Publications
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3D reconstruction of Golgi data: Golgi-stained neuron is reconstructed in 3D. [More images] [More nuggets]
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2010
Yoonsuck Choe, Louise C. Abbott, Giovanna Ponte, John Keyser, Jaerock Kwon, David Mayerich, Daniel Miller, Donghyeop Han, Anna Maria Grimaldi, Graziano Fiorito, David B. Edelman, and Jeffrey L. McKinstry. Charting out the octopus connectome at submicron resolution using the knife-edge scanning microscope. BMC Neuroscience, 11(Suppl 1):P136, 2010. Nineteenth Annual Computational Neuroscience Meeting: CNS*2010.
Huei-Fang Yang and Yoonsuck Choe. Electron microscopy image segmentation with estimated symmetric three-dimensional shape prior. In Proceedings of the 6th International Symposium on Visual Computing, 2010. In press.
Y. Choe, D. Han, P.-S. Huang, J. Keyser, J. Kwon, D. Mayerich, and L. C. Abbott. Complete submicrometer scans of mouse brain microstructure: Neurons and vasculatures. In Neuroscience Meeting Planner, Chicago, IL: Society for Neuroscience, 2009. Program No. 389.10. Online.
2009
Donghyeop Han, Heeyoul Choi, Choonseog Park, and Yoonsuck Choe. Fast and accurate retinal vasculature tracing and kernel-isomap-based feature selection. In Proceedings of the International Joint Conference on Neural Networks, pages 1075-1082, Piscataway, NJ, 2009. IEEE Press. PDF
Donghyeop Han, John Keyser, and Yoonsuck Choe. A local maximum intensity projection tracing of vasculature in Knife-Edge Scanning Microscope volume data. In Proceedings of the IEEE International Symposium on Biomedical Imaging, pages 1259-1262, 2009. PDF
Huei-Fang Yang and Yoonsuck Choe. 3D volume extraction of densely packed cells in EM data stack by forward and backward graph cuts. In Proceedings of the 2009 IEEE Symposium on Computational Intelligence for Multimedia Signal and Vision Processing, pages 47-52, 2009. PDF
Huei-Fang Yang and Yoonsuck Choe. Cell tracking and segmentation in electron microscopy images using graph cuts. In Proceedings of the IEEE International Symposium on Biomedical Imaging, pages 306-309, 2009. PDF
Donghyeop Han. Rapid 3D Tracing of the Mouse Brain Neurovasculature with Local Maximum Intensity Projection and Moving Windows. PhD thesis, Department of Computer Science, Texas A&M University, 2009.
Jae-Rock Kwon. Acquisition and Mining of the Whole Mouse Brain Microstructure. PhD thesis, Department of Computer Science, Texas A&M University, 2009. PDF
Mayerich, D. Imaging and Computational Methods for Exploring Sub-cellular Anatomy Ph.D. Dissertation, May, 2009 (student's dissertation) PDF
2008
D. Mayerich, J. Kwon, Y. Choe, L. Abbott, J. Keyser, Constructing High-Resolution Microvascular Models, Proceedings of the 3rd International Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB 2008). [PDF]
Mayerich, D., Abbott, L., and McCormick, B. H.. Knife-Edge Scanning Microscopy for Imaging and Reconstruction of Three-Dimensional Anatomical Structures of the Mouse Brain. Journal of Microscopy, 231:134–143, 2008. [DOI]
Yoon H. Bai, Choonseog Park, and Yoonsuck Choe. Relative advantage of touch over vision in the exploration of texture. In Proceedings of the 19th International Conference on Pattern Recognition, 2008. In press. [PDF]
Daniel Chern-Yeow Eng and Yoonsuck Choe. Stereo pseudo 3D rendering for web-based display of scientific volumetric data. In Proceedings of the IEEE/EG International Symposium on Volume Graphics, 2008. In press.
Jaerock Kwon, David Mayerich, Yoonsuck Choe, and Bruce H. McCormick. Lateral sectioning for knife-edge scanning microscopy. In Proceedings of the IEEE International Symposium on Biomedical Imaging, 2008. In press. [PDF]
Mayerich, D., Abbott, L., Keyser, J. Visualization of Cellular and Microvessel Relationships IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization), 2008 Condtional acceptance with revisions, To appear [PDF]
Mayerich, D., Keyser, J. Filament Tracking and Encoding for Complex Biological Networks Proceedings of ACM Symposium on Solid and Physical Modeling, pp. 353-358, 2008. (Refereed Short Paper/Poster) [PDF] [Preprint PDF]
2007
Y. Choe, L. C. Abbott, J. Keyser, J. Kwon, D. M. Mayerich, Zeki Melek, and B. H. McCormick. Enhanced microvascular staining and tracing in large volumes of mouse brain tissue. In Neuroscience Meeting Planner, San Diego, CA: Society for Neuroscience, 2007. Program No. 845.14. Online.
D. M. Mayerich, L. C. Abbott, Y. Choe, D. Han, J. Keyser, Zeki Melek, and B. H. McCormick. Efficient methods for tracing and visualization of neural morphology in microscopy image stacks. In Neuroscience Meeting Planner, San Diego, CA: Society for Neuroscience, 2007. Program No. 845.2. Online.
Jyothi S. Guntupalli. Physical sectioning in 3D biological microscopy. Master's thesis, Department of Computer Science, Texas A&M University, 2007. [PDF]
D'Souza, A. Automated Counting of Cell Bodies Using Nissl Stained Cross-Sectional Images M.S. Thesis, December, 2007 (student's thesis) [PDF]
Mayerich, D., Melek, Z., Keyser, J. Fast Filament Tracking Using Graphics Hardware Technical Report tamu-cs-tr-2007-11-3, Department of Computer Science, Texas A&M University [PDF]
David Mayerich, Bruce H. McCormick, and John Keyser, Noise and Artifact Removal in Knife-Edge Scanning Microscopy, In Proceedings of 2007 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Piscataway, NJ: IEEE Press, 2007 [PDF][Preprint PDF]
Wonryull Koh, Neuroanatomical Data Organization for Mammalian Brain Observed at Cellular Level, PhD Dissertation, Department of Computer Science, Texas A&M University, 2007. [PDF]
2006
B. H. McCormick, L. C. Abbott, D. M. Mayerich, , J. Keyser, Jaerock Kwon, Zeki Melek, and Y. Choe. Full-scale submicron neuroanatomy of the mouse brain. In Society for Neuroscience Abstracts. Washington, DC: Society for Neuroscience, 2006. Program No. 694.5. Online.
Bruce H. McCormick, KESM 1.5 Optics and Cameras, Technical Report TR2006-10-1, Department of Computer Science, Texas A&M University, College Station, TX, [PDF]
Zeki Melek, David Mayerich, Cem Yuksel, and John Keyser, Visualization of Fibrous and Thread-like Data, IEEE Transactions on Visualization and Computer Graphics 12:1165-1172, 2006. [PDF]
Hari S. Muddana, Integrated Biomechanical Model of Cells Embedded in Extracellular Matrix, MS Thesis, Department of Computer Science, Texas A&M University, 2006. [PDF]
2005
Aravind Aluri, Stochastic Generation of Biologically Accurate Brain Networks, MS Thesis, Department of Computer Science, Texas A&M University, 2005. [PDF]
Heejin Lim and Yoonsuck Choe. Facilitatory neural activity compensating for neural delays as a potential cause of the flash-lag effect. In Proceedings of the International Joint Conference on Neural Networks, 268-273, 2005. [PDF]
B.H. McCormick, D.M. Mayerich and M. Wiercigroch, Nanomachining for high-resolution scanning of mammalian brain microstructure, Proceedings, 11th International Conference on Fracture -Turin, Italy, March 20-25, 2005
2004
Prathuyusha Aragonda, Strategy for Construction of Polymerized Volume Data Sets, MS thesis, Department of Computer Science, Texas A&M University, 2004. [PDF]
Purna Doddapaneni, Segmentation Strategies for Polymerized Volume Data Sets, MS thesis, Department of Computer Science, Texas A&M University, 2004. [PDF]
B. H. McCormick and D.M. Mayerich, Three-Dimensional Imaging Using Knife-Edge Scanning Microscopy. Proceedings, Microscopy and Micro-analysis Conference 2004, Savannah, GA, August 1-5, 2004 [PDF]
B. H. McCormick, B. Busse, P. Doddapaneni, Z. Melek, and J. Keyser, Compression, Segmentation, and Modeling of Filamentary Volumetric Data, ACM Symposium on Solid Modeling, Genova, Italy, June 9-11, 2004.
B. H. McCormick, Y. Choe, W. Koh, L. C. Abbott, J. Keyser, Z. Melek, P. Doddapaneni, and D. Mayerich. Construction of anatomically correct models of mouse brain networks. Neurocomputing, 58-60:379-386, 2004. [PDF].
Y. Choe and R. Miikkulainen. Contour integration and segmentation in a self-organizing map of spiking neurons. Biological Cybernetics, 90:75-88, 2004. [Reprint: PDF]
Y. Choe. The role of temporal parameters in a thalamocortical model of analogy. IEEE Transactions on Neural Networks, 15:1071-1082, 2004. [Reprint: PDF]
2003
Koh, W. and B.H. McCormick, Specifications for Volume Data Acquisition in Three-Dimensional Light Microscopy, Technical Report TR2003-7-5, Department of Computer Science, Texas A&M University, College Station, TX, 2003. [PDF]
McCormick,
B.H., B. Busse, P. Doddapaneni, Z.
Melek and J. Keyser, Polymerization
Strategy for the Compression, Segmentation, and Modeling of Volumetric Data,
submitted to Pacific Graphics 2003. [PDF]
Stevens, C.B. and D. Mayerich, BTS User Interface, Technical Report, Department of Computer Science, Texas A&M University, College Station, TX, January 24, 2003. [PDF] (Note: This report is updated frequently)
2002
McCormick, B.H., B. Busse, Z. Melek and J. Keyser, Polymerization Strategy for the Compression, Segmentation, and Modeling of Volumetric Data, Technical Report 2002-12-1, Department of Computer Science, Texas A&M University, College Station, TX, December 2002. [PDF]
Koh, W. and B.H. McCormick, Distributed brain microstructure database system: an exoskeleton to 3D reconstruction and modeling, Neurocomputing, 44-46:1099-1105, 2002.
McCormick, B.H., Brain Tissue Scanner enables brain microstructure surveys, Neurocomputing, 44-46:1113-1118, 2002.
McCormick, B.H., Development of the Brain Tissue Scanner, Technical Report, Department of Computer Science, Texas A&M University, College Station, TX, March 18, 2002 [PDF].
2001
Burton, B.P., B.H. McCormick, R. Torp, and J.H. Fallon, Three-dimensional reconstruction of neuronal forests, Neurocomputing, 38-40:1643-1650, 2001.
Koh, W. and B.H. McCormick, Organization and visualization of brain tissue volume data, Neurocomputing, 38-40:1643-1650, 2001.
Lien, J-M., M. Morales, and N.M. Amato, Neuron PRM: A Framework for Constructing Cortical Networks, Technical Report TR01-002, PARASOL LAB, Department of Computer Science, Texas A&M University, October 2001. [PDF]
2000
Koh, W. and B.H. McCormick, Distributed, web-based microstructure
database for brain tissue, Neurocomputing, 32-33: 1065-1071, 2000.
Koh, W., Distributed,
Web-based Microstructure Database for Brain Tissue, MS Thesis, Department
of Computer Science,
McCormick, B.H., R.W. DeVaul, W.R. Shankel, and J.H. Fallon, Modeling neuron spatial distribution and morphology in the developing human cerebral cortex, Neurocomputing, 32-33: 897-904, 2000.
McCormick, B.H., W. Koh, W.R. Shankle, and J.H. Fallon, Geometric modeling of local cortical networks, Neurocomputing, 32-33: 461-469, 2000.
1999
Burton, B. P., Automated
3D Reconstruction of Neuronal Structures from Serial Sections, MS Thesis,
Department of Computer Science, Texas A&M University, 1999. [PDF]
McCormick, B. H.,
Design of a brain tissue scanner, Neurocomputing, 26-27, 1025-1032,
1999.
1998
Batte, D. A., T. S.
Chow, and B. H. McCormick, Finite element decomposition of human neocortex, in
J. M. Bower, Ed,. Computational Neuroscience Trends in Research, Plenum
Press,
Chow, S., Finite
Element Decomposition of the Human Neocortex. MS Thesis, Department of
Computer Science,
Duchowski, Andrew
T., 3D Wavelet Analysis of Eye Movements, Wavelet Applications IV,
Orlando, FL, April, 1998. SPIE.
Duchowski, Andrew
T., Representing Multiple Regions Of Interest with Wavelets, Visual
Communications and Image Processing (VCIP),
Duchowski, Andrew T.
and Bruce H. McCormick, Gaze-Contingent Video Resolution Degradation, Human
Vision and Electronic Imaging III (HVEI), San Jose, CA, January, 1998.
SPIE.
Duchowski, Andrew
T., Incorporating the Viewer's Point-Of-Regard (POR) in Gaze-Contingent Virtual
Environments, Engineering Reality of Virtual Reality,
1997
Batte, D. A., Finite
Element Decomposition and Grid Generation for Brain Modeling and Visualization.
M.S. Thesis, Department of Computer Science,
Batte, D. A. and
B.H. McCormick, Grid Generation for Brain Visualization at the Cellular and
Tissue Level, in J. M. Bower, Ed,. Computational Neuroscience Trends in
Research, Plenum Press,
Duchowski, A. T., Gaze-contingent
Visual Communication, Doctoral Dissertation, Department of Computer
Science,
McCormick, B. H., G.
T. Prusky, and S. Tewari, Stochastic Modeling of the Pyramidal Cell Module, in
J. M. Bower, Ed,. Computational Neuroscience Trends in Research, Plenum
Press,
1996 and beyond
DeVaul, R. W. and B.
H. McCormick, Neuron developmental modeling and structural representation 1.
An introduction to the N++ language, an open stochastic L-system. Technical
Report, Scientific Visualization Laboratory, Department of Computer Science,
McCormick, B. H.,
and R. W. DeVaul, Neuron developmental modeling and structural
representation 2. The stochastic model. Technical Report, Scientific
Visualization Laboratory, Department of Computer Science,
Duchowski Andrew, T.
and Bruce H. McCormick, Modeling visual attention for gaze-contingent video
processing, In Ninth IMDSP Workshop,
Belize City, Belize, March 1996. I EEE.
Tewari, S., Implicit Function Modeling of Neuron Morphology,
M.S. Thesis, Department of Computer Science, Texas A&M University, College
Station, TX, July 1995.
Tewari, S. and B. H.
McCormick, Implicit function modeling of neuron morphology, In Proc. Computational Neuroscience 1995 (CNS*95),
McCormick, B. H. and
K. Mulchandani, A framework for modeling neuron morphology, in Proc. Computational Neuroscience 1995 (CNS*95),
Mulchandani, K., Morphological Modeling of Neurons, M.S.
Thesis, Department of Computer Science, Texas A&M University, College
Station, TX, May 1995. [Postscript]
Duchowski, Andrew,
T. and Bruce H. McCormick, Simple multiresolution approach for representing
multiple Regions of Interest (ROIs), In Conference
on Visual Communications and Image Processing, Taipei, Taiwan, May
1995. SPIE.
Duchowski, Andrew
T., Bruce H. McCormick, Pre-attentive considerations for gaze-contingent image
processing. In Conference on Human Vision,
Visual Processing, and Digital Display VI,
McCormick, B. H. and
K. Mulchandani, L-system modeling of neurons. In Proc. Visualization in Biomedical Computing, SPIE Vol. 2359,
pp. 693-705, 1994.
Guan, S. Y. and B.
H. McCormick, Atlas-based brain image segmentation, Electronic Imaging Conference,
Guan, S. Y. Guided Image Interpretation in Neuroanatomy.
Ph.D. thesis, Department of Computer Science,
Guan, S. Y. and B.
H. McCormick, Homology mapping between atlas and a biological section, In Proc. of Vision Interface '91, Calgary,
AB, pp. 154-161, June, 1991.
Guan, S. Y. and B.
H. McCormick, Design for a 3D deformable brain atlas, In Proc. of the 4th IEEE Symposium on Computer-Based
Medical Systems, Baltimore, MD, pp. 113-120, May 12-14, 1991.
Guan, S. Y. and B.
H. McCormick, Guided image interpretation in neuroanatomy. In Proc. Conference on Visualization in Biomedical
Computing,
Liaw, J-S and B. H.
McCormick, Visualization environment for editing and modeling volumetric data,
In Proceedings of the First Conference on
Visualization and Biomedical Computing, Atlanta, GA, pp. 467-476,
May 1990.
DeFanti, T. A., M.
D. Brown, and B. H. McCormick, Visualization: Expanding scientific and
engineering research opportunities, in Visualization
in Scientific Computing, G. M. Nielson and B. Shriver (eds.), and
L. J. Rosenblum (assoc. ed.), IEE E Computer Society Press,
McCormick, B. H.,
Advanced Visualization Environments: Knowledge-based image modeling, in Visualization in Supercomputing, R.
Mendez (ed.),
McCormick, B. H.,
Issues in scientific visualization, in Supercomputing,
J. S. Kowalik (ed.), NATO ASI Series, Berlin/New York: Springer-Verlag, pp.
205-224, 1989.
DeFanti, T. A., M.
D. Brown and B. H. McCormick, Visualization: Expanding scientific and
engineering opportunities, IEEE Computer,
22(8), pp. 12-25, 1989.
McCormick, B. H., T.
A. DeFanti and M. D. Brown, Visualization in scientific computing--A synopsis, IEEE Computer Graphics and Applications,
7(7), pp. 61-70, 1987.
McCormick, B. H., T.
A. DeFanti, and M. D. Brown (eds.), Visualization in scientific computing, Computer Graphics, 21(6) (entire issue),
November 1987.
McCormick, B. H., T.
A. DeFanti and M. D. Brown (eds.), Visualization in scientific computing, SIGGRAPH Video Review, Issues 28-29
(two-hour video tape), 1987.
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updated by Wonryull Koh on August 7, 2003
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