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


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.

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.

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.


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.

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.


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.

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, 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. 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.