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. 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.

O. Zachar, O. Alter. “Interpretation of the Curious Results of the New Quantum Formalism of Pre- and Post-Selected Systems,” In Foundations of Physics, Vol. 21, No. 7, pp. 803-–820. July, 1991.
DOI: 10.1007/BF00733346


O. Alter, O. Zachar. “Achilles and the Turtle in the Maze of the Weak Measurement,” Tel Aviv University Report, No. TAUP 90-1832, Tel Aviv University, 1990.

M. Berzins, A.J. Preston, P.M. Dew. “Integration Algorithms for the Dynamic Simulation of Production Processes,” In Proc of Third European Conference for Mathematics in Industry, Edited by J. Manley et al., Kluwer Academic Publishers, Stuttgart., pp. 265--271. 1990.

C.D. Hansen. “High-level Tools for Scientific Visualization,” In Computer Use By Engineers (CUBE) Symposium, Sante Fe, NM., Note: Refereed abstract., November, 1990.

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

R.D. Skeel, M. Berzins. “A Method for the Spatial Discretisation of Parabolic Equations,” In SIAM Journal on Scientific Computing, Vol. 11, No. 1, pp. 1--32. January, 1990.

S.L-Y. Woo, K.J. Ohland, J.A. Weiss. “The Effects of Aging and Sex on the Biomechanical Properties of the Medial Collateral Ligament,” In Mechanisms of Ageing and Development, Vol. 56, pp. 129--142. 1990.

S.L-Y. Woo, J.A. Weiss, M.A. Gomez, D.A. Hawkins. “Measurement of Changes in Ligament Tension with Knee Motion and Skeletal Maturation,” In Journal of Biomechanical Engineering, Vol. 112, pp. 46--51. 1990.


M. Berzins. “Developments in NAG Library Software for Parabolic Equations,” In Scientific Software Systems, Edited by J.C. Mason and M.G. Cox, Chapman and Hall, pp. 59--72. July, 1989.
ISBN: 0412345706