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


J.M. Kniss, P. McCormick, A. McPherson, J. Ahrens, J. Painter, A. Keahey, C.D. Hansen. “T-Rex, Texture-based Volume Rendering for Extremely Large Datasets,” In IEEE Comp. Graph. & Applic., Vol. 21, No. 4, pp. 52--61. 2001.

D.H. Laidlaw, R.M. Kirby, J.S. Davidson, T.S. Miller, M. da Silva, W.H. Warren, M. Tarr. “Quantitative Comparative Evaluation of 2D Vector Field Visualization Methods,” In Proceedings of IEEE Visualization 2001, San Diego, CA, pp. 143--150. October, 2001.

I. Lagzi, A.S. Tomlin, T.Turanyi, L.Haszpra, M.Berzins. “The Simulation of Photochemical Smog Episodes in Hungary and Central Europe Using Adaptive Gridding Models,” In Lecture Notes in Computer Science (LCNS), Computational Science - ICCS 2001, Vol. 2074/2001, Springer Berlin / Heidelberg, pp. 67--76. 2001.
ISBN: 978-3-540-42233-4

P. Lindstrom, V. Pascucci. “Visualization of Large Terrains Made Easy,” In Proceedings of the 12th Annual IEEE Conference on Visualization (VIS-01), San Diego, CA, Note: UCRL-JC-144753, IEEE Computer Society, pp. 363--370, 574. October 21-26, 2001.

Y. Livnat, C.D. Hansen, S.G. Parker, C.R. Johnson. “Isosurface extraction for large-scale datasets,” In Proceedings of Scientific Visualization -Dagstuhl`2000, Edited by F. Post, 2001.

P. Lorenzen, S. Joshi, G. Gerig, E. Bullitt. “Tumor-Induced Structural Radiometric Asymmetry in Brain Images,” In Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA), pp. 163--170. 2001, 2001.

K. Ma, S.G. Parker. “Massively Parallel Software Rendering for Visualizing Large-Scale DataSets,” In IEEE Trans. Vis & Comp. Graph., pp. 72--83. July/August, 2001.

R.S. MacLeod, B. Yilmaz, B. Taccardi, B.B. Punske, Y. Serina, D.H. Brooks. “Direct and Inverse Methods for Cardiac Mapping Using Multielectrode Catheter Measurements,” In Journal of Biomedizinische Technik, Vol. 46(supp), pp. 207--209. 2001.

R.S. MacLeod, B.B. Punske, B. Yilmaz, S. Shome, B. Taccardi. “The Role of Heart Rate in Myocardial Ischemia From Restricted Coronary Perfusion,” In J. Electrocardiol., Vol. 34 (supp), Note: ISCE conference paper, pp. 43--51. 2001.

J. McCorquodale, J.D. de St. Germain, S.G. Parker, C.R. Johnson. “The Uintah Parallelism Infrastructure: A Performance Evaluation on the SGI Origin 2000,” In Proceedings of The 5th International Conference on High-Performance Computing, Seattle, Mar, 2001.

M. Miller, C. Moulding, J. Dongarra, C.R. Johnson. “Grid-enabling Problem Solving Environments: A Case Study of SCIRun and Netsolv,” In Proceedings of The 5th International Conference on High-Performance Computing, 2001 Advanced Simulation Technologies Conference, Society for Modeling and Simulation International, pp. 98--103. April, 2001.

V. Pascucci, R.J. Frank. “Global Static Indexing for Real-time Exploration of Very Large Regular Grids,” In Proceedings of Supercomputing 2001, Note: UCRL-JC-144754, ACM, Nov, 2001.

V. Pascucci. “On the Topology of the Level Sets of a Scalar Field,” In Proceedings of the 13th Canadian Conference on Computational Geometry, Note: UCRL-JC-142262, pp. 141--144. August, 2001.

H. Pfister, B. Lorensen, C. Bajaj, G. Kindlmann, W. Schroeder, L.S. Avila, K.M. Raghu, R. Machiraju, J. Lee. “The transfer function bake-off,” In IEEE Computer Graphics and Applications, Vol. 21, No. 1, IEEE, pp. 16--22. 2001.
DOI: 10.1109/38.920623

S. Pizer, S. Joshi, P.T. Fletcher, M. Styner, G. Tracton, Z. Chen. “Segmentation of Single-Figure Objects by Deformable M-reps,” In Medical Image Computing and Computer-Assisted Intervention (MICCAI), Edited by WJ Niessen and MA Viergever, New York, pp. 862--871. October, 2001.

O. Portniaguine, D.M. Weinstein, C.R. Johnson. “Focusing Inversion of Electroencephalography and Magnetoencephalography Data,” In 3rd International Symposium On Noninvasive Functional Source Imaging, Journal of Biomedizinische Technik (special issue), Vol. 46, Innsbruck, Austria pp. 115--117. Sep, 2001.

R. Rawat, S.G. Parker, P.J. Smith, C.R. Johnson. “Parallelization and Integration of Fire Simulations in the Uintah PSE,” In Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, March 12-14, 2001.

E. Reinhard, P. Shirley, C.D. Hansen. “Parallel point reprojection,” In Proceedings of the IEEE 2001 symposium on parallel and large-data visualization and graphics, pp. 29--35. 2001.
DOI: 10.1109/PVGS.2001.964400


Improvements in hardware have recently made interactive ray tracing practical for some applications. However, when the scene complexity or rendering algorithm cost is high, the frame rate is too low in practice. Researchers have attempted to solve this problem by caching results from ray tracing and using these results in multiple frames via reprojection. However, the reprojection can become too slow when the number of samples that are reused is high, so previous systems have been limited to small images or a sparse set of computed pixels. To overcome this problem we introduce techniques to perform this reprojection in a scalable fashion on multiple processors.

L.M. Schultz, C.R. Butson, G.A. Clark. “Post-light potentiation at type B to A photoreceptor connections in Hermissenda,” In Neurobiology of Learning and Memory, Vol. 76, No. 1, pp. 7--32. July, 2001.

A. Shamir, V. Pascucci. “Temporal and Spatial Level of Details for Dynamic Meshes,” In Proceedings of the ACM Symposium on Virtual Reality Software and Technology 2001, Banff Center, Canada, ACM, November, 2001.