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

2007


 S. Gouttard, M. Styner, S. Joshi, R.G. Smith, H.C. Hazlett, G. Gerig. “Subcortical Structure Segmentation Using Probabilistic Atlas Priors,” In Medical Imaging 2007: Image Processing, Vol. 6512, No. 65122J, Note: Presented at Worshop - 3D Segmentation in the Clinic: a Grand Challenge, Edited by J.P. W. Pluim and J.M. Reinhardt, SPIE Intl Soc Optical Eng, March, 2007.


T.B. Terriberry, J.N. Damon, S.M. Pizer, S. Joshi, G. Gerig. “Population-Based Fitting of Medial Shape Models with Correspondence Optimization,” In Proceedings of Information Processing in Medical Imaging (IPMI '07), Lecture Notes in Computer Science, Vol. 20, pp. 700--712. July, 2007.

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


G. Gerig, B. Davis, P. Lorenzen, S. Xu, M. Jomier, J. Piven, S. Joshi. “Computational Anatomy to Assess Longitudinal Trajectory of Brain Growth,” In Proceedings of The Third International Symposium on 3D Data Processing, Visualization, and Transmission, pp. 1041--1047. June, 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.


P. Lorenzen, M.W. Prastawa, B. Davis, G. Gerig, E. Bullitt, S. Joshi. “Multi-Modal Image Set Registration and Atlas Formation,” In Med Image Anal, Vol. 10, No. 3, pp. 440--451. June, 2006.


S. Xu, M. Styner, B. Davis, S. Joshi, G. Gerig. “Group Mean Differences of Voxel and Surface Objects via Nonlinear Group Averaging,” In Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI), pp. 758--761. April, 2006.

2005


 E. Bullitt, D. Zeng, G. Gerig, S. Aylward, S. Joshi, J.K. Smith, W. Lin, M. Ewend. “Vessel Tortuosity and Brain Tumor Malignancy: A Blinded Study,” In Acad Radiol, Vol. 12, No. 10, pp. 1232--1240. October, 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.


M. Foskey, B. Davis, L. Goyal, S. Chang, E. Chaney, N. Strehl, S. Tomei, J. Rosenman, S. Joshi. “Large Deformation Three-Dimensional Image Registration in Image-Guided Radiation Therapy,” In Phys Med Biol, Vol. 50, No. 24, pp. 5869--5892. December 21, 2005.


H. Guo, A. Rangarajan, S. Joshi. “3-D Diffeomorphic Shape Registration on Hippocampal Data Sets,” In Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv, Vol. 8 (Pt. 2), pp. 984--991. 2005.


Q. Han, S.M. Pizer, D. Merck, S. Joshi, J.-Y. Jeong. “Multi-figure Anatomical Objects for Shape Statistics,” In Lecture Notes in Computer Science, Edited by G. Christensen and M. Sonka, Springer, pp. 701-712. 2005.
DOI: 10.1007/11505730_58


P.J. Keall, S. Joshi, S.S. Vedam, J.V. Siebers, V.R. Kini, R. Mohan. “Four-Dimensional Radiotherapy Planning for DMLC-Based Respiratory Motion Tracking,” In Med Phys, Vol. 32, No. 4, pp. 942--951. April, 2005.


P. Lorenzen, B. Davis, S. Joshi. “Unbiased Atlas Formation via Large Deformations Metric Mapping,” In Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv (MICCAI), Vol. 8 (Pt. 2), Edited by J.S. Duncan and G. Gerig, pp. 411--418. 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.


S.M. Pizer, J.Y. Jeong, C. Lu, K. Muller, S. Joshi. “Estimating the Statistics of Multi-Object Anatomic Geometry Using Inter-Object Relationships,” In Proceedings of International Workshop on Deep Structure, Singularities and Computer Vision (DSSCV), Edited by O.F. Olsen and L. Florack and A Kuijper, pp. 60--71. June, 2005.


T. Terriberry, S. Joshi, G. Gerig. “Hypothesis Testing with Nonlinear Shape Models,” In Information Processing in Medical Imaging (IPMI), Edited by G Christensen and M Sonka, pp. 15--26. July, 2005.

2004


 E. Bullitt, M.G. Ewend, S. Aylward, W. Lin, G. Gerig, S. Joshi, I. Jung, K. Muller, J. Smith. “Abnormal Vessel Tortuosity as a Marker of Treatment Response of Malignant Gliomas: Preliminary Report,” In Technol Cancer Res Treat, Vol. 3, No. 6, pp. 577--584. December, 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.