, L.C. McInnes, J. Nieplocha, J. Ray, S. Shasharina. “Enabling Advanced Scientific Computing Software,” In CTWatch Quarterly, Vol. 3, No. 4, 2007.


V. Pascucci, G. Scorzelli, P.-T. Bremer, A. Mascarenhas. “Robust On-line Computation of Reeb Graphs: Simplicity and Speed,” In ACM Transactions on Graphics: ACM SIGGRAPH 2007 Papers, ACM Press, New York, NY, USA pp. 1057--1066. 2007.


S. Pervez, G. Gopalakrishnan, R.M. Kirby, R. Palmer, R. Thakur, W. Gropp. “Practical Model Checking Method for Verifying Correctness of MPI Programs,” In Recent Advances in Parallel Virtual Machine and Message Passing Interface - Proceedings of EuroPVM-MPI 2007, Paris, France, Vol. 4757/2007, pp. 344--353. 2007.


N.S. Phatak, Q. Sun, S.-E. Kim, D.L. Parker, R.K. Sanders, A.I. Veress, B.J. Ellis, J.A. Weiss. “Noninvasive Determination of Ligament Strain with Deformable Image Registration,” In Annals of Biomedical Engineering, Vol. 35, No. 7, pp. 1175--1187. February, 2007.


A.B. Porter, L. Healy, N.L. Foster, K.A. Josephs. “Compulsive Urination as a Presenting Symptom of Frontotemporal Dementia,” In European Journal of Neurology, Vol. 14, Note: Letter to the Editor, pp. e16--e17. 2007.


G.A. Preston, E.W. Anderson, C.T. Silva. “Effects of 10 Hz rTMS on Alpha Spectral Dynamics and Working Memory Performance,” In Proceedings of Neuroscience 2007 Poster Session, Note: Poster presentation., 2007.


D. Reed, C.R. Johnson. “CRA-NIH Computing Research Challenges in Biomedicine Workshop Recommendations,” Note: Computing Research Association (CRA), 2007.