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:

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.

NIH Biomedical Information Science and Technology Initiative (BISTI)
D. Botstein, L. Smarr, D. Agard, M. Levitt, D. Lippman, D. Herrington, C.R. Johnson, G Rose, G. Rubin, A. Levison, M. Spence, H. Smith, C. Peskin, G. Jacobs. Note: Prepared by the Working Group on Biomedical Computing Advisory Committee to the Director, National Institutes of Health, July, 1999.

The biomedical community is increasingly taking advantage of the power of computing, both to manage and analyze data, and to model biological processes. The working group should investigate the needs of NIH-supported investigators for computing resources, including hardware, software, networking, algorithms, and training. It should take into account efforts to create a national information infrastructure, and look at working with other agencies (particularly NSF and DOE) to ensure that the research needs of the NIH-funded community are met.

It should also investigate the impediments biologists face in utilizing high-end computing, such as a paucity of researchers with cross-disciplinary skills. The panel should consider both today's unmet needs and the growing requirements over the next five years (a reasonable horizon for extrapolating the advances in the rapidly changing fields of computing and computational biology).

The result of deliberations should be a report to the NIH Director, which will be presented to the Advisory Committee to the Director. The report should include recommendations for NIH actions to support the growing needs of NIH-funded investigators for biomedical computing.

Fundamental Quantum Limit to External Force Detection via Monitoring a Single Harmonic Oscillator or Free Mass
O. Alter, Y. Yamamoto. In Physics Letters A, Vol. 236, No. 4-6, pp. 226--231. 1999.
DOI: 10.1016/S0375-9601(99)00743-4

Independent Component Analysis For EEG Source Localization In Realistic Head Models
L. Zhukov, D.M. Weinstein, C.R. Johnson. In Third International Conference on Inverse Problems in Engineering, 1999.

Lead Field Basis for FEM Source Localization
School of Computing Technical Report, D.M. Weinstein, L. Zhukov, C.R. Johnson. No. UUCS-99-014, University of Utah, Salt Lake City, UT October, 1999.

Impossibility of Determining the Unknown Wavefunction of a Single Quantum System: Quantum Non-Demolition Measurements, Measurements without Entanglement and Adiabatic Measurements
O. Alter, Y. Yamamoto. In Fortschritte der Physik, Vol. 46, No. 6-8, pp. 817--827. November, 1998.

Bioelectric Modeling of the P300 in Schizophrenia
G.F. Potts, D.M. Weinstein, B.F. O'Donnell M.E., C.R. Johnson, R.W. McCarley. In Biological Psychiatry (suppl.), pp. 396. 1998.

Computer Visualization in Medicine
C.R. Johnson. In National Forum, Vol. Fall, pp. 17--21. 1998.