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:


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.



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