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 Johnson

Inverse Problems
Computational Electrophysiology

Rob MacLeod

ECG Imaging
Cardiac Disease
Computational Electrophysiology

Jeff Weiss

Computational Biomechanics

Orly Alter

Computational Biology

Chris Butson

Deep Brain Simulation
Transcranial Magnetic
Stimulation (TMS)

Associated Centers:

Publications in Biomedical Computing:

Influence of Stochastic Organ Conductivity in 2D ECG Forward Modeling: A Stochastic Finite Element Study
S.E. Geneser, S. Choe, R.M. Kirby, R.S. MacLeod. In Proceedings of The Joint Meeting of The 5th International Conference on Bioelectromagnetism and The 5th International Symposium on Noninvasive Functional Source Imaging within the Human Brain and Heart, pp. 5528--5531. 2005.

Computational Simulation of Penetrating Trauma in Biological Soft Tissues Using the Material Point Method
I. Ionescu, J. Guilkey, M. Berzins, R.M. Kirby, J.A. Weiss. In Proceedings, Medicine Meets Virtual Reality, Vol. 13, Edited by James D Westwood et al., IOS Press, pp. 213--218. 2005.
ISBN: 1-58603-498-7

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

Advanced Modeling and Visualization of Cardiothoracic Electrical Fields
F. Sachse, M. Cole, R.M. Kirby, X. Tricoche, C.R. Johnson. In Proceedings of 13th Medicine Meets Virtual Reality (MMVR13), 2005.

Novel Genome-Scale Correlation Between DNA Replication and RNA Transcription During the Cell Cycle in Yeast is Predicted by Data-Driven Models
O. Alter, G.H. Golub, P.O. Brown, D. Botstein. In Proceedings of the Miami Nature Biotechnology Winter Symposium on the Cell Cycle, Chromosomes and Cancer, Vol. 15, Edited by M.P. Deutscher and S. Black and P.E. Boehmer and G. D'Urso and T. Fletcher and F. Huijing and A. Marshall and B. Pulverer and B. Renault and J.D. Rosenblatt and J.M. Slingerland and W.J. Whelan, 2004.

Integrative Analysis of Genome-Scale Data by Using Pseudoinverse Projection Predicts Novel Correlation Between DNA Replication and RNA Transcription,
O. Alter, G.H. Golub. In Proceedings of the National Academy of Sciences, Vol. 101, No. 47, Proceedings of the National Academy of Sciences, pp. 16577--16582. November, 2004.
DOI: 10.1073/pnas.0406767101

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

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

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

A Software Framework for Solving Problems of Bioelectricity Applying High-Order Finite Elements
M. Cole, F.B. Sachse, D.M. Weinstein, S.G. Parker, R.M. Kirby. In Proceedings of the IEEE Engineering in Medicine and Biology Society 26th Annual International Conference, Vol. 1, pp. 821--824. 2004.

Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms
O. Alter, P.O. Brown, D. Botstein. In Proceedings of the National Academy of Sciences, Vol. 100, No. 6, Proceedings of the National Academy of Sciences, pp. 3351--3356. March, 2003.
DOI: 10.1073/pnas.0530258100

Volume Currents in Forward and Inverse Magnetoencephalographic Simulations Using Realistic Head Models
R. Van Uitert, D. Weinstein, C.R. Johnson. In Annals of Biomedical Engineering, Vol. 31, pp. 21--31. 2003.

Minimum Support MEG (Magnetoencephalography) Imaging: Study on Effects of Noise, Discretization, Depth, and Separation of Multiple Sources
D. Hwang, O. Portniaguine, S. Nagarajan, C.R. Johnson, K. Sekihara. In World Congress on Medical Physics and Biomedical Engineering, August, 2003.

Influence of Brain Conductivity on Magnetoencephalographic Simulations in Realistic Head Models
R. Van Uitert, C.R. Johnson. In The 25th Annual International Conference of the IEEE Engineering In Medicine And Biology Society, Vol. 3, pp. 2136--2139. September, 2003.

BioPSE Case Study: Modeling, Simulation, and Visualization of Three Dimensional Mouse Heart Propagation
D.M. Weinstein, J.V. Tranquillo, C.S. Henriquez, C.R. Johnson. In International Journal of Bioelectromagnetism, Vol. 5, No. 1, pp. 314--315. 2003.

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