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:

Localization of Ischemia during Coronary Angioplasty using Body Surface Potential Mapping and an Electrocardiographic Inverse Solution
R.S. MacLeod, C.R. Johnson, M.J. Gardner B.M.. In Computers in Cardiology, IEEE Press, pp. 251--254. 1992.

Effects of Anistropy and Inhomogeneity on Electrocardiographic Fields: A Finite Element Study
C.R. Johnson, R.S. MacLeod, A. Dutson. In Engineering in Medicine and Biology Society 14th Annual International Conference, IEEE Press, pp. 2009--2010. 1992.

Visualization of cardiac bioelectricity --- a case study
R.S. MacLeod, C.R. Johnson, M.A. Matheson. In IEEE Visualization `92, pp. 411--418. 1992.

Visualization Tools for Computational Electrocardiology
R.S. MacLeod, C.R. Johnson, M.A. Matheson. In Visualization in Biomedical Computing, pp. 433--444. 1992.

A Computer Model for the Study of Electrical Current Flow in the Human Thorax
C.R. Johnson, R.S. MacLeod, P.R. Ershler. In Computers in Biology and Medicine, Vol. 22, No. 5, Elsevier BV, pp. 305--323. 1992.

Electrocardiography has played an important role in the detection and characterization of heart function, both in normal and abnormal states. In this paper we present an inhomogeneous, anisotropic computer model of the human thorax for use in electrocardiography with emphasis on the calculation of transthoracic potential and current distributions. Knowledge of the current pathways in the thorax has many applications in electrocardiography and has direct utility in studies pertaining to cardiac defibrillation, forward and inverse problems, impedance tomography, and electrode placement in electrocardiography.

Keywords: scalar field methods, vector field methods, tensor field methods, cardiac heart, scientific visualization

Computational Studies of Forward and Inverse Problems in Electrocardiology
C.R. Johnson, R.S. MacLeod. In Biomedical Modeling and Simulation, Edited by J. Eisenfeld and D.S. Levine and M. Witten, Elsevier Science Publishers, Elsevier, Amsterdam pp. 283--290. 1992.

Nonuniform Spatial Mesh Adaption Using a Posteriori Error Estimate: Applications to Forward and Inverse Problems
C.R. Johnson, R.S. MacLeod. In Adaptive Methods for Partial Differential Equations, Vol. 14, Edited by J.E. Flaherty and M.S. Shephard, Elsevier, pp. 311--326. 1992.

Computer Models for Calculating Transthoracic Current Flow
C.R. Johnson, R.S. MacLeod. In IEEE Engineering in Medicine and Biology Society 13th Annual International Conference, IEEE Press, pp. 768--769. 1991.

Construction of an Inhomogeneous Model of the Human Torso for Use in Computational Electrocardiography
R.S. MacLeod, C.R. Johnson, P.R. Ershler. In IEEE Engineering in Medicine and Biology Society 13th Annual International Conference, IEEE Press, pp. 688--689. 1991.

Electrical Activation of the Heart: Computational Studies of the Forward and Inverse Problems in Electrocardiography
C.R. Johnson, A.E. Pollard. In Computer Assisted Analysis and Modeling, MIT Press, pp. 583--628. 1990.