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

2003


 C.C. Douglas, C.E. Shannon, Y. Efendiev, R.E. Ewing, V. Ginting, R. Lazanov, M.J. Cole, G.M. Jones, C.R. Johnson, J. Simpson. “A Note on Dynamic Data Driven Application Simulation (DDDAS) Using Virtual Telemetry,” In International Conference on Parallel Algorithms and Computing Environments, pp. pp.193--198. 2003.


C.D. Hansen, C.R. Johnson. “Graphics Applications for Grid Computing,” In IEEE Comp. Graph. & Applic., pp. 20--21. March/April, 2003.


D. Hwang, O. Portniaguine, S. Nagarajan, C.R. Johnson, K. Sekihara. “Minimum Support MEG (Magnetoencephalography) Imaging: Study on Effects of Noise, Discretization, Depth, and Separation of Multiple Sources,” In World Congress on Medical Physics and Biomedical Engineering, August, 2003.


M. Ikits, C.D. Hansen, C.R. Johnson. “A Comprehensive Calibration and Registration Procedure for the Visual Haptic Workbench,” In Proceedings of the Ninth Eurographics Workshop on Virtual Environments, Zurich, Switzerland, pp. 247--254. May, 2003.


M. Ikits, J.D. Brederson, C.D. Hansen, C.R. Johnson. “A Constraint-Based Technique for Haptic Volume Exploration,” In Proceedings IEEE Visualization 2003, Seattle, WA, pp. 263--269. October, 2003.


C.R. Johnson, A.R. Sanderson. “A Next Step: Visualizing Errors and Uncertainty,” In IEEE Computer Graphics and Applications, Vol. 23, No. 5, pp. 6--10. September/October, 2003.


A.A. Samsonov, E.G. Kholmovski, C.R. Johnson. “Image Reconstruction from Sensitivity Encoded MRI Data Using Extrapolated Iterations of Parallel Projections Onto Convex Sets,” In SPIE Medical Imaging, Vol. 5032, pp. 1829--1838. 2003.


A.A. Samsonov, E.G. Kholmovski, C.R. Johnson. “Determination of the Sampling Density Compensation Function Using a Point Spread Function Modeling Approach and Gridding Approximation,” In Proceedings of 11th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), Toronto, pp. 477. 2003.


A.A. Samsonov, E.G. Kholmovski, C.R. Johnson. “A Modified POCSENSE Technique for Accelerated Iterative Reconstruction from Sensitivity Encoded MRI Data,” In Proceedings of 11th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), Toronto, pp. 477. 2003.


A.R. Sanderson, C.R. Johnson. “Display of Vector Fields Using a Reaction-Diffusion Model,” SCI Institute Technical Report, No. UUSCI-2003-002, University of Utah, June, 2003.


R. Van Uitert, D. Weinstein, C.R. Johnson. “Volume Currents in Forward and Inverse Magnetoencephalographic Simulations Using Realistic Head Models,” In Annals of Biomedical Engineering, Vol. 31, pp. 21--31. 2003.


R. Van Uitert, C.R. Johnson. “Influence of Brain Conductivity on Magnetoencephalographic Simulations in Realistic Head Models,” In The 25th Annual International Conference of the IEEE Engineering In Medicine And Biology Society, Vol. 3, pp. 2136--2139. September, 2003.


D.M. Weinstein, J.V. Tranquillo, C.S. Henriquez, C.R. Johnson. “BioPSE Case Study: Modeling, Simulation, and Visualization of Three Dimensional Mouse Heart Propagation,” In International Journal of Bioelectromagnetism, Vol. 5, No. 1, pp. 314--315. 2003.

2002


 C.R. Johnson, S.G. Parker, D. Weinstein, S. Heffernan. “Component-Based Problem Solving Environments for Large-Scale Scientific Computing,” In J. Conc. & Comp.: Prac. & Exper., Vol. 14, pp. 1337--1349. 2002.


S.S. Nagarajan, O. Portniaguine, K. Sekihara, D. Hwang, C.R. Johnson. “Performance of a Minimum-Support Imaging Method for Biomagnetic Source Localization,” In Proceedings of the IEEE Engineering in Medicine and Biology Society 24th Annual International Conference, Houston, Vol. 3, pp. 2006-2007. October, 2002.


A.A. Samsonov, R.T. Whitaker, C.R. Johnson. “Noise-Adaptive Nonlinear Filtering Technique for SENSE-Reconstructed Images,” In Proceedings of The 10th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Honolulu, pp. 74. 2002.


A.A. Samsonov, C.R. Johnson. “Noise-Adaptive Anisotropic Diffusion Filtering of MRI Images Reconstructed by SENSE (SENSitivity Encoding) Method,” In Proceedings of The 2002 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Washington DC, pp. 701--704. July, 2002.


A.A. Samsonov, R.T. Whitaker, E.G. Kholmovski, C.R. Johnson. “Parametric Method for Correction of Intensity Inhomogeneity in MRI Data,” In Proceedings of The 10th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Honolulu, pp. 154. 2002.


R. Van Uitert, C.R. Johnson. “Can a Spherical Model Substitute for a Realistic Head Model in Forward and Inverse MEG Simulations?,” In Proceedings of The 13th International Conference on Biomagnetism, Jena, Germany, August, 2002.

2001


 J.D. Brederson, M. Ikits, C.R. Johnson, C.D. Hansen. “A Prototype System For Synergistic Data Display,” In IEEE Virtual Reality 2001, 2001.