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:


An Optimal-Path Approach for Neural Circuit Reconstruction
E. Jurrus, R.T. Whitaker, B. Jones, R. Marc, T. Tasdizen. In Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, pp. 1609--1612. 2008.
PubMed ID: 19172170



Realizing the Potential of Positron Emission Tomography with 18F-Fluorodeoxyglucose to Improve the Treatment of Alzheimer
N.L. Foster, A.Y. Wang, T. Tasdizen, P.T. Fletcher, J.M. Hoffman, R.A. Koeppe. In Journal of the Alzheimer, Vol. 4, No. 1, Suppl. 1, pp. S29--36. 2008.
PubMed ID: 18631997



Automatic Classification of Alzheimer
N. Sadeghi, N.L. Foster, A.Y. Wang, S. Minoshima, A.P. Lieberman, T. Tasdizen. In Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2008): From Nano to Macro, pp. 408--411. 2008.
DOI: 10.1109/ISBI.2008.4541019



Principal Components for Non-Local Means of Image Denoising
T. Tasdizen. In Proceedings of the International Conference on Image Processing (ICIP 2008), pp. 1728--1731. 2008.
PubMed ID: 19180227



Fast Isosurface Extraction Methods for Large Image Data Sets
Y. Livnat, S.G. Parker, C.R. Johnson. In Handbook of Medical Image Processing and Analysis, 2nd edition, Ch. 47, Note: (to appear), Edited by Isaac N. Bankman, Elsevier, pp. 801--816. 2008.



A Structural MRI Study of Human Brain Development from Birth to Two Years
R.C. Knickmeyer, S. Gouttard, C. Kang, D. Evans, K. Wilber, K.J. Smith, R.M. Hamer, W. Lin, G. Gerig, J.H. Gilmore. In The Journal of Neuroscience, Vol. 28, No. 47, pp. 12176--12182. Nov, 2008.
PubMed ID: 19020011



CRA-NIH Computing Research Challenges in Biomedicine Workshop Recommendations
D. Reed, C.R. Johnson. Note: Computing Research Association (CRA), 2007.



Robust Non-linear Dimensionality Reduction using Successive 1-Dimensional Laplacian Eigenmaps
S. Gerber, T. Tasdizen, R.T. Whitaker. In Proceedings of the 2007 International Conference on Machine Learning (ICML), pp. 281--288. 2007.



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.