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.

SCI Publications


C.R. Johnson, R.S. MacLeod. “Computational Studies of Forward and Inverse Problems in Electrocardiology,” 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.

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

J. Lawson, M. Berzins. “Towards an Automatic Algorithm for the Numerical Solution of Parabolic P.D.E.s Using the Method of Lines,” In proc of I.M.A. 1989 O.D.E. Conference, Edited by I. Gladwell and J. Cash and A. Iserles, Oxford University Press, pp. 309--322. 1992.
ISBN: 0-19-853659-3

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

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

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

A. Pascucci, V. Pascucci. “Uso del calcolatore nella produzione, elaborazione ed archiviazione di proiezioni parallele (Using the computer for generating, processing and archiving parallel projections),” In Atti del convegno L'immagine nel rilievo, Edited by C. Cundari, Gangemi, pp. 540--561. 1992.

C. Walshaw, M. Berzins. “Dynamic Load Balancing for PDE Solvers on Adaptive Unstructured Meshes,” School of Computer Studies Research Report, No. 92.32, University of Leeds, December, 1992.

J.M. Ware, M. Berzins. “Finite Volume Techniques for Time-dependent Fluid-Flow Problems,” In Advances in Comp. Meths. for P.D.E.s VII, New Jersey, Rutgers Univ., pp. 794--798. 1992.

C. Williams, J. Rasure, C.D. Hansen. “The State of the Art of Visual Languages for Visualization,” In Visualization 1992, Boston, Ma., pp. 202--209. October, 1992.


M. Berzins, P. Baehmann, J.E. Flaherty, J. Lawson. “Towards An Automated Finite Element Solver for Time-Dependent Fluid-Flow Problems,” In MAFELAP 90, Edited by J.R. Whiteman, Academic Press, pp. 181--188. 1991.

M. Berzins, P.M. Dew. “Chebyshev Polynomial Software for Elliptic-Parabolic Systems of P.D.E.s,” In A.C.M. Transactions on Mathematical Software, Vol. 17, No. 2, pp. 178--206. June, 1991.


PDECHEB is a FORTRAN 77 software package that semidiscretizes a wide range of time dependent partial differential equations in one space variable. The software implements a family of spatial discretization formulas, based on piecewise Chebyshev polynomial expansions with C0 continuity. The package has been designed to be used in conjunction with a general integrator for initial value problems to provide a powerful software tool for the solution of parabolic-elliptic PDEs with coupled differential algebraic equations. Examples are provided to illustrate the use of the package with the DASSL d.a.e, integrator of Petzold [18].

M. Berzins. “Balancing Space and Time Errors for Spectral Methods used with the Method of Lines for Parabolic equations,” 1991.

C.D. Hansen, S. Tenbrink. “The Impact of Gigabit Networking on Imaging,” In Digital Imaging, Anaheim, Ca., pp. 191--194. April, 1991.

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

J. Lawson, M. Berzins, P.M. Dew. “Balancing Space and Time Errors in the Method of Lines for Parabolic Equations,” In SIAM Journal on Scientific Computing, Vol. 12, No. 3, pp. 573--594. 1991.

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

A.J. Preston, M. Berzins. “On Algorithms for the Location of Discontinuities for Dynamic Simulation Problems,” In Computers in Chemical Engineering, Vol. 15, No. 10, pp. 701--713. 1991.

S. Susswein, T.C. Henderson, J. Zachary, C.D. Hansen, P. Hinker, G. Marsden. “Parallel Path Consistency,” In International Journal of Parallel Programming, Vol. 20, No. 6, pp. 453--473. 1991.

J.A. Weiss, S.L-Y. Woo, K.J. Ohland, S. Horibe, P.O. Newton. “Evaluation of a New Injury Model to Study Medial Collateral Ligament Healing: Primary Repair vs Nonoperative Treatment,” In Journal of Orthopaedic Research, Vol. 9, pp. 516--528. 1991.