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.

SCI Publications

2006


 I. Corouge, P.T. Fletcher, S. Joshi, S. Gouttard, G. Gerig. “Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis,” In Medical Image Analysis, Vol. 10, No. 5, pp. 786--798. 2006.


P.T. Fletcher, S.M. Pizer, S. Joshi. “Shape Variation of Medial Axis Representations via Principal Geodesic Analysis on Symmetric Spaces,” In Statistics and Analysis of Shapes, Springer, pp. 29--59. 2006.
DOI: 10.1007/0-8176-4481-4_2


P.T. Fletcher, R.T. Whitaker. “Riemannian Metrics on the Space of Solid Shapes,” In MICCAI Workshop on Mathematical Foundations of Computational Anatomy, October, 2006.


G. Gerig, S. Joshi, P.T. Fletcher, K. Gorczowski, S. Xu, S.M. Pizer, M. Styner. “Statistics of Populations of Images and its Embedded Objects: Driving Applications in Neuroimaging,” In Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI), pp. 1120--1123. April, 2006.


E. Jurrus, T. Tasdizen, P. Koshevoy, P.T. Fletcher, M. Hardy, C-B. Chien, W. Denk, R.T. Whitaker. “Axon Tracking in Serial Block-Face Scanning Electron Microscopy,” In Workshop on Microscopic Image Analysis with Applications in Biology, MICCAI, October, 2006.

2005


 I. Corouge, P.T. Fletcher, S. Joshi, J.H. Gilmore, G. Gerig. “Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis,” In Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv, Vol. 8 (Pt. 1), pp. 131--139. 2005.


S.M. Pizer, P.T. Fletcher, S. Joshi, A.G. Gash, J. Stough, A. Thall, G. Tracton, E. Chaney. “A Method and Software for Segmentation of Anatomic Object Ensembles by Deformable M-Reps,” In Med Phys, Vol. 32, No. 5, pp. 1335--1345. May, 2005.

2004


 E. Chaney, S. Pizer, S. Joshi, R. Broadhurst, P.T. Fletcher, G. Gash, Q. Han, J.Y. Jeong, C. Lu, D. Merck, J. Stough, G. Tracton, M.D.J. Bechtel, J. Rosenman, Y.Y. Chi, K. Muller. “Automatic Male Pelvis Segmentation from CT Images via Statistically Trained Multi-Object Deformable M-rep Models,” In Presented at American Society for Therapeutic Radiology and Oncology (ASTRO), 2004.


E. Dam, P.T. Fletcher, S.M. Pizer, G. Tracton, J. Rosenman. “Prostate Shape Modeling based on Principal Geodesic Analysis Bootstrapping,” In Medical Image Computing and Computer-Assisted Intervention (MICCAI), pp. 1008--1016. 2004.


P.T. Fletcher, C. Lu, S.M. Pizer, S. Joshi. “Principal Geodesic Analysis for the Study of Nonlinear Statistics of Shape,” In IEEE Trans Med Imaging, Vol. 23, No. 8, pp. 995--1005. August, 2004.


P.T. Fletcher, S. Joshi. “Principal Geodesic Analysis on Symmetric Spaces: Statistics of Diffusion Tensors,” In Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis, Springer-Verlag, Lecture Notes In Computer Science, Vol. 3117, pp. 87--98. 2004.
DOI: 10.1109/TMI.2004.831793


P.T. Fletcher. “Statistical Variability in Nonlinear Spaces: Application to Shape Analysis and DT-MRI,” Note: Ph.D. Thesis, University of North Carolina Department of Computer Science, August, 2004.

2003


 P.T. Fletcher, S. Joshi, C. Lu, S. Pizer. “Gaussian Distributions on Lie Groups and Their Application to Statistical Shape Analysis,” In Inf Process Med Imaging, Vol. 18, Note: Runner-up for the Francois Erbsmann Prize, pp. 450--462. 2003.


P.T. Fletcher, C. Lu, S. Joshi. “Statistics of Shape via Principal Component Analysis on Lie Groups,” In Proceedings of the Conference on Computer Vision and Pattern Recognition (CVPR), Los Alamitos, CA, pp. 95--101. June, 2003.


S.M. Pizer, P.T. Fletcher, Y. Fridman, D.S. Fritsch, A.G. Gash, J.M. Glotzer, S. Joshi, A. Thall, G. Tracton, P. Yushkevich, E.L. Chaney. “Deformable M-Reps for 3D Medical Image Segmentation,” In International Journal of Computer Vision - Special UNC-MIDAG issue, Vol. 55, No. 2, Edited by O Faugeras and K Ikeuchi and J Ponce, Kluwer Academic, pp. 85--106. November-December, 2003.


S.M. Pizer, P.T. Fletcher, A. Thall, M. Styner, G. Gerig, S. Joshi. “Object Models in Multiscale Intrinsic Coordinates via M-reps,” In Image and Vision Computing, Special Issue on Generative Model-based Vision, Vol. 21, No. 1, pp. 5--15. January, 2003.


P. Yushkevich, P.T. Fletcher, S. Joshi, A. Thall, S.M. Pizer. “Continuous Medial Representations for Geometric Object Modeling in 2D and 3D,” In Image and Vision Computing, Special Issue on Generative Model-based Vision, Vol. 21, No. 1, pp. 17--27. 2003.

2002


 P.T. Fletcher, S.M. Pizer, G. Gash, S. Joshi. “Deformable M-rep segmentation of object complexes,” In Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), pp. 26--29. 2002.


S. Joshi, S. Pizer, P.T. Fletcher, P. Yushkevich, A. Thall, J. Marron. “Multiscale Deformable Model Segmentation and Statistical Shape Analysis Using Medial Descriptions,” In IEEE Trans Med Imaging, Vol. 21, No. 5, pp. 538--550. May, 2002.

2001


 S. Joshi, S. Pizer, P.T. Fletcher, A. Thall, G. Tracton. “Multi-scale 3-D Deformable Model Segmentation Based on Medial Description,” In Information Processing in Medical Imaging (IPMI), Edited by MF Insana and RM Leahy, pp. 64--77. June, 2001.