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


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.



C.R. Johnson, R. Moorhead, T. Munzner, H. Pfister, P. Rheingans, T. Yoo. “NIH/NSF Visualization Research Challenges Report Summary,” Note: NIH/NSF, pp. 66-73. 2006.



T. Munzner, C.R. Johnson, R. Moorhead, H. Pfister, P. Rheingans, T.S. Yoo. “NIH-NSF Visualization Research Challenges Report Summary,” Note: NIH-NSF, pp. 20--24. March/April, 2006.



S. Nagarajan, O. Portniaguine, D. Hwang, C.R. Johnson, K. Sekihara. “Controlled Support MEG Imaging,” In NeuroImage, Vol. 15;33, No. 3, pp. 878--885. 2006.



J.T. Oden, J. Fish, C.R. Johnson, A. Laub, D. Srolovitz, T. Belytschko, T.J.R. Hughes, D. Keys, L. Petzold, S. Yip. “NSF Blue Ribbon Panel Report on Simulation Based Engineering Science,” Note: NSF Report, 2006.

ABSTRACT

Purpose: To explore the emerging discipline of Simulation Simulation-Based Engineering Science, its major components, its importance to the nation, the challenges and barriers to its advancement, and to recommend to the NSF and the broader community concerned with science and engineering in the United States, steps that could be taken to advance development in this discipline.



S.G. Parker, K. Zhang, K. Damevski, C.R. Johnson. “Integrating Component-Based Scientific Computing Software,” In Parallel Processing for Scientific Computing, Edited by M.A. Heroux and P. Raghavan and H.D. Simon, SIAM Press, pp. 271--288. 2006.
ISBN: 0-89871-619-5



S. Parker, K. Zhang, C. Damevski, C.R. Johnson. “Integrating Component-Based Scientific Computing Software,” In Parallel Processing for Scientific Computing, Edited by M.A. Heroux and P. Raghavan and H.D. Simon, SIAM, pp. 271--288. January, 2006.



A.R. Sanderson, R.M. Kirby, C.R. Johnson, L. Yang. “Advanced Reaction-Diffusion Models for Texture Synthesis,” In Journal of Graphics Tools, Vol. 11, No. 3, pp. 47--71. 2006.


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.



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



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



G.L. Kindlmann, D.M. Weinstein, G.M. Jones, C.R. Johnson, M.R. Capecchi, C. Keller. “Practical Vessel Imaging by Computed Tomography in Live Transgenic Mouse Models for Human Tumors,” In Journal of Molecular Imaging, Vol. 4, No. 4, pp. 417--424. 2005.



R.M. Kirby, D.F. Keefe, D.H. Laidlaw. “Painting and Visualization,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 873--891. 2005.
ISBN: 0-12-387582-X



J.M. Kniss, G. Kindlmann, C.D. Hansen. “Multidimentional Transfer Functions for Volume Rendering,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 189--210. 2005.
ISBN: 0-12-387582-X



Y. Livnat. “Accelerated Isosurface Extraction Approaches,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 39--55. 2005.
ISBN: 0-12-387582-X



M.D. Meyer, H. Pfister, C.D. Hansen, C.R. Johnson. “Image-Based Volume Rendering with Opacity Light Fields,” SCI Institute Technical Report, No. UUSCI-2005-002, University of Utah, 2005.



D. Reed, R. Bajcsy, J.M. Griffiths, J. Dongarra, C.R. Johnson. “Computational Science: Ensuring America's Competitiveness,” Note: President's Information Technology Advisory Committee (PITAC), June, 2005.



F. Sachse, M. Cole, R.M. Kirby, X. Tricoche, C.R. Johnson. “Advanced Modeling and Visualization of Cardiothoracic Electrical Fields,” In Proceedings of 13th Medicine Meets Virtual Reality (MMVR13), 2005.



A.A. Samsonov, E.V.R. DiBella, P. Kellman, E.G. Kholmovski, C.R. Johnson. “Adaptive k-t BLAST/k-t SENSE for Accelerating Cardiac Perfusion MRI,” In Proceedings of the Society for Cardiovascular Magnetic Resonance (SCMR) 8th Annual Scientific Sessions, pp. 277--278. 2005.



A.A. Samsonov, E.G. Khölmovski, C.R. Johnson. “POCS-Enhanced Parallel MRI Correction of MR Image Artifacts,” In Proc. Intl. Soc. Mag. Reson., Note: Abstract, pp. 690. 2005.