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.

Biomedical Computing

Biomedical computing combines the diagnostic and investigative aspects of biology and medical science with the power and problem-solving capabilities of modern computing. Computers are used to accelerate research learning, simulate patient behavior and visualize complex biological models.


Chris Johnson

Inverse Problems
Computational Electrophysiology

Rob MacLeod

ECG Imaging
Cardiac Disease
Computational Electrophysiology

Jeff Weiss

Computational Biomechanics

Orly Alter

Computational Biology

Tamara Bidone

Computational Models
Simulations of Biological Systems
Multi-Physics Models of Cancer Cells


Amir Arzani

Cardiovascular biomechanics
Scientific machine learning

Centers and Labs:

Funded Research Projects:

Publications in Biomedical Computing:

Molecular Characterisation of Soft Tissue Tumours: a Gene Expression Study,
T. Nielsen, R.B. West, S.C. Linn, O. Alter, M.A. Knowling, J. O'Connell, S. Zhu, M. Fero, G. Sherlock, J.R. Pollack, P.O. Brown, D. Botstein, M. van de Rijn. In Lancet, Vol. 359, No. 9314, pp. 1301–-1307. April, 2002.
DOI: 10.1016/S0140-6736(02)08270-3

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

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

Modeling and Simulation in Medicine: Towards an Integrated Framework
G. Higgins, B. Athey, J. Bassingthwaighte, J. Burgess, H. Champion, K. Cleary, P. Dev, J. Duncan, M. Hopmeier, D. Jenkins, C.R. Johnson, H. Kelly, R. Leitch, W. Lorensen, D. Metaxas, V. Spitzer, N. Vaidehi, K. Vosburgh, R. Winslow. In Computer Aided Surgery, Vol. 6, No. 1, Note: Final report of the meeting of the same title held July 20-21, 2000, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA., 2001.
DOI: 10.1002/igs.1008

Quantum Measurement of a Single System,
O. Alter, Y. Yamamoto. Wiley-Blackwell, May, 2001.
ISBN: 9780471283089
DOI: 10.1002/9783527617128

Processing and Modeling Genome-Wide Expression Data Using Singular Value Decomposition,
O. Alter, P.O. Brown, D. Botstein. In Microarrays: Optical Technologies and Informatics, Vol. 4266, Edited by M.L. Bittner and Y. Chen and A.N. Dorsel and E.R. Dougherty (International Society for Optical Engineering Bellingham), pp. 171--186. 2001.

Multilevel Methods for Inverse Bioelelectric Field Problems
C.R. Johnson, M. Mohr, U. Ruede, A. Samsonov, K. Zyp. In Lecture Notes in Computational Science and Engineering - Multiscale and Multiresolution Methods: Theory and Applications, Vol. 20, Edited by T.J. Barth and T.F. Chan and R. Haimes, Springer-Verlag Publishing, Heidelberg pp. 331--346. October, 2001.

Finite Element EEG and MEG Simulations for Realistic Head Models: Quadratic vs. Linear Approximations
R. Van Uitert, D. Weinstein, C.R. Johnson, L. Zhukov. In Biomed. Technik, Vol. 46, pp. 32--34. 2001.

Computational Bioimaging for Medical Diagnosis and Treatment
C.R. Johnson. In Communications of the ACM, Vol. 44, No. 3, pp. 74--76. March, 2001.

Spatio-temporal Multi-dipole Source Localization Using ICA and Lead-Fields in FEM Head Models
L. Zhukov, D.M. Weinstein, C.R. Johnson, R.S. Macleod. In Proceedings of the IEEE Engineering in Medicine and Biology Society 23rd Annual International Conference, Istanbul, Turkey Oct, 2001.

Adaptive Finite Element and Local Regularization Methods for the Inverse ECG Problem
C.R. Johnson. In Inverse Problems in Electrocardiology, Advances in Computational Biomedicine, Vol. 5, Edited by Peter Johnston, WIT Press, pp. 51--88. 2001.

Focusing Inversion of Electroencephalography and Magnetoencephalography Data
O. Portniaguine, D.M. Weinstein, C.R. Johnson. In 3rd International Symposium On Noninvasive Functional Source Imaging, Journal of Biomedizinische Technik (special issue), Vol. 46, Innsbruck, Austria pp. 115--117. Sep, 2001.

Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling,
O. Alter, P.O. Brown, D. Botstein. In Proceedings of the National Academy of Sciences, Vol. 97, No. 18, Proceedings of the National Academy of Sciences, pp. 10101--10106. August, 2000.
DOI: 10.1073/pnas.97.18.10101

Statistical Analysis For FEM EEG Source Localization in Realistic Head Models
School of Computing Technical Report, L. Zhukov, D. Weinstein, C.R. Johnson. No. UUCS-2000-003, University of Utah, February, 2000.

An Inverse EEG Problem Solving Environment and its Applications to EEG Source Localization
D.M. Weinstein, L. Zhukov, C.R. Johnson. In NeuroImage (suppl.), pp. 921. 2000.

Lead-Field Bases for EEG Source Imaging
D.M. Weinstein, L. Zhukov, C.R. Johnson. In Annal. Biomed. Eng., Vol. 28, No. 9, pp. 1059--1065. Sep, 2000.

Interactive Source Imaging with BioPSE
D.M. Weinstein, L. Zhukov, C.R. Johnson, S.G. Parker, R. Van Uitert, R.S. MacLeod, C.D. Hansen. In Chicago 2000 World Congress on Medical Physics and Biomedical Engineering, Chicago, IL., Note: Refereed abstract., July, 2000.

Independent Component Analysis for EEG Source Localization in Realistic Head Models
L. Zhukov, D. Weinstein, C.R. Johnson. In IEEE Engineering in Medicine and Biology, Vol. 19, No. 3, pp. 87--96. 2000.

The BioPSE Inverse EEG Modeling Pipeline
D.M. Weinstein, P. Krysl, C.R. Johnson. In ISGG 7th International Conference on Numerical Grid Generation in Computation Field Simulations, The International Society of Grid Generation, Mississippi State University pp. 1091--1100. 2000.

Reciprocity Basis for EEG Source Imaging
L. Zhukov, D.M. Weinstein, C.R. Johnson. In NeuroImage (suppl.), pp. 598. 2000.