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

2005


 L. Grady, T. Tasdizen. “A Geometric Multigrid Approach to Solving the 2D Inhomogeneous Laplace Equation with Internal Dirichlet Boundary Conditions,” In IEEE International Conference on Image Processing, Vol. 2, pp. 642--645. September, 2005.


C. Guerra, V. Pascucci. “Line-Based Object Recognition Using Hausdorff Distance: From Range Images to Molecular Secondary Structure,” In Image and Vision Computing, Vol. 23, No. 4, Note: UCRL-JRNL-208551, pp. 405-415. April, 2005.


J.E. Guilkey, J.B. Hoying JB, J.A. Weiss. “Computational modeling of multicellular constructs with the Material Point Method,” In Journal of Biomechanics, pp. (published online). June, 2005.


D. Gullmar, J.R. Reichenbach, A. Anwander, T. Knosche, C.H. Wolters, M. Eiselt, J. Haueisen. “Influence of Anisotropic Conductivity of the White Matter Tissue on EEG Source Reconstruction - An FEM Simulation Study,” In Int. J. Bioelectromag., Vol. 7, No. 1, pp. 108--110. 2005.


H. Guo, A. Rangarajan, S. Joshi. “3-D Diffeomorphic Shape Registration on Hippocampal Data Sets,” In Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv, Vol. 8 (Pt. 2), pp. 984--991. 2005.


A. Gyulassy, V. Natarajan, V. Pascucci, P.-T. Bremer, B. Hamann. “Topology-based Simplification for Feature Extraction from 3D Scalar Fields,” In Proceedings of the IEEE Conference on Visualization (VIS-05), pp. 275--280. October, 2005.


C.W. Hamman, R.M. Kirby, M. Berzins. “Parallelization and Scalability of a Spectral Element Solver,” SCI Institute Technical Report, No. UUSCI-2005-011, University of Utah, 2005.


C.D. Hansen, C.R. Johnson. “The Visualization Handbook,” Elsevier, 2005.
ISBN: 0-12-387582-X


Q. Han, S.M. Pizer, D. Merck, S. Joshi, J.-Y. Jeong. “Multi-figure Anatomical Objects for Shape Statistics,” In Lecture Notes in Computer Science, Edited by G. Christensen and M. Sonka, Springer, pp. 701-712. 2005.
DOI: 10.1007/11505730_58


D.E. Hart, C.E. Goodyer, M. Berzins, P.K. Jimack, L.E. Scales. “Adjoint Error Estimation for EHL-Like Models,” In Int. J. Numer. Meth. Fluids, Vol. 47, No. 10-11, pp. 1069--1075. 2005.


P. Hawkes, G. Kindlmann, D. Weinstein, G.M. Jones, C. Keller. “Practical Vessel Imaging by Computed Tomography in Live Transgenic Mouse Models for Human Tumors,” In Proceedings of 2005 SMI Conference, 4th Annual Meeting of the Society for Molecular Imaging, Cologne, Germany, 2005.


B. Hopenfeld, J.G. Stinstra, R.S. MacLeod. “The Effect of Conductivity on ST-Segment Epicardial Potentials Arising from Subendocardial Ischemia,” In Annal. Biomed. Eng., Vol. 33, No. 6, pp. 751--763. 2005.


M. Ikits, J.D. Brederson. “The Visual Haptic Workbench,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 431--447. 2005.
ISBN: 0-12-387582-X


I. Ionescu, J. Guilkey, M. Berzins, R.M. Kirby, J.A. Weiss. “Computational Simulation of Penetrating Trauma in Biological Soft Tissues Using the Material Point Method,” In Proceedings, Medicine Meets Virtual Reality, Vol. 13, Edited by James D Westwood et al., IOS Press, pp. 213--218. 2005.
ISBN: 1-58603-498-7


S. Izvekov, A. Violi, G.A. Voth. “Systematic Coarse-Graining of Nanoparticle Interactions in Molecular Dynamics Simulation,” In Journal of Physical Chemistry, B, Vol. 109, No. 36, pp. 17019--17024. August, 2005.
DOI: 10.1021/jp0530496

ABSTRACT

A recently developed multiscale coarse-graining procedure [Izvekov, S.; Voth, G. A. J. Phys. Chem. B2005, 109, 2469] is extended to derive coarse-grained models for nanoparticles. The methodology is applied to C60 and to carbonaceous nanoparticles produced in combustion environments. The coarse-graining of the interparticle force field is accomplished applying a force-matching procedure to data obtained from trajectories and forces from all-atom MD simulations. The CG models are shown to reproduce accurately the structural properties of the nanoparticle systems studied, while allowing for MD simulations of much larger self-assembled nanoparticle systems.


 P.J. Keall, S. Joshi, S.S. Vedam, J.V. Siebers, V.R. Kini, R. Mohan. “Four-Dimensional Radiotherapy Planning for DMLC-Based Respiratory Motion Tracking,” In Med Phys, Vol. 32, No. 4, pp. 942--951. April, 2005.


E.G. Khölmovski, E.V.R. DiBella, A.A. Samsonov. “Accurate Assessment of the Arterial Input Function using MRI with Radial Sampling,” In Proceedings of the Society for Cardiovascular Magnetic Resonance (SCMR) 8th Annual Scientific Sessions, Vol. 7, pp. 292--294. 2005.


E.G. Khölmovski, D.L. Parker. “Application of Phase Consistency to Improve Time Efficiency and Image Quality in Dual Echo Black Blood Carotid Angiography,” In Magn Reson Imaging, Vol. 23, No. 6, pp. 711--722. 2005.


E.G. Khölmovski, E.V.R. DiBella, A.A. Samsonov. “Perfusion MRI with Radial Sampling: Arterial Input Function and Tissue Enhancement Curve Assessment,” In Proc. Intl. Soc. Mag. Reson., Note: Abstract, pp. 252. 2005.


E.G. Khölmovski, A.A. Samsonov. “GARSE: Generalized Autocalibrating Reconstruction for Sensitivity Encoded MRI,” In Proc. Intl. Soc. Mag. Reson., Note: Abstract, pp. 2672. 2005.