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

2004


 B. Davis, D. Prigent, J. Bechtel, J. Rosenman, D.M. Lovelock, S. Joshi. “Accommodating Bowel Gas in Large Deformation Image Registration for Adaptive Radiation Therapy of the Prostate,” In Proceedings of AAPM Annual Meeting, July, 2004.


B. Davis, P. Lorenzen, S. Joshi. “Large Deformation Minimum Mean Squared Error Template Estimation for Computational Anatomy,” In Proceedings of the International Symposium on Biomedical Imaging (ISBI), Piscataway, NJ, pp. 173--176. April, 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


Q. Han, C. Lu, G. Liu, S.M. Pizer, S. Joshi, A. Thall. “Representing Multi-Figure Anatomical Objects,” In Proceedings of the International Symposium on Biomedical Imaging (ISBI), Piscataway, NJ, pp. 1251--1254. 2004.


S. Joshi, B. Davis, M Jomier, G. Gerig. “Unbiased Diffeomorphic Atlas Construction for Computational Anatomy,” In Neuroimage, Vol. 23 Suppl. 1, pp. S151--S160. 2004.


P. Lorenzen, B. Davis, S. Joshi. “Model Based Symmetric Information Theoretic Large Deformation Multi-Modal Image Registration,” In Proceedings of the International Symposium on Biomedical Imaging (ISBI), Piscataway, NJ, pp. 720--723. April, 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.


R.E. Hogan, R.D. Bucholz, S. Joshi. “Hippocampal Deformation-Based Shape Analysis in Epilepsy and Unilateral Mesial Temporal Sclerosis,” In Epilepsia, Vol. 44, No. 6, pp. 800--806. June, 2003.


S. Joshi, P. Lorenzen, G. Gerig, E. Bullitt. “Structural and Radiometric Asymmetry in Brain Images,” In Med Image Anal, Vol. 7, No. 2, pp. 155--170. June, 2003.


P. Lorenzen, S. Joshi. “High-Dimensional Multi-modal Image Registration,” In Proceedings of the Workshop on Biomedical Image Registration, pp. 234--243. 2003.


C. Lu, S. Pizer, S. Joshi. “A Markov Random Field Approach to Multi-scale Shape Analysis,” In Scale Space Methods in Computer Vision, Edited by LD Griffin and M Lillholm, pp. 416--431. 2003.


S.M. Pizer, G. Gerig, S. Joshi, S. Aylward. “Multiscale Medial Shape-Based Analysis of Image Objects,” In Proceedings of the IEEE, Vol. 91, No. 10, Edited by C. Roux and J.K. Udupa, IEEE, pp. 1670--1679. October, 2003.
DOI: 10.1109/jproc.2003.817876


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.


M. Styner, G. Gerig, S. Pizer, S. Joshi. “Automatic and Robust Computation of 3D Medial Models Incorporating Object Variability,” 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. 107--122. November-December, 2003.


P. Yushkevich, S. Joshi, S.M. Pizer, J.G. Csernansky, L. Wang. “Feature Selection for Shape-Based Classification of Biological Objects,” In Inf Process Med Imaging, Vol. 18, pp. 114--125. July, 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


 Z. Chen, S. Pizer, E. Chaney, S. Joshi. “Medical Image Synthesis via Monte Carlo Simulation,” In Medical Image Computing and Computer-Assisted Intervention (MICCAI), Edited by T Dohi and R Kikinis, pp. 347--354. 2002.