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

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.


P. Lorenzen, S. Joshi, G. Gerig, E. Bullitt. “Tumor-Induced Structural Radiometric Asymmetry in Brain Images,” In Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA), pp. 163--170. 2001, 2001.


S. Pizer, S. Joshi, P.T. Fletcher, M. Styner, G. Tracton, Z. Chen. “Segmentation of Single-Figure Objects by Deformable M-reps,” In Medical Image Computing and Computer-Assisted Intervention (MICCAI), Edited by WJ Niessen and MA Viergever, New York, pp. 862--871. October, 2001.


P. Yushkevich, S.M. Pizer, S. Joshi, J.S. Marron. “Intuitive, Localized Analysis of Shape Variability,” In Information Processing in Medical Imaging (IPMI), pp. 402--408. June, 2001.

2000


 J.G. Csernansky, L. Wang, S. Joshi, J.P. Miller, M. Gado, D. Kido, D. McKeel, J.C. Morris, M. Miller. “Early DAT is Distinguished from Aging by High-Dimensional Mapping of the Hippocampus. Dementia of the Alzheimer Type,” In Neurology, Vol. 55, No. 11, pp. 1636--1643. December 12, 2000.


R.E. Hogan, K.E. Mark, L. Wang, S. Joshi, M.I. Miller, R. Bucholz. “Mesial Temporal Sclerosis and Temporal Lobe Epilepsy: MR Imaging Deformation-Based Segmentation of the Hippocampus in Five Patients,” In Radiology, Vol. 216, No. 1, pp. 291--297. July, 2000.


R.E. Hogan, K.E. Mark, I. Choudhuri, L. Wang, S. Joshi, M.I. Miller, R. Bucholz. “Magnetic Resonance Imaging Deformation-Based Segmentation of the Hippocampus in Patients with Mesial Temporal Sclerosis and Temporal Lobe Epilepsy,” In J Digit Imaging, Vol. 13, No. 2 (Suppl. 1), pp. 217--218. May, 2000.


R.E. Hogan, R.D. Bucholz, I. Choudhuri, K.E. Mark, C.S. Butler, S. Joshi. “Shape-analysis of hippocampal surface structure in patients with unilateral mesial temporal sclerosis,” In Journal of Digital Imaging, Vol. 13, No. 2, pp. 39--42. 2000.


S. Joshi, M.I. Miller. “Landmark Matching Via Large Deformation Diffeomorphisms,” In IEEE Transactions on Image Processing, Vol. 9, No. 8, pp. 1357--1370. August, 2000.


D.C. Van Essen, H.A. Drury, S. Joshi, M. Miller. “Functional and Structural Mapping of Human Cerebral Cortex: Solutions are in the Surfaces,” In Adv Neurol, Vol. 84, pp. 23--34. 2000.

1999


 M. Joshi, J. Cui, K. Doolittle, S. Joshi, D.C. Van Essen, L. Wang, M. Miller. “Brain Segmentation and the Generation of Cortical Surfaces,” In Neuroimage, Vol. 9, No. 5, pp. 461--476. May, 1999.

1998


 J.C. Csernansky, S. Joshi, L. Wang, M. Gado, J.P. Miller, U. Grenander, M.I. Miller. “Hippocampal Morphometry in Schizophrenia by High Dimensional Brain Mapping,” In Proceedings of the National Academy of Science, Vol. 95, pp. 11406--11411. September, 1998.


D.C. Van Essen, H.A. Drury, S. Joshi, M. Miller. “Functional and Structural Mapping of Human Cerebral Cortex: Solutions are in the Surfaces,” In Proceedings of the National Academy of Sciences, Vol. 95, No. 3, Proceedings of the National Academy of Sciences, pp. 788--795. February, 1998.
DOI: 10.1073/pnas.95.3.788

1997


 J.W. Haller, A. Banerjee, G.E. Christensen, M. Gado, S. Joshi, M.I. Miller, Y. Sheline, M.W. Vannier, J. Csernansky. “Three-Dimensional Hippocampal MR Morphometry with High-Dimensional Transformation of a Neuroanatomic Atlas,” In Radiology, Vol. 202, No. 2, pp. 504--510. February, 1997.


S. Joshi, A. Banerjee, G.E. Christensan, J.G. Csernansky, J.W. Haller, M.I. Miller, L. Wang. “Gaussian Random Fields on Sub-Manifolds for Characterizing Brain Surfaces,” In Proceedings of the International Conference on Image Processing in Medical Imaging (IPMI), 1997.


A.L. Levy, T.J. Schaewe, M.I. Miller, K.R. Smith, A.M. Hammoud, J.M. Henderson, S. Joshi, K.E. Mark, C.D. Sturm, L.L. McDurmont Jr, R. Bucholz. “An Internet-Connected, Patient-Specific, Deformable Brain Atlas Integrated into a Surgical Navigation System,” In J Digit Imaging, Vol. 10, No. 3 (Suppl. 1), pp. 231--237. August, 1997.


M. Miller, A. Banerjee, G. Christensen, S. Joshi, N. Khaneja, U. Grenander, L. Matejic. “Statistical Methods in Computational Anatomy,” In Stat Methods Med Res, Vol. 6, No. 3, pp. 267--299. September, 1997.


M.I. Miller, S. Joshi. “Discussion of Mathematics for Object Recognition Shape, Invariance and Deformations,” In Proceedings of the Workshop on Mathematics for Object Recognition Shape, Invariance and Deformations, Edited by L. Younes, November, 1997.