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

2007


 J.H. Gilmore, L. Smith, C. Kang, R. Hamer, H. Wolfe, B. Hertzberg, J.K. Smith, N. Chescheir, W. Lin, G. Gerig. “Neonatal Brain Structure in Children with Prenatal Isolated Mild Ventriculomegaly,” In Proceedings American Conference of Neuropharmacology (ACNP) 2007, Boca Raton, FL, Note: abstract., 2007.


J.H. Gilmore, W. Lin, M.W. Prastawa, C.B. Looney, Y.S.K. Vetsa, R.C. Knickmeyer, D.D. Evans, J.K. Smith, R.M. Hamer, J.A. Lieberman, G. Gerig. “Regional Gray Matter Growth, Sexual Dimorphism, and Cerebral Asymmetry in the Neonatal Brain,” In Journal of Neuroscience, Vol. 27, No. 6, pp. 1255--1260. 2007.


C. Goodlett, P.T. Fletcher, W. Lin, G. Gerig. “Quantification of Measurement Error in DTI: Theoretical Predictions and Validation,” In Proceedings of The 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007), Lecture Notes in Computer Science, Vol. 4792, pp. 10--17. November, 2007.
PubMed ID: 18051038


C.E. Goodyer, M. Berzins. “Parallelisation and Scalability Issues of a Multilevel EHL Solver,” In Concurrency and Computation: Practice and Experience, Vol. 19, No. 4, pp. 369--396. 2007.


C.B. Goodlett, P.T. Fletcher, W. Lin, G. Gerig. “Noise-Induced Bias in Low-Direction Diffusion Tensor MRI: Replication of Monte-Carlo Simulation with In-Vivo Scans,” In Proceedings of ISMRM 2007, 2007.


K. Gorczowski, M. Styner, J.Y. Jeong, J.S. Marron, J. Piven, H.C. Hazlett, S.M. Pizer, G. Gerig. “Statistical Shape Analysis of Multi-Object Complexes,” In Proceedings of the 2007 IEEE Conference on Computer Vision and Pattern Recognition, pp. 1--8. 2007.


K. Gorczowski, M. Stynera, J.Y. Jeonga, J.S. Marron, J. Piven, H.C. Hazlett, S.M. Pizer, G. Gerig. “Discrimination Analysis using Multi-Object Statistics of Shape and Pose,” In Proceedings of the 2007 SPIE Conference, Vol. 6512, January, 2007.


S. Gouttard, M. Styner, S. Joshi, R.G. Smith, H.C. Hazlett, G. Gerig. “Subcortical Structure Segmentation Using Probabilistic Atlas Priors,” In Medical Imaging 2007: Image Processing, Vol. 6512, No. 65122J, Note: Presented at Worshop - 3D Segmentation in the Clinic: a Grand Challenge, Edited by J.P. W. Pluim and J.M. Reinhardt, SPIE Intl Soc Optical Eng, March, 2007.


C.P. Gribble, S.G. Parker. “Interactive Visualization with Advanced Shading Models using Lazy Evaluation,” In Proceedings of the 2007 Eurographics Symposium on Parallel Graphics and Visualization, pp. 37--44. 2007.


C.P. Gribble, C. Brownlee, S.G. Parker. “Practical Global Illumination for Interactive Particle Visualization,” In Computers and Graphics, Vol. 32, No. 1, pp. 14--24. February, 2007.


A. Gyulassy, V. Natarajan, B. Hamann, V. Pascucci. “Efficient Computation of Morse-Smale Complexes for Three-dimensional Scalar Functions,” In IEEE Transactions on Visualization and Computer Graphics, Note: (presented at IEEE VIS 2007), 2007.


A. Gyulassy, V. Natarajan, B. Hamann, M. Duchaineau, V. Pascucci, E. Bringa, A. Higginbotham. “Topologically Clean Distance Fields,” In IEEE Transactions on Visualization and Computer Graphics, Note: (presented at IEEE VIS 2007), 2007.


C.W. Hamman, R.M. Kirby, M. Berzins. “Parallelization and Scalability of a Spectral Element Channel Flow Solver for Incompressible Navier-Stokes Equations,” In Concurrency and Computation: Practice and Experience, Vol. 14, No. 10, pp. 1403--1422. 2007.


C.R. Hamman, R.M. Kirby, M. Berzins. “Parallel Direct Simulation of Incompressible Navier Stokes Equations,” In Concurrency and Computation, Vol. 19, No. 10, pp. 1403-1427. 2007.


H.B. Henninger, C.J. Underwood, S.A. Maas, R.T. Whitaker, J.A. Weiss. “Spatial Distribution and Orientation of Dermatan Sulfate in Human Medial Collateral Ligament,” In Journal of Structural Biology, Vol. 158, No. 1, pp. 33--45. April, 2007.
DOI: 10.1016/j.jsb.2006.10.008

ABSTRACT

The proteoglycan decorin and its associated glycosaminoglycan (GAG), dermatan sulfate (DS), regulate collagen fibril formation, control fibril diameter, and have been suggested to contribute to the mechanical stability and material properties of connective tissues. The spatial distribution and orientation of DS within the tissue are relevant to these mechanical roles, but measurements of length and orientation from 2D transmission electron microscopy (TEM) are prone to errors from projection. The objectives of this study were to construct a 3D geometric model of DS GAGs and collagen fibrils, and to use the model to interpret TEM measurements of the spatial orientation and length of DS GAGs in the medial collateral ligament of the human knee. DS was distinguished from other sulfated GAGs by treating tissue with chondroitinase B, an enzyme that selectively degrades DS. An image processing pipeline was developed to analyze the TEM micrographs. The 3D model of collagen and GAGs quantified the projection error in the 2D TEM measurements. Model predictions of 3D GAG orientation were highly sensitive to the assumed GAG length distribution, with the baseline input distribution of 69 ± 23 nm providing the best predictions of the angle measurements from TEM micrographs. The corresponding orientation distribution for DS GAGs was maximal at orientations orthogonal to the collagen fibrils, tapering to near zero with axial alignment. Sulfated GAGs that remained after chondroitinase B treatment were preferentially aligned along the collagen fibril. DS therefore appears more likely to bridge the interfibrillar gap than non-DS GAGs. In addition to providing quantitative data for DS GAG length and orientation in the human MCL, this study demonstrates how a 3D geometric model can be used to provide a priori information for interpretation of geometric measurements from 2D micrographs.

Keywords: computational biomechanics, mrl


 X. Huang, Y.Z. Lee, M. McKeown, G. Gerig, H. Gu, W. Lin, M.M. Lewis, S. Ford, A.I. Troster, D.R. Weinberger, Styner. “Asymmetrical ventricular enlargement in Parkinson's Disease,” In Movement Disorders, Vol. 22, No. 11, pp. 1657--1660. August 15, 2007.


M. Ikits. “Interactive Exploration of Volumetric Data Sets With a Combined Visual and Haptic Interface,” Note: Ph.D. Thesis, University of Utah School of Computing, 2007.


T. Ize, I. Wald, S.G. Parker. “Asynchronous BVH Construction for Ray Tracing Dynamic Scenes on Parallel Multi-Core Architectures,” In Proceedings of the 2007 Eurographics Symposium on Parallel Graphics and Visualization, pp. 101--108. 2007.


T. Ize, P. Shirley, S.G. Parker. “Grid Creation Strategies for Efficient Ray Tracing,” In Proceedings of the 2007 IEEE/Eurographics Symposium on Interactive Ray Tracing, pp. 27--32. 2007.


W.-K. Jeong, P.T. Fletcher, R. Tao, R.T. Whitaker. “Interactive Visualization of Volumetric White Matter Connectivity in DT-MRI Using a Parallel-Hardware Hamilton-Jacobi Solver,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 6, pp. 1480--1487. 2007.
PubMed ID: 17968100