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


M.L. Cooper, A.D. Lanterman, S.C. Joshi, M.I. Miller. “Representing The Variation of Thermodynamic State Via Principal Components Analysis,” In Proceedings of the Third Workshop On Conventional Weapon ATR, pp. 481--490. November, 1996.

C.S. Gitlin, C.R. Johnson. “MeshView: A tool for exploring 3D unstructured tetrahedral meshes,” In 5th International Meshing Roundtable, pp. 333--345. 1996.

J.W. Haller, G.E. Christensen, S.C. Joshi, J.W. Newcomer, M.I. Miller, J.G. Csernansky, M. Vannier. “Hippocampal MR Imaging Morphometry by Means of General Pattern Matching,” In Radiology, Vol. 199, No. 3, pp. 787--791. June, 1996.

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

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

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

Y. Livnat, H.W. Shen, C.R. Johnson. “A Near Optimal Isosurface Extraction Algorithm Using the Span Space,” In IEEE Transactions on Visual Computer Graphics, Vol. 2, No. 1, pp. 73--84. 1996.

E. Nurgat, M. Berzins. “A new relaxation scheme for solving EHL Problems,” In 23rd Leeds-Lyon Symposium on Tribology, Tribology Series, Vol. 32, Edited by D.Dowson et al., Elsevier, pp. 125a-134. 1996.
ISBN: 0444828095


A New Relaxation Scheme (NRS) is presented in this paper to solve Elasto Hydrodynamic Lubrication (EHL) point contact problems. The solutions obtained are compared with those obtained by Ehret [6] who employed the Distributive Relaxation Scheme (DRS) of Venner [2]. Results obtained using the two schemes are in close agreement which is very encouraging although it is too early to draw any conclusions. The new relaxation scheme thus provides an alternative approach to the distributive relaxation scheme.

E. Nurgat, M. Berzins. “A new relaxation scheme for solving EHL Problems,” In Proceedings of 23rd Leeds-Lyon Symposium on Tribology, Tribology Series, Vol. 32, Edited by D.Dowson et al., Elsevier, pp. 125A--134. 1996.
ISBN: 0444828095

J. Painter, H.P. Bunge, Y. Livnat. “Case Study: Mantle Convection Visualization on the Cray T3D,” In IEEE Visualization `96, pp. 409--412. 1996.

J. Painter, M. Krogh, C.D. Hansen. “Parallel Sphere Rendering,” In EUROGRAPHICS Workshop on Parallel Graphics and Visualization, Bristol, England, September, 1996.

S.G. Parker, C.R. Johnson. “SCIRun: Applying Interactive Computer Graphics to Scientific Problems,” In SIGGRAPH (applications/demo), 1996.

V. Pascucci, V. Ferrucci, A. Paoluzzi. “Dimension-Independent Convex-Cell Based HPC: Skeletons and Product,” In International Journal of Shape Modeling, Vol. 2, pp. 37--67. 1996.

P. Pratt, M. Berzins. “Shock preserving quadratic interpolation for visualization on triangular meshes,” In Computers & Graphics, Vol. 20, No. 5, pp. 723--730. 1996.
DOI: 10.1016/S0097-8493(96)00046-5


A new interpolation method for visualizing shock-type solutions on triangular meshes is presented. The method combines standard linear and quadratic interpolants in such a way as to avoid supurious numerical values. The effectiveness of the method is demonstrated on test problems.

G.J. Ryder, M. Berzins, T.H.C. Childs. “Modelling Simple Feature Creation in Selective Laser Sintering,” In Proc 7th Symposium on Solid Free Form Fabrication, University of Texas at Austin, Edited by J.W. Barlow et al., pp. 567--574. 1996.

H.W. Shen, C.R. Johnson, K.L. Ma. “Global and Local Vector Field Visualization Using Enhanced Line Integral Convolution,” In Symposium on Volume Visualization, IEEE Press, pp. 63--70. 1996.

H.W. Shen, C.D. Hansen, Y. Livnat, C.R. Johnson. “Isosurfacing in Span Space with Utmost Efficiency,” In IEEE Visualization `96, IEEE Press, pp. 287--294. 1996.

P.A. Sleigh, M. Berzins, P.H. Gaskell. “A Reliable and Accurate Technique for the Modelling of Complex Hydraulic Flows,” In Proceedings of the First International Symposium on Finite Volumes for Complex Applications, Hermes, Paris, pp. 635--642. 1996.
ISBN: 2-86601-556-8

J.D.B. Smith, A.S. Tomlin, M. Berzins, V. Pennington, M.J. Pilling. “Modelling the effects of Concentrated Emissions Sources on Tropospheric Ozone,” In Proceedings of the 3rd Workshop on Modelling of Chemical Reaction Systems, Heidelberg, Germany, Published on CD-ROM, July, 1996.
ISBN: 3-932217-00-4


Numerical models that describe the chemical processes occurring in the troposphere, in the main, are still using fixed or telescopic grids to provide greater detail where it is required, such as near large emissions sources. While the use of adaptive grids has become well accepted in the fields of aeronautical and mechanical engineering, the adoption of adaptive gridding techniques in atmospheric modelling has been somewhat slower. Tomlin et al [1] recently demonstrated the use of time-dependent adaptive mesh gridding techniques applied to the investigation of a single power station plume, with regards to regional ozone levels. The results of that paper highlighted the differences in the total and peak concentrations of ozone arising from using fixed grids, as opposed to using adaptive grids.

Ozone concentrations in the atmospheric boundary layer, the bottom kilometre of the troposphere, are dependent on the interactions of nitrogen oxides and the volatile organic compounds (VOCs) that are emitted from both anthropogenic and biogenic sources. There are many more chemical species involved in the processes of the atmospheric boundary layer than in the stratosphere. This makes the use of detailed chemical mechanisms with fine mesh resolution difficult in two space dimensions, and prohibitively expensive for three space dimensions.

This paper investigates the effects of multiple point sources interacting with the more diffuse area sources arising from urban emissions, and will show the differences arising from the use of adaptive gridding techniques rather than fixed grids. The numerical code, SPRINT2D, provides spatial and temporal error controls for limiting the adaptation of the grid for a length scale ranging from a few hundred metres to a few hundred kilometres.

Comparisons will also be made between a systematically reduced mechanism, CBMLeeds[2], and the Generic Reaction Set (GRS) of Azzi et al [3] to see the advantages of the two approaches. CBMLeeds originates from the CBM-Ex scheme of Gery et al [4], which uses lumped organic species, as opposed to the heavily parameterised organic chemistry of the GRS.

J.A. Weiss, B.N. Maker, S. Govindjee. “Finite Element Implementation of Incompressible, Transversely Isotropic Hyperelasticity,” In Computer Methods in Applied Mechanics and Engineering, Vol. 135, pp. 107--128. 1996.