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

2009


 E. Jurrus, M. Hardy, T. Tasdizen, P.T. Fletcher, P. Koshevoy, C.-B. Chien, W. Denk, R.T. Whitaker. “Axon Tracking in Serial Block-Face Scanning Electron Microscopy,” In Medical Image Analysis (MEDIA), Vol. 13, No. 1, Elsevier, pp. 180--188. February, 2009.
PubMed ID: 18617436


I. Oguz, M. Niethammer, J. Cates, R.T. Whitaker, P.T. Fletcher, C. Vachet, M. Styner. “Cortical Correspondence with Probabilistic Fiber Connectivity,” In Information Processing in Medical Imaging (IPMI), Lecture Notes in Computer Science (LCNS), Vol. 5636, pp. 651--663. 2009.
DOI: 10.1007/978-3-642-02498-6_54


R. Tao, P.T. Fletcher, R.T. Whitaker. “A Variational Image-Based Approach to the Correction of Susceptibility Artifacts in the Alignment of Diffusion Weighted and Structural MRI,” In Lecture Notes in Computer Science, Springer, pp. 664--675. 2009.
DOI: 10.1007/978-3-642-02498-6_55
PubMed ID: 19694302

2008


 J. Cates, P.T. Fletcher, Z. Warnock, R.T. Whitaker. “A Shape Analysis Framework for Small Animal Phenotyping with Application to Mice with a Targeted Disruption of Hoxd11,” In Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08), pp. 512--516. 2008.
DOI: 10.1109/ISBI.2008.4541045


J. Cates, P.T. Fletcher, M. Styner, H. Hazlett, R.T. Whitaker. “Particle-Based Shape Analysis of Multi-Object Complexes,” In Proceedings of the 11th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI '08), Lecture Notes In Computer Science (LCNS), pp. 477--485. 2008.
ISBN: 978-3-540-85987-1


P.T. Fletcher, S. Venkatasubramanian, S. Joshi. “Robust Statistics on Riemannian Manifolds via the Geometric Median,” In IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2008), pp. 1--8. 2008.
DOI: 10.1109/CVPR.2008.4587747


N.L. Foster, A.Y. Wang, T. Tasdizen, P.T. Fletcher, J.M. Hoffman, R.A. Koeppe. “Realizing the Potential of Positron Emission Tomography with 18F-Fluorodeoxyglucose to Improve the Treatment of Alzheimer,” In Journal of the Alzheimer, Vol. 4, No. 1, Suppl. 1, pp. S29--36. 2008.
PubMed ID: 18631997


C. Goodlett, P.T. Fletcher, J. Gilmore, G. Gerig. “Group Statistics of DTI Fiber Bundles Using Spatial Functions of Tensor Measures,” In Medical Image Computing and Computer-Assisted Intervention (MICCAI 2008), Springer Verlag, pp. 1068--1075. 2008.
PubMed ID: 18979851


I. Oguz, J. Cates, P.T. Fletcher, R.T. Whitaker, D. Cool, S. Aylward, M. Styner. “Cortical Correspondence using Entropy-Based Particle Systems and Local Features,” In 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008. (ISBI 2008), pp. 1637--1640. 2008.


S. Pizer, M. Styner, T. Terriberry, R. Broadhurst, S. Joshi, E. Chaney, P.T. Fletcher. “Statistical Applications with Deformable M-Reps,” In Computational Imaging and Vision, Springer, pp. 269--308. 2008.
DOI: 10.1007/978-1-4020-8658-8_9

2007


 J. Cates, P.T. Fletcher, M. Styner, M. Shenton, R.T. Whitaker. “Shape Modeling and Analysis with Entropy-Based Particle Systems,” In Proceedings of Information Processing in Medical Imaging (IPMI) 2007, LNCS 4584, pp. 333--345. 2007.


B. Davis, P.T. Fletcher, E. Bullitt, S. Joshi. “Population Shape Regression From Random Design Data,” In Proceedings of the Eleventh IEEE International Conference on Computer Vision (ICCV '07), pp. 1-7. 2007.


P.T. Fletcher, S. Joshi. “Riemannian Geometry for the Statistical Analysis of Diffusion Tensor Data,” In Signal Processing, Vol. 87, No. 2, pp. 250--262. February, 2007.


P.T. Fletcher, R. Tao, W.-K. Jeong, R.T. Whitaker. “A Volumetric Approach to Quantifying Region-to-Region White Matter Connectivity in Diffusion Tensor MRI,” In Information Processing in Medical Imaging, Vol. 4584/2007, pp. 346--358. 2007.


P.T. Fletcher, S. Powell, N.L. Foster, S. Joshi. “Quantifying Metabolic Asymmetry Modulo Structure in Alzheimer's Disease,” In Lecture Notes in Computer Science, Springer, pp. 446--457. 2007.
DOI: 10.1007/978-3-540-73273-0_37
PubMed ID: 17633720


C. Goodlett, P.T. Fletcher, W. Lin, G. Gerig. “Quantification of Measurement Error in DTI: Theoretical Predictions and Validation,” In Proceedings of The 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007), Lecture Notes in Computer Science, Vol. 4792, pp. 10--17. November, 2007.
PubMed ID: 18051038


C.B. Goodlett, P.T. Fletcher, W. Lin, G. Gerig. “Noise-Induced Bias in Low-Direction Diffusion Tensor MRI: Replication of Monte-Carlo Simulation with In-Vivo Scans,” In Proceedings of ISMRM 2007, 2007.


W.-K. Jeong, P.T. Fletcher, R. Tao, R.T. Whitaker. “Interactive Visualization of Volumetric White Matter Connectivity in DT-MRI Using a Parallel-Hardware Hamilton-Jacobi Solver,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 13, No. 6, pp. 1480--1487. 2007.
PubMed ID: 17968100

2006


 S. Basu, P.T. Fletcher, R.T. Whitaker. “Rician Noise Removal in Diffusion Tensor MRI,” In Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. LNCS 4190, pp. 117--125. October, 2006.


J. Cates, M.D. Meyer, P.T. Fletcher, R.T. Witaker. “Entropy-Based Particle Systems for Shape Correspondence,” In Workshop on Mathematical Foundations of Computational Anatomy, MICCAI 2006, pp. 90--99. October, 2006.