Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Large scale visualization on the Powerwall.
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

Chris Johnson

Inverse Problems
Computational Electrophysiology
rob

Rob MacLeod

ECG Imaging
Cardiac Disease
Computational Electrophysiology
jeff

Jeff Weiss

Computational Biomechanics
orly

Orly Alter

Computational Biology
butson

Chris Butson

Neuromodulation
Deep Brain Simulation
Transcranial Magnetic
Stimulation (TMS)


Associated Centers:


Publications in Biomedical Computing:


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.



Adaptive local regularization methods for the inverse ECG problem
C.R. Johnson, R.S. MacLeod. In Progress in Biophysics and Biochemistry, Vol. 69, No. 2/3, pp. 405. Dec, 1998.



Reply to the Comment on 'Protective Measurement of the Wave Function of a Single Squeezed Harmonic Oscillator State'
O. Alter, Y. Yamamoto. In Physical Review A, Vol. 56, No. 1, pp. 1057--1059. July, 1997.
DOI: 10.1103/PhysRevA.56.1057



Computational and Numerical Methods for Bioelectric Field Problems
C.R. Johnson. In Critical Reviews in BioMedical Engineering, Vol. 25, No. 1, pp. 1--81. 1997.



Applications of Large-Scale Computing and Scientific Visualization in Medicine
SCI Institute Technical Report, C.R. Johnson, D.M. Beazley, Y. Livnat, S.G. Parker, J.A. Schmidt, H.W. Shen, D.M. Weinstein. No. UUSCI-1997-001, University of Utah, 1997.



The Effects of Inhomogeneities and Anisotropies on Electrocardiographic Fields: A Three-Dimensional Finite Element Study
R.N. Klepfer, C.R. Johnson, R.S. MacLeod. In IEEE Transactions on Biomedical Engineering, Vol. 44, No. 8, pp. 706--719. August, 1997.



Effects of Geometric Uncertainty on the Inverse EEG Problem
D.M. Weinstein, C.R. Johnson. In Computational, Experimental, and Numerical Methods for Solving Ill-Posed Inverse Imaging Problems:Medical and Nonmedical Applications, SPIE '97, Vol. 3171, Edited by R.L. Barbour and M.J. Carvlin and M.A. Fiddy, SPIE, pp. 138--145. 1997.



Applications of Large-Scale Computing and Scientific Visualization in Medicine
C.R. Johnson, D.M. Beazley, Y. Livnat, S.G. Parker, J.A. Schmidt, H.W. Shen, D.M. Weinstein. In International Journal on Supercomputer Applications and High Performance Computing, 1996.



The effects of inhomogeneities and anisotropies on electrocardiographic fields: A three-dimensional finite element study
R.N. Klepfer, C.R. Johnson, R.S. MacLeod. In IEEE Trans. on Biomedical Engineering, 1996.



Local regularization and adaptive methods for the inverse Laplace problem
C.R. Johnson, R.S. MacLeod. In Biomedical and Life Physics, Edited by D.N. Ghista, Vieweg-Verlag, Braunschweig pp. 224--234. 1996.



Large Scale Biomedical Modeling and Simulation: From Concepts to Results
SCI Institute Technical Report, C.S. Henriquez, C.R. Johnson, K.A. Henneberg L.J., A.E. Pollard. No. UUSCI-1995-001, University of Utah, 1995.



Software Tools for Modeling, Computation, and Visualization in Medicine
C.R. Johnson, R.S. MacLeod, J.A. Schmidt. In CompMed 94 Proceedings, World Scientific, 1995.



An Interactive Computer Model for Defibrillation Device Design
J.A. Schmidt, C.R. Johnson, R.S. MacLeod. In International Congress on Electrocardiology, ICE, pp. 160--161. 1995.



Applications in Computational Medicine using SCIRun: A Computational Steering Programming Environment
C.R. Johnson, S.G. Parker. In Supercomputer `95, Edited by H.W. Meuer, Springer-Verlag, pp. 2--19. 1995.