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


K. Gorczowski, M. Stynera, J.Y. Jeonga, J.S. Marron, J. Piven, H.C. Hazlett, S.M. Pizer, G. Gerig. “Discrimination Analysis using Multi-Object Statistics of Shape and Pose,” In Proceedings of the 2007 SPIE Conference, Vol. 6512, January, 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.

X. Huang, Y.Z. Lee, M. McKeown, G. Gerig, H. Gu, W. Lin, M.M. Lewis, S. Ford, A.I. Troster, D.R. Weinberger, Styner. “Asymmetrical ventricular enlargement in Parkinson's Disease,” In Movement Disorders, Vol. 22, No. 11, pp. 1657--1660. August 15, 2007.

D. Nain, M. Styner, M. Niethammer, J.J. Levitt, M.E. Shenton, G. Gerig, A. Bobick, A. Tannenbaum. “Statistical Shape Analysis of Brain Structures Using Spherical Wavelets,” In Proceedings of the 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2007), IEEE Press, pp. 209--212. 2007.

M. Styner, S. Xu, M. El-Sayed, G. Gerig. “Correspondence Evaluation in Local Shape Analysis and Structural Subdivision,” In Proceedings of ISBI 2007, IEEE Press, pp. 1192--1195. 2007.

M. Styner, I. Oguz, S. Xu, D. Pantazis, G. Gerig. “Statistical Group Differences in Anatomical Shape Analysis using Hotelling T2 Metric,” In Proceedings of the 2007 SPIE Medical Imaging Conference, Vol. 6512, 2007.

W.D. Taylor, J.R. MacFall, G. Gerig, K.R. Krishnan. “Structural Integrity of the Uncinate Fasciculus in Geriatric Depression: Relationship with Age of Onset,” In Neuropsychiatric Disease and Treatment, Vol. 3, No. 5, pp. 669--674. 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.

F. Zhang, C. Goodlett, E. Hancock, G. Gerig. “Probabilistic White Matter Fiber Tracking using Particle Filtering,” In Proceedings of The 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007), Lecture Notes in Computer Science, Vol. 4791, pp. 144--151. November, 2007.


C.J. Cascio, M. Styner, R.G. Smith, M.D. Poe, G. Gerig, H.C. Hazlett, M. Jomier, R. Bammer, J. Piven. “Tractography-Based Segmentation of the Corpus Callosum Reveals a Reduced Relationship to Cortical White Matter Volume in Young Children with Developmental Delay,” In Am J Psychiatry, Vol. 163, pp. 2157--2163. December, 2006.

C.J. Cascio, G. Gerig, J. Piven. “Diffusion Tensor Imaging: Application to the Study of the Developing Brain,” In Journal of the American Academy of Child and Adolescent Psychiatry JAACAP, August, 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.

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.

J.H. Gilmore, W. Lin, G. Gerig. “IMAGES IN NEUROSCIENCE: Fetal and Neonatal Brain Development,” In Am J Psychiatry, Vol. 163, pp. 2046. December, 2006.

H.C. Hazlett, M.D. Poe, G. Gerig, R.G. Smith, J. Piven. “Cortical Gray and White Brain Tissue Volume in Adolescents and Adults with Autism,” In Biological Psychiatry, Vol. 59, No. 1, pp. 1--96. January, 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.

M. Styner, M. Jomier, G. Gerig. “Closed and Open Source Neuroimage Analysis Tools and Libraries at UNC,” In Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI), Special Session: Open Source, pp. 702--705. 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.

P.A. Yushkevich, J. Piven, H.C. Hazlett, R.G. Smith, S. Ho, J.C. Gee, G. Gerig. “User-Guided 3D Active Contour Segmentation of Anatomical Structures: Significantly Improved Efficiency and Reliability,” In NeuroImage, Vol. 31, Note: A NeuroImage Top Cited Paper!, pp. 1116--1128. 2006.