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.

Image Analysis

SCI's imaging work addresses fundamental questions in 2D and 3D image processing, including filtering, segmentation, surface reconstruction, and shape analysis. In low-level image processing, this effort has produce new nonparametric methods for modeling image statistics, which have resulted in better algorithms for denoising and reconstruction. Work with particle systems has led to new methods for visualizing and analyzing 3D surfaces. Our work in image processing also includes applications of advanced computing to 3D images, which has resulted in new parallel algorithms and real-time implementations on graphics processing units (GPUs). Application areas include medical image analysis, biological image processing, defense, environmental monitoring, and oil and gas.


ross

Ross Whitaker

Segmentation
sarang

Sarang Joshi

Shape Statistics
Segmentation
Brain Atlasing
tolga

Tolga Tasdizen

Image Processing
Machine Learning
chris

Chris Johnson

Diffusion Tensor Analysis
shireen

Shireen Elhabian

Image Analysis
Computer Vision


Funded Research Projects:



Publications in Image Analysis:


Particle Systems for Efficient and Accurate Finite Element Visualization
M.D. Meyer, B. Nelson, R.M. Kirby, R.T. Whitaker. In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 5, pp. 1015--1026. 2007.



Anisotropic Curvature Motion for Structure Enhancing Smoothing of 3D MR Angiography Data
O. Nemitz, T. Tasdizen, M. Rumpf, R.T. Whitaker. In Journal of Mathematical Imaging and Vision, Vol. 7, No. 3, pp. 217--229. 2007.
DOI: 10.1007/s10851-006-0645-2



Temporally Constrained Reconstruction of Dynamic Cardiac Perfusion MRI
G. Adluru, S.P. Awate, T. Tasdizen, R.T. Whitaker, E.V.R. DiBella. In Magnetic Resonance in Medicine, Vol. 57, pp. 1027--1036. 2007.



Structure and Function of Microneuromas in Retinal Remodeling
B.W. Jones, R.E. Marc, C.B. Watt, K. Kinardi, D. DeMill, J.H. Yang, T. Tasdizen, P. Koshevoy, E. Jurrus, R.T. Whitaker. In The Association for Research in Vision and Ophthalmology (ARVO) Conference, Note: (abstract), 2007.



Automatic Assembly of TEM Mosaics and Mosaic Stacks Using Phase Correlation
SCI Institute Technical Report, P.A. Koshevoy, T. Tasdizen, R.T. Whitaker. No. UUSCI-2007-004, University of Utah, 2007.



Fast Isosurface Extraction Methods for Large Image Data Sets
Y. Livnat, S.G. Parker, C.R. Johnson. In Handbook of Medical Imaging: Processing and Analysis, 2nd Edition, Ch. 44, Edited by Isaac Bankman, Academic Press, 2007.



Regional Gray Matter Growth, Sexual Dimorphism, and Cerebral Asymmetry in the Neonatal Brain
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. In Journal of Neuroscience, Vol. 27, No. 6, pp. 1255--1260. 2007.



Topology, Accuracy, and Quality of Isosurface Meshes Using Dynamic Particles
M.D. Meyer, R.M. Kirby, R.T. Whitaker. In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 6, IEEE, pp. 1704--1711. Nov, 2007.



Automatic Classification of Alzheimers Disease vs. Frontotemporal Dementia: A Decision Tree Approach with FDG-PET
SCI Institute Technical Report, N. Sadeghi, T. Tasdizen, N.L. Foster, A.Y. Wang, S. Minoshima, A.P. Lieberman.. No. UUSCI-2007-016, University of Utah, 2007.



Regional Gray Matter Growth, Sexual Dimorphism, and Cerebral Asymmetry in the Neonatal Brain
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. In Journal of Neuroscience, Vol. 27, No. 6, pp. 1255--1260. 2007.



Unsupervised Texture Segmentation with Nonparametric Neighborhood Statistics
SCI Institute Technical Report, S.P. Awate, T. Tasdizen, R.T. Whitaker. No. UUSCI-2006-011, University of Utah, 2006.



Anisotropic Curvature Motion for Structure Enhancing Smoothing of 3D MR Angiography Data
O. Nemitz, M. Rumpf, T. Tasdizen, R.T. Whitaker. In Journal of Mathematical Imaging and Vision, Vol. 27, No. 3, pp. 217--229. April, 2006.



Assembly of Large Three-Dimensional Volumes from Serial-Section Transmission Electron Microscopy
P. Koshevoy, T. Tasdizen, R.T. Whitaker, B. Jones, R. Marc. In Proceedings of 2006 MICCAI Workshop on Microscopic Image Analysis with Applications in Biology, October, 2006.



Axon Tracking in Serial Block-Face Scanning Electron Microscopy
E. Jurrus, T. Tasdizen, P. Koshevoy, P.T. Fletcher, M. Hardy, C-B. Chien, W. Denk, R.T. Whitaker. In Workshop on Microscopic Image Analysis with Applications in Biology, MICCAI, October, 2006.



Entropy-Based Particle Systems for Shape Correspondence
J. Cates, M.D. Meyer, P.T. Fletcher, R.T. Witaker. In Workshop on Mathematical Foundations of Computational Anatomy, MICCAI 2006, pp. 90--99. October, 2006.



Adaptive, Nonparametric Markov Modeling for Unsupervised, MRI Brain-Tissue Classification
S.P. Awate, T. Tasdizen, N.L. Foster, R.T. Whitaker. In Medical Image Analysis (MEDIA), Vol. 10, No. 5, pp. 726--739. 2006.



Computational Methods and Software for Bioelectric Field Problems
C.R. Johnson. In Biomedical Engineering Handbook, 2nd Edition, Vol. 1, Ch. 23, Edited by J.D. Bronzino, CRC Press, Boca Raton, pp. 1--23. 2006.



Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping
J.T. Johnson III, M.S. Hansen, I. Wu, L.J. Healy, C.R. Johnson, G.M. Jones, M.R. Capecchi, C. Keller. In PLoS Genetics, Vol. 2, No. 1, pp. 471--477. April, 2006.



Adaptive, Nonparametric Markov Modeling for Unsupervised, MRI Brain-Tissue Classification
SCI Institute Technical Report, S.P. Awate, T. Tasdizen, N. Foster, R.T. Whitaker. No. UUSCI-2006-008, University of Utah, 2006.



Implementation of an Automatic Image Registration Tool
SCI Institute Technical Report, P.A. Koshevoy, T. Tasdizen, R.T. Whitaker. No. UUSCI-2006-020, University of Utah, 2006.