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:


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.



The BioPSE Inverse EEG Modeling Pipeline
D.M. Weinstein, P. Krysl, C.R. Johnson. In ISGG 7th International Conference on Numerical Grid Generation in Computation Field Simulations, The International Society of Grid Generation, Mississippi State University pp. 1091--1100. 2000.



Reciprocity Basis for EEG Source Imaging
L. Zhukov, D.M. Weinstein, C.R. Johnson. In NeuroImage (suppl.), pp. 598. 2000.



Color Quantization with Genetic Algorithms
T. Tasdizen, L. Akarun, C. Ersoy. In Signal Processing: Image Communication, Vol. 12, pp. 49--57. 1998.



Computational and Numerical Methods for Bioelectric Field Problems
C.R. Johnson. In Critical Reviews in BioMedical Engineering, Vol. 25, No. 1, pp. 1--81. 1997.



Software Tools for Modeling, Computation, and Visualization in Medicine
C.R. Johnson, R.S. MacLeod, J.A. Schmidt. In CompMed 94 Proceedings, World Scientific, 1995.



Numerical Methods for Bioelectric Field Problems
C.R. Johnson. In The Biomedical Engineering Handbook, Edited by J.D. Bronzino, CRC Press, Boca Ratan pp. 161--188. 1995.



Construction of a Human Torso Model from Magnetic Resonance Images for Problems in Computational Electrocardiography
School of Computing Technical Report, R.S. MacLeod, C.R. Johnson, P.R. Ershler. No. UUCS-94-017, University of Utah, 1994.



Interactive Manipulation of Contour Data Using the Layers Program - User Guide
School of Computing Technical Report, S.G. Parker, C.R. Johnson. No. UUCS-94-014, University of Utah, 1994.



Computer Simulations Reveal Complexity of Electrical Activity in the Human Thorax
C.R. Johnson, R.S. MacLeod, M.A. Matheson. In Computers in Physics, Vol. 6, pp. 230--237. May/June, 1992.



A Computer Model for the Study of Electrical Current Flow in the Human Thorax
C.R. Johnson, R.S. MacLeod, P.R. Ershler. In Computers in Biology and Medicine, Vol. 22, No. 5, Elsevier BV, pp. 305--323. 1992.

Electrocardiography has played an important role in the detection and characterization of heart function, both in normal and abnormal states. In this paper we present an inhomogeneous, anisotropic computer model of the human thorax for use in electrocardiography with emphasis on the calculation of transthoracic potential and current distributions. Knowledge of the current pathways in the thorax has many applications in electrocardiography and has direct utility in studies pertaining to cardiac defibrillation, forward and inverse problems, impedance tomography, and electrode placement in electrocardiography.

Keywords: scalar field methods, vector field methods, tensor field methods, cardiac heart, scientific visualization



Construction of an Inhomogeneous Model of the Human Torso for Use in Computational Electrocardiography
R.S. MacLeod, C.R. Johnson, P.R. Ershler. In IEEE Engineering in Medicine and Biology Society 13th Annual International Conference, IEEE Press, pp. 688--689. 1991.