Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Large scale visualization on the Powerwall.
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
tom

Tom Fletcher

Shape Statistics
Diffusion Tensor Analysis
chris

Chris Johnson

Diffusion Tensor Analysis



Image Analysis Project Sites:


Publications in Image Analysis:


An Algorithm for Moment-Based Global Registration of Echo Planar Diffusion-Weighted Images
G. Kindlmann, A. L. Alexander, M. Lazar, J. Lee, T. Tasdizen, R.T. Whitaker. In Proceedings of 12th Annual ISMRM, pp. 2200. 2004.



Removal of Intensity Bias in Magnitude Spin-Echo MRI Images by Nonlinear Diffusion Filtering
A.A. Samsonov, C.R. Johnson.. In Proceedings of SPIE Medical Imaging 2004, San Diego, CA, Vol. 5370, pp. 743--752. 2004.



Unbiased Nonlinear Filtering of Fast Spin Echo MRI Images
A.A. Samsonov, C.R. Johnson. In Proceedings of The 12th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Kyoto, Japan, pp. 760. 2004.



Minimum Support MEG (Magnetoencephalography) Imaging: Study on Effects of Noise, Discretization, Depth, and Separation of Multiple Sources
D. Hwang, O. Portniaguine, S. Nagarajan, C.R. Johnson, K. Sekihara. In World Congress on Medical Physics and Biomedical Engineering, August, 2003.



Cramer-Rao Bounds for Nonparametric Surface Reconstruction from Range Data
T. Tasdizen, R.T. Whitaker. In Proceedings of Fourth International Conference on 3-D Imaging and Modeling, pp. 70--77. October, 2003.



White Matter Tractography Using Diffusion Tensor Deflection
M. Lazar, D.M. Weinstein, J.S. Tsuruda, K.M. Hasan, K. Arfanakis, E. Meyer, B. Badie, H.A. Rowley, V. Haughton, A. Field, A.L. Alexander. In Human Brain Mapping, Vol. 18, pp. 306--321. 2003.



A Modified POCSENSE Technique for Accelerated Iterative Reconstruction from Sensitivity Encoded MRI Data
A.A. Samsonov, E.G. Kholmovski, C.R. Johnson. In Proceedings of 11th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), Toronto, pp. 477. 2003.



Image Reconstruction from Sensitivity Encoded MRI Data Using Extrapolated Iterations of Parallel Projections Onto Convex Sets
A.A. Samsonov, E.G. Kholmovski, C.R. Johnson. In SPIE Medical Imaging, Vol. 5032, pp. 1829--1838. 2003.



BioPSE Case Study: Modeling, Simulation, and Visualization of Three Dimensional Mouse Heart Propagation
D.M. Weinstein, J.V. Tranquillo, C.S. Henriquez, C.R. Johnson. In International Journal of Bioelectromagnetism, Vol. 5, No. 1, pp. 314--315. 2003.



Determination of the Sampling Density Compensation Function Using a Point Spread Function Modeling Approach and Gridding Approximation
A.A. Samsonov, E.G. Kholmovski, C.R. Johnson. In Proceedings of 11th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), Toronto, pp. 477. 2003.



Parametric Method for Correction of Intensity Inhomogeneity in MRI Data
A.A. Samsonov, R.T. Whitaker, E.G. Kholmovski, C.R. Johnson. In Proceedings of The 10th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Honolulu, pp. 154. 2002.



Noise-Adaptive Anisotropic Diffusion Filtering of MRI Images Reconstructed by SENSE (SENSitivity Encoding) Method
A.A. Samsonov, C.R. Johnson. In Proceedings of The 2002 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Washington DC, pp. 701--704. July, 2002.



Noise-Adaptive Nonlinear Filtering Technique for SENSE-Reconstructed Images
A.A. Samsonov, R.T. Whitaker, C.R. Johnson. In Proceedings of The 10th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Honolulu, pp. 74. 2002.



Computational Bioimaging for Medical Diagnosis and Treatment
C.R. Johnson. In Communications of the ACM, Vol. 44, No. 3, pp. 74--76. March, 2001.



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



Fast Isosurface Extraction Methods for Large Image Data Sets
Y. Livnat, S.G. Parker, C.R. Johnson. In Handbook of Medical Imaging, Edited by A.N. Bankman, Academic Press, San Diego, CA pp. 731--745. Nov, 2000.



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



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



Improving the Stability of Algebraic Curves for Applications
T. Tasdizen, J.-P. Tarel, D.B. Cooper. In IEEE Transactions on Image Processing, Vol. 9, No. 3, pp. 405--416. March, 2000.



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