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:

Morphometric and Qualitative Analysis of Congenital Occipitocervical Instability in Children: Implications for Down Syndrome Patients
S. Browd, L.J. Healy, G. Dobie, J.T. Johnson III, G.M. Jones, L.F. Rodriguez, D.L. Brockmeyer. In Journal of Neurosurgery: Pediatrics, Vol. 105, No. 1 , Journal of Neurosurgery Publishing Group, pp. 50--54. July, 2006.
DOI: 10.3171/ped.2006.105.1.50

Model-Based Image Reconstruction for Dynamic Cardiac Perfusion MRI from Sparse Data
S.P. Awate, E.V.R. DiBella, T. Tasdizen, R.T. Whitaker. In Proceedings of the 2006 IEEE Int. Conf. Engineering and Biology Society (EMBC), pp. 936--941. 2006.

Unsupervised Texture Segmentation with Nonparametric Neighborhood Statistics
S.P. Awate, T. Tasdizen, R.T. Whitaker. In Proceedings of The European Conference on Computer Vision (ECCV) 2006 Springer, Lecture Notes in Computer Science, pp. 494--507. 2006.

Implementation of an Automatic Slice-to-Slice Registration Tool
SCI Institute Technical Report, P.A. Koshevoy, T. Tasdizen, R.T. Whitaker. No. UUSCI-2006-018, University of Utah, 2006.

Controlled Support MEG Imaging
S. Nagarajan, O. Portniaguine, D. Hwang, C.R. Johnson, K. Sekihara. In NeuroImage, Vol. 15;33, No. 3, pp. 878--885. 2006.

Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping
J.T. Johnson III, M.S. Hansen, I.Q Wu, L.J. Healy, C.R. Johnson, G.M. Jones, M.R. Capecchi, C.Keller. In Proceedings of the Teratology 46th Annual Meeting, Tucson, AZ, 2006.

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-2005-007, University of Utah, 2005.

A Geometric Multigrid Approach to Solving the 2D Inhomogeneous Laplace Equation with Internal Dirichlet Boundary Conditions
L. Grady, T. Tasdizen. In IEEE International Conference on Image Processing, Vol. 2, pp. 642--645. September, 2005.

POCS-Enhanced Parallel MRI Correction of MR Image Artifacts
A.A. Samsonov, E.G. Khölmovski, C.R. Johnson. In Proc. Intl. Soc. Mag. Reson., Note: Abstract, pp. 690. 2005.

Robust Particle Systems for Curvature Dependent Sampling of Implicit Surfaces
M.D. Meyer, P. Georgel, R.T. Whitaker. In In Proceedings of the International Conference on Shape Modeling and Applications (SMI), pp. 124--133. June, 2005.

Nonparametric Statistics of Image Neighborhoods for Unsupervised Texture Segmentation
SCI Institute Technical Report, S.P. Awate, T. Tasdizen, R.T. Whitaker. No. UUSCI-2005-003, University of Utah, 2005.

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.