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.


Visualization, sometimes referred to as visual data analysis, uses the graphical representation of data as a means of gaining understanding and insight into the data. Visualization research at SCI has focused on applications spanning computational fluid dynamics, medical imaging and analysis, biomedical data analysis, healthcare data analysis, weather data analysis, poetry, network and graph analysis, financial data analysis, etc.

Research involves novel algorithm and technique development to building tools and systems that assist in the comprehension of massive amounts of (scientific) data. We also research the process of creating successful visualizations.

We strongly believe in the role of interactivity in visual data analysis. Therefore, much of our research is concerned with creating visualizations that are intuitive to interact with and also render at interactive rates.

Visualization at SCI includes the academic subfields of Scientific Visualization, Information Visualization and Visual Analytics.


Charles Hansen

Volume Rendering
Ray Tracing

Valerio Pascucci

Topological Methods
Data Streaming
Big Data

Chris Johnson

Scalar, Vector, and
Tensor Field Visualization,
Uncertainty Visualization

Mike Kirby

Uncertainty Visualization

Ross Whitaker

Topological Methods
Uncertainty Visualization
alex lex

Alex Lex

Information Visualization

Bei Wang

Information Visualization
Scientific Visualization
Topological Data Analysis

Centers and Labs:

Funded Research Projects:

Publications in Visualization:

Fast Isosurface Extraction Methods for Large Image Data Sets
Y. Livnat, S.G. Parker, C.R. Johnson. In Handbook of Medical Image Processing and Analysis, 2nd edition, Ch. 47, Note: (to appear), Edited by Isaac N. Bankman, Elsevier, pp. 801--816. 2008.

DOE Visualization and Knowledge Discovery
C.R. Johnson, R. Ross, S. Ahern, J. Ahrens, W. Bethel, K.L. Ma, M. Papka, J. van Rosendale, H.W. Shen, J. Thomas. Note: Report from the DOE/ASCR Workshop on Visual Analysis and Data Exploration at Extreme Scale, October, 2007.

CRA-NIH Computing Research Challenges in Biomedicine Workshop Recommendations
D. Reed, C.R. Johnson. Note: Computing Research Association (CRA), 2007.

Dynamically identifying and tracking contaminants in water bodies
C.C. Douglas, M.J. Cole, P. Dostert, Y. Efendiev, R.E. Ewing, G. Haase, J. Hatcher, M. Iskandarani, C.R. Johnson, R.A. Lodder. In Proceedings of the 7th International Conference on Computational Science (ICCS) 2007, Part I, Beijing, China, Lecture Notes in Computer Science (LNCS), Vol. 4887, Edited by Y. Shi and G.D. van Albada and P.M.A. Sloot and J.J. Dongarra, Springer-Verlag, Berlin Heidelberg, pp. 1002--1009. May, 2007.

Dynamic data-driven application systems for empty houses, contaminat tracking, and wildland fireline prediction
C.C. Douglas, D. Bansal, J.D. Beezley, L.S. Bennethum, S. Chakraborty, J.L. Coen, Y. Efendiev, R.E. Ewing, J. Hatcher, M. Iskandarani, C.R. Johnson, M. Kim, D. Li, R.A. Lodder, J. Mandel, G. Qin, A. Vodacek. In Grid-Based Problem Solving Environments, IFIP series, Edited by P.W. Gaffney and J.C.T. Pool, Springer-Verlag, Berlin, pp. 255-272. 2007.
DOI: 10.1007/978-0-387-73659-4_14

SciDAC Visualization and Analytics Center for Enabling Technology
E.W. Bethel, C.R. Johnson, K. Joy, S. Ahern, V. Pascucci, H. Childs, J. Cohen, M. Duchaineau, B. Hamann, C.D. Hansen, D. Laney, P. Lindstrom, J. Meredith, G. Ostrouchov, S.G. Parker, C.T. Silva, A.R. Sanderson, X. Tricoche. In Journal of Physics, Conference Series, Vol. 78, No. 012032, pp. (published online). 2007.

Fast Isosurface Extraction Methods for Large Image Data Sets
Y. Livnat, S.G. Parker, C.R. Johnson. In Handbook of Medical Imaging: Processing and Analysis, 2nd Edition, Ch. 44, Edited by Isaac Bankman, Academic Press, 2007.

DOE's SciDAC Visualization and Analytics Center for Enabling Technologies - Strategy for Petascale Visual Data Analysis Success
E.W. Bethel, C.R. Johnson, C. Aragon, Prabhat, O. Rübel, G. Weber, V. Pascucci, H. Childs, P.-T. Bremer, B. Whitlock, S. Ahern, J. Meredith, G. Ostrouchov, K. Joy, B. Hamann, C. Garth, M. Cole, C.D. Hansen, S.G. Parker, A.R. Sanderson, C.T. Silva, X. Tricoche. In CTWatch Quarterly, Vol. 3, No. 4, 2007.

NIH/NSF Visualization Research Challenges Report,
C.R. Johnson, R. Moorhead, T. Munzner, H. Pfister, P. Rheingans, T.S. Yoo, (Eds.). Note: IEEE Press, 2006.
ISBN: 0-7695-2733-7

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

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.

Biomedical Computing and Visualization
C.R. Johnson, D.M. Weinstein. In Proceedings of the Twenty-Ninth Australasian Computer Science Conference (ACSC2006): Conferences in Research and Practice in Information Technology (CRPIT), Hobart, Australia, Vol. 48, Edited by Vladimir Estivill-Castro and Gill Dobbie, pp. 3-10. 2006.

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

VACET: Proposed SciDAC2 Visualization and Analytics Center for Enabling Technologies
W. Bethel, C.R. Johnson, C.D. Hansen, S.G. Parker, A.R. Sanderson, C.T. Silva, X. Tricoche, V. Pascucci, H. Childs, J. Cohen, M. Duchaineau, D. Laney, P. Lindstrom, S. Ahern, J. Meredith, G. Ostrouchov, K. Joy, B. Hamann. In J. Phys.: Conf. Ser., Vol. 46, pp. 561--569. 2006.

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

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

Problem Solving Environments for DDDAS
C.R. Johnson, S.G. Parker. In Proceedings of the Ninth Copper Mountain Conference on Iterative Methods, Copper Mountain, CO, Note: Minisymposium: Actually Doing Dynamic Data-driven Application Simulations, April, 2006.

Dynamic Contaminant Identification in Water
C.C. Douglas, J.C. Harris, M. Iskandarani, C.R. Johnson, R.J. Lodder, S.G. Parker, M.J. Cole, R. Ewing, Y. Efendiev, R. Lazarov, G. Qin. In Proceedings of Computational Science - ICCS 2006: 6th International Conference, Part III, Reading, UK, May 28-31, 2006, Lecture Notes in Computer Science series, Vol. 3993, Edited by Vassil N. Alexandrov and Geert Dick van Albada and Peter M.A. Sloot and Jack J. Dongarra, Springer-Verlag Heidelberg, pp. 393--400. 2006.

Computational Methods and Software for Bioelectric Field Problems
C.R. Johnson. In Biomedical Engineering Handbook, 2nd Edition, Vol. 1, Ch. 23, Edited by J.D. Bronzino, CRC Press, Boca Raton, pp. 1--23. 2006.

Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping
J.T. Johnson III, M.S. Hansen, I. Wu, L.J. Healy, C.R. Johnson, G.M. Jones, M.R. Capecchi, C. Keller. In PLoS Genetics, Vol. 2, No. 1, pp. 471--477. April, 2006.

Morphometric and Qualitative Analysis of Congenital Occipitocervical Instability in Children: Implications for Down Syndrome Patients
S. Browd, L.J. Healy, G. Dobie, J.T. Johnson III, G.M. Jones, L.F. Rodriguez, D.L. Brockmeyer. In Journal of Neurosurgery: Pediatrics, Vol. 105, No. 1 , Journal of Neurosurgery Publishing Group, pp. 50--54. July, 2006.
DOI: 10.3171/ped.2006.105.1.50