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

2000


 D.M. Weinstein, L. Zhukov, G. Potts. “Localization of Multiple Deep Epileptic Sources in a Realistic Head Model via Independent Component Analysis,” School of Computing Technical Report, No. UUCS-2000-004, University of Utah, February, 2000.


D.M. Weinstein, L. Zhukov, C.R. Johnson. “Lead-Field Bases for EEG Source Imaging,” In Annal. Biomed. Eng., Vol. 28, No. 9, pp. 1059--1065. Sep, 2000.


D. Weinstein. “Scanline Surfacing: Building Separating Surfaces from Planar Contours,” In Proceeding of IEEE Visualization 2000, pp. 283--289. 2000.


D.M. Weinstein, L. Zhukov, C.R. Johnson. “An Inverse EEG Problem Solving Environment and its Applications to EEG Source Localization,” In NeuroImage (suppl.), pp. 921. 2000.


M. Weiler, R. Westermann, C.D. Hansen, K. Zimmerman, T. Ertl. “Level-Of-Detail Volume Rendering via 3D Textures,” In Proceeding of IEEE Volume Visualization 2000, SLC, Utah, pp. 7--13. October, 2000.


D.M. Weinstein, L. Zhukov, C.R. Johnson, S.G. Parker, R. Van Uitert, R.S. MacLeod, C.D. Hansen. “Interactive Source Imaging with BioPSE,” In Chicago 2000 World Congress on Medical Physics and Biomedical Engineering, Chicago, IL., Note: Refereed abstract., July, 2000.


D.M. Weinstein, P. Krysl, C.R. Johnson. “The BioPSE Inverse EEG Modeling Pipeline,” In ISGG 7th International Conference on Numerical Grid Generation in Computation Field Simulations, The International Society of Grid Generation, Mississippi State University pp. 1091--1100. 2000.


R. Westermann, C.R. Johnson, T. Ertl. “A Level-Set Method for Flow Visualization,” In Proceeding of IEEE Visualization 2000, IEEE Computer Society, Salt Lake City pp. 147--154. 2000.


S. Zhang, T.N. Truong. “Direct ab initio Dynamics Studies of N+H2NH+H Reaction,” In Journal of Chemical Physics, Vol. 113, No. 15, pp. 6149--6153. 2000.
DOI: 10.1063/1.1308544

ABSTRACT

Kinetics of the N+H2↔NH+Hreaction have been studied using a direct ab initio dynamics method. Potential energy surface for low electronic states have been explored at the QCISD/cc-pVDZ level of theory. We found the ground-statereaction is N(4S)+H2→NH(3Σ−)+H. Thermal rate constants for this reaction were calculated using the microcanonical variational transition state theory.Reaction path information was calculated at the QCISD/cc-pVDZ level of theory. Energies along the minimum energy path (MEP) were then refined at the QCISD(TQ)/cc-pVTZ level of theory. The forward and reverse barriers of the ground-statereaction are predicted to be 29.60 and 0.53 kcal/mol, respectively. The calculated rate constants for both forward and reverse reactions are in good agreement with available experimental data. They can be expressed as k(T)=2.33×1014 exp(-30.83 (kcal/mol)/RT) cm3 mol−1 s−1 for the forward reaction and k(T)=5.55×108T1.44 exp(−0.78(kcal/mol)/RT) cm3 mol−1 s−1 for the reverse reaction in the temperature range 400–2500 K.


 S. Zhang, T.N. Truong. “Thermal Rate Constants of the NO2 fission reaction of Gas Phase a-HMX: A Direct Ab Initio Dynamics Study,” In Journal of Physical Chemistry, A, Vol. 104, pp. 7304--7307. 2000.
DOI: 10.1021/jp001419e

ABSTRACT

The NO2 fission reaction of gas phase α-HMX has been studied using a direct ab initio method within the framework of microcanonical variational transition state theory (μVT). The potential energy calculations were calculated using the hybrid nonlocal B3LYP density functional theory with the cc-pVDZ basis set. The calculated results show that the potential energy of breaking the axial NO2 groups is lower than that of breaking the equatorial NO2 groups. No traditional transition state was found along the reaction path. Microcanonical rate constants calculation shows the variational transition state varies from 2.0 to 3.5 Å of the breaking N−N bond length as a function of the excess energy. The μVT method was used for thermal rate constants calculation over a temperature range from 250 to 2000 K. The fitted Arrhenius expression from the calculated data is k(T) = 1.66 × 1015 exp(−18748K/T) s-1, which is in good agreement with the experimental data at low temperatures.


 L. Zhukov, D. Weinstein, C.R. Johnson. “Statistical Analysis For FEM EEG Source Localization in Realistic Head Models,” School of Computing Technical Report, No. UUCS-2000-003, University of Utah, February, 2000.


L. Zhukov, D.M. Weinstein, C.R. Johnson. “Reciprocity Basis for EEG Source Imaging,” In NeuroImage (suppl.), pp. 598. 2000.


L. Zhukov, D. Weinstein, C.R. Johnson. “Independent Component Analysis for EEG Source Localization in Realistic Head Models,” In IEEE Engineering in Medicine and Biology, Vol. 19, No. 3, pp. 87--96. 2000.

1999


 O. Alter, Y. Yamamoto. “Fundamental Quantum Limit to External Force Detection via Monitoring a Single Harmonic Oscillator or Free Mass,” In Physics Letters A, Vol. 236, No. 4-6, pp. 226--231. 1999.
DOI: 10.1016/S0375-9601(99)00743-4


R. Armstrong, D. Gannon, A. Geist, K. Keahey, S. Kohn, L. McInnes, S.G. Parker, B. Smolinksi. “Toward a Common Component Architecture for High-Performance Scientific Computing,” In Proceedings of the 8th IEEE International Symposium on High Performance Distributed Computation (HPDC), August, 1999.


C.L. Bajaj, C. Baldazzi, S. Cutchin, A. Paoluzzi, V. Pascucci, M. Vicentino. “A Programming Approach for Complex Animations,” In Computer Aided Design, Vol. 31, No. 11, pp. 695--710. 1999.


C.L. Bajaj, V. Pascucci, G. Zhuang. “Single Resolution Compression of Arbitrary Triangular Meshes with Properties,” In Computational Geometry: Theory and Applications, Vol. 14, No. 1--3, pp. 167--186. 1999.
ISSN: 0925-7721
DOI: 10.1016/S0925-7721(99)00026-7

ABSTRACT

Triangular meshes are widely used as primary representation of surface models for networked gaming and for complex interactive design in manufacturing. Accurate triangulation of a surface with sharp features (highly varying curvatures, holes) may require an extremely large number of triangles. Fast transmission of such large triangle meshes is critical to many applications that interactively manipulate geometric models in remote networked environments. The need for a succinct representation is therefore not only to reduce static storage requirements, but also to consume less network bandwidth and thus reduce the transmission time.

In this paper we address the problem of defining a space efficient encoding scheme for both lossless and error-bounded lossy compression of triangular meshes that is robust enough to handle directly arbitrary sets of triangles including non-orientable meshes, non-manifold meshes and even non-mesh cases. The compression is achieved by capturing the redundant information in both the topology (connectivity) and geometry with possibly property attributes. Example models and results are also reported.


 C.L. Bajaj, V. Pascucci, D.R. Schikore. “Data Visualization Techniques,” Trends in Software, Vol. 6, Ch. 3: Accelerated IsoContouring of Scalar Fields, John Wiley & Sons, pp. 31--47. 1999.


C.L. Bajaj, V. Pascucci, G. Zhuang. “Progressive Compression and Transmission of Arbitrary Triangular Meshes,” In Proceedings of the 10th Annual IEEE Conference on Visualization (VIS-99), San Francisco, CA, pp. 307--316. October 24-29, 1999.


C.L. Bajaj, V. Pascucci, D. Thompson, X.Y. Zhang. “Parallel Accelerated Isocontouring for Out-Of-Core Visualization,” In Proceedings of First Parallel Visualization and Graphics Symposium 1999, San Francisco, CA, IEEE Computer Society, October, 1999.