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 Whitaker


Sarang Joshi

Shape Statistics
Brain Atlasing

Tolga Tasdizen

Image Processing
Machine Learning

Chris Johnson

Diffusion Tensor Analysis

Shireen Elhabian

Image Analysis
Computer Vision

Funded Research Projects:

Publications in Image Analysis:

Automatic Correction of Non-uniform Illumination in Transmission Electron Microscopy Images
SCI Institute Technical Report, T. Tasdizen, R.T. Whitaker, R. Marc, B. Jones. No. UUSCI-2005-008, University of Utah, 2005.

MRI Tissue Classification with Neighborhood Statistics: A Nonparametric, Entropy-Minimizing Approach
T. Tasdizen, S.P. Awate, R.T. Whitaker, N. Foster. In Proceedings of The 8th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pp. 517--525. 2005.
PubMed ID: 16685999

Enhancement of Cell Boundaries in Transmission Micropscopy Images
T. Tasdizen, R.T. Whitaker, R. Marc, B. Jones. In IEEE International Conference on Image Processing, Vol. 2, pp. 129--132. 2005.

Adaptive k-t BLAST/k-t SENSE for Accelerating Cardiac Perfusion MRI
A.A. Samsonov, E.V.R. DiBella, P. Kellman, E.G. Kholmovski, C.R. Johnson. In Proceedings of the Society for Cardiovascular Magnetic Resonance (SCMR) 8th Annual Scientific Sessions, pp. 277--278. 2005.

Diffusion Tensor MRI Visualization
S. Zhang, D.H. Laidlaw, G. Kindlmann. In The Visualization Handbook, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 327--340. 2005.
ISBN: 0-12-387582-X

Practical Vessel Imaging by Computed Tomography in Live Transgenic Mouse Models for Human Tumors
G.L. Kindlmann, D.M. Weinstein, G.M. Jones, C.R. Johnson, M.R. Capecchi, C. Keller. In Journal of Molecular Imaging, Vol. 4, No. 4, pp. 417--424. 2005.

An Efficient, Geometric Multigrid Solver for the Anisotropic Diffusion Equation in Two and Three Dimensions
SCI Institute Technical Report, T. Tasdizen, R.T. Whitaker. No. UUSCI-2004-002, University of Utah, June, 2004.

Anisotropic Diffusion of Height Field Data using Multigrid Solver on GPU
Won-Ki Jeong, Tolga Tasdizen, Ross Whitaker. In Proceedings ACM Workshop on General Purpose Computing on Graphics Processors, 2004, 2004.

Automatic Tissue Classification for the Human Head from Multispectral MRI
SCI Institute Technical Report, T. Tasdizen, D.M. Weinstein, J.N. Lee. No. UUSCI-2004-001, University of Utah, March, 2004.

Higher-order nonlinear priors for surface reconstruction
T. Tasdizen, R.T. Whitaker. In IEEE Trans. Pattern Anal. & Mach. Intel., Vol. 26, No. 7, pp. 878--891. July, 2004.

Non-Cartesian POCSENSE
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. 2648. 2004.

Case Study: An Evaluation of User-Assisted Hierarchical Watershed Segmentation
J. Cates, R.T. Whitaker, G.M. Jones. No. UUCS-04-006, University of Utah School of Computing, 2004.

Biomedical Computing and Visualization Software Environments
C.R. Johnson, R.S. MacLeod, S.G. Parker, D.M. Weinstein. In Comm. ACM, Vol. 47, No. 11, pp. 64--71. 2004.

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.