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


 S. Xu, M. Styner, B. Davis, S. Joshi, G. Gerig. “Group Mean Differences of Voxel and Surface Objects via Nonlinear Group Averaging,” In Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI), pp. 758--761. April, 2006.


B. Yilmaz, R.S. Macleod. “Instance Selection for Estimation of Epicardial Activation Sequence from Venous Catheter Measurements,” In Proceedings of the 28th IEEE EMBS Annual International Conference, pp. 3982--3985. 2006.


P.A. Yushkevich, J. Piven, H.C. Hazlett, R.G. Smith, S. Ho, J.C. Gee, G. Gerig. “User-Guided 3D Active Contour Segmentation of Anatomical Structures: Significantly Improved Efficiency and Reliability,” In NeuroImage, Vol. 31, Note: A NeuroImage Top Cited Paper!, pp. 1116--1128. 2006.


X. Zheng, X. Tricoche, A. Pang. “Degenerate 3D Tensors,” In Visualization and Processing of Tensor Fields, Springer, pp. 241--256. 2006.

2005


 Y. Alexeev, B.A. Allan, R.C. Armstrong, D.E. Bernholdt, T.L. Dahlgren, D. Gannon, C.L. Janssen, J.P. Kenny, M. Krishnan, J.A. Kohl, G. Kumfert, L.C. McInnes, J. Nieplocha, S.G. Parker, C. Rasmussen, T.L. Windus. “Component-Based Software for High-Performance Scientific Computing,” In Journal of Physics: Conference Series, Vol. 16, IOP Publishing, pp. 536--540. January, 2005.
DOI: 10.1088/1742-6596/16/1/073


O. Alter, G.H. Golub. “Reconstructing the Pathways of a Cellular System from Genome-Scale Signals by Using Matrix and Tensor Computations,” In Proceedings of the National Academy of Sciences, Vol. 102, No. 49, Proceedings of the National Academy of Sciences, pp. 17559--17564. November, 2005.
DOI: 10.1073/pnas.0509033102


A.E. Anderson, C.L. Peters, B.D. Tuttle, J.A. Weiss. “A Subject-Specific Finite Element Model of the Pelvis: Development, Validation and Sensitivity Studies,” In ASME J. Biom. Eng., Vol. 127, No. 3, pp. 364--373. 2005.


S.P. Awate, T. Tasdizen, R.T. Whitaker. “Nonparametric Statistics of Image Neighborhoods for Unsupervised Texture Segmentation,” SCI Institute Technical Report, No. UUSCI-2005-003, University of Utah, 2005.


S.P. Awate, R.T. Whitaker. “Higher-Order Image Statistics for Unsupervised, Information-Theoretic, Adaptive, Image Filtering,” SCI Institute Technical Report, No. UUSCI-2005-004, University of Utah, 2005.


S.P. Awate, R.T. Whitaker. “Nonparametric Neighborhood Statistics for MRI Denoising,” SCI Institute Technical Report, No. UUSCI-2005-005, University of Utah, 2005.


S.P. Awate, R.T. Whitaker. “Nonparametric Neighborhood Statistics for MRI Denoising,” In In Proc. Int. Conf. Information Processing in Medical Imaging (IPMI), 2005. Lecture Notes in Computer Science, Vol. 3565, pp. 677--688. July, 2005.


S.P. Awate, R.T. Whitaker. “Higher-Order Image Statistics for Unsupervised, Information-Theoretic, Adaptive, Image Filtering,” In Proceedings of the IEEE Int. Conf. Computer Vision and Pattern Recognition (CVPR), pp. 44--51. 2005.


S.P. Awate, R.T. Whitaker. “Unsupervised, Information-Theoretic, Adaptive Image Filtering for Image Restoration,” In IEEE Trans. Pattern Anal. & Mach. Intel., Vol. 28, No. 3, pp. 364--376. 2005.


L. Barbosa, A.C. Salgado, F. de Carvalho, J. Robin, J. Freire. “Looking at both the Present and the Past to Efficiently Update Replicas of Web Content,” In Proceedings of the 7th Annual ACM International Workshop on Web Information and Data Management, pp. 75--80. 2005.


D. Barbosa, J. Freire, A. Mendelzon. “Designing Information-Preserving Mapping Schemes for XML,” In Proceedings of the 31st International Conference on Very Large Data Bases, Trondheim, Norway, pp. 109--120. 2005.


L. Bavoil, S.P. Callahan, P.J. Crossno, J. Freire, C.E. Scheidegger, C.T. Silva, H.T. Vo. “Vistrails: Enabling Interactive Multiple-View Visualizations,” In Proceeding of IEEE Visualization 2005, pp. 18. 2005.


F. Bertrand, R. Bramley, K. Damevski, D. Bernholdt, J. Kohl, J. Larson, A. Sussman. “Data Redistribution and Remote Method Invocation in Parallel Component Architectures,” In Proceedings of The 19th International Parallel and Distributed Processing Symposium, Vol. 1, Note: Awarded Best Paper, pp. 40--42. 2005.


F.F. Bernardon, S.P. Callahan, J.L.D. Comba, C.T. Silva. “Volume Rendering of Time-Varying Scalar Fields on Unstructured Meshes,” SCI Institute Technical Report, No. UUSCI-2005-006, University of Utah, 2005.


M. Berzins, R.M. Kirby, C.R. Johnson. “Integrating Teaching and Research in HPC: Experiences and Opportunities,” In Proceedings of the International Conference on Computational Science (ICCS) 2005, Atlanta, GA, pp. 36--43. 2005.


M. Berzins. “Preserving Positivity for Hyperbolic PDEs Using Variable-Order Finite Elements with Bounded Polynomials,” In Applied Numerical Mathematics, Vol. 52, No. 2-3, pp. 197--217. February, 2005.