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


G. Scheuermann, X. Tricoche. “Topological Methods for Flow Visualization,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 341--356. 2005.
ISBN: 0-12-387582-X



D.M. Weinstein, S.G. Parker, J. Simpson, K. Zimmerman, G.M. Jones. “Visualization in the SCIRun Problem-Solving Environment,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 615--632. 2005.
ISBN: 0-12-387582-X



R.T. Whitaker. “Isosurfaces and Level-Sets,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 97--123. 2005.
ISBN: 0-12-387582-X



C. H. Wolters, A. Anwander, X. Tricoche, S. Lew, C.R. Johnson. “Influence of Local and Remote White Matter Conductivity Anisotropy for a Thalamic Source on EEG/MEG Field and Return Current Computation,” In Int.Journal of Bioelectromagnetism, Vol. 7, No. 1, pp. 203--206. 2005.



S. Zhang, D.H. Laidlaw, G. Kindlmann. “Diffusion Tensor MRI Visualization,” In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 327--340. 2005.
ISBN: 0-12-387582-X


2004


C. DeTar, A.L. Fogelson, C.R. Johnson, C.A. Sikorski, T. Truong. “Computational Engineering and Science Program at the University of Utah,” In Proceedings of the International Conference on Computational Science (ICCS) 2004, Lecture Notes in Computer Science (LNCS) 3039, part 4, Edited by M. Bubak et al, pp. 1202--1209. 2004.



C.S. Henriquez, J.V. Tranquillo, D.M. Weinstein, E.W. Hsu, C.R. Johnson. “Three-dimensional Propagation in Mathematic Models: Integrative Model of the Mouse Heart,” In Cardiac Electrophysiology: From Cell to Bedside, 4th edition, Ch. 30, Edited by D.P. Zipes and J. Jalife, Saunders, pp. 273--281. 2004.



C.R. Johnson. “Top Scientific Visualization Research Problems,” In IEEE Computer Graphics and Applications: Visualization Viewpoints, Vol. 24, No. 4, pp. 13--17. July/August, 2004.



C.R. Johnson, R.S. MacLeod, S.G. Parker, D.M. Weinstein. “Biomedical Computing and Visualization Software Environments,” In Comm. ACM, Vol. 47, No. 11, pp. 64--71. 2004.



R.S. Macleod, D.M. Weinstein, J.D. de St. Germain, D.H. Brooks, C.R. Johnson, S.G. Parker. “SCIRun/BioPSE: Integrated Problem Solving Environment for Bioelectric Field Problems and Visualization,” In Proceedings of the Int. Symp. on Biomed. Imag., Arlington, Va, pp. 640--643. April, 2004.



A.A. Samsonov, C.R. Johnson.. “Removal of Intensity Bias in Magnitude Spin-Echo MRI Images by Nonlinear Diffusion Filtering,” In Proceedings of SPIE Medical Imaging 2004, San Diego, CA, Vol. 5370, pp. 743--752. 2004.



A.A. Samsonov, C.R. Johnson. “Non-Cartesian POCSENSE,” In Proceedings of The 12th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Kyoto, Japan, pp. 2648. 2004.



A.A. Samsonov, C.R. Johnson. “Unbiased Nonlinear Filtering of Fast Spin Echo MRI Images,” In Proceedings of The 12th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Kyoto, Japan, pp. 760. 2004.



A.A. Samsonov, E.G. Kholmovski, C.R. Johnson. “Phase-Constrained Reconstruction of Sensitivity-Encoded MRI Data with POCSENSE,” In Proceedings of The 12th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Kyoto, Japan, pp. 2647. 2004.



A.A. Samsonov, C.R. Johnson. “Noise-Adaptive Nonlinear Diffusion Filtering of MR Images with Spatially Varying Noise Levels,” In Magn. Reson. Med., Vol. 52, pp. 798--806. 2004.



A.A. Samsonov, E.G. Kholmovski, D.L. Parker, C.R. Johnson. “POCSENSE: POCS-based reconstruction for sensitivity encoded MRI,” In Magn. Reson. Med., Vol. 52, pp. 1397--1406. 2004.



A.A. Samsonov, C.R. Johnson. “Multicoil MRI Artifacts Correction Using Parallel Pocs,” In Proceedings of The 12th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), 2004.



A.R. Sanderson, C.R. Johnson, R.M. Kirby. “Display of Vector Fields Using a Reaction Diffusion Model,” In Proceeding of IEEE Visualization 2004, pp. 115--122. 2004.



R. Van Uitert, C.R. Johnson, L. Zhukov. “Influence of Head Tissue Conductivity in Forward and Inverse Magnetoencephalographic Simulations Using Realistic Head Models,” In IEEE Trans Biomed. Eng., Vol. 51, No. 12, pp. 2129--2137. 2004.


2003


C.C. Douglas, M. Cole, Y. Efendiev, R. Ewing, V. Ginting, C.R. Johnson, G.M. Jones, R. Lazarov, C. Shannon, J. Simpson. “Workshop on Dynamic Data-Driven Application Systems,” In ICCS 2003, Melbourne, Australia, June 2-3, 2003.