Publications related to KESM Brain Atlas and Data (selected):

• In reverse chronological order.

1. Miller, D. E., Shah, R., Zhang, W., Yoo, J., Kwon, J., Mayerich, D., Keyser, J., Abbott, L. C., and Choe, Y. (2016). Fast submicrometer-scale imaging of whole zebrafish using the knife-edge scanning microscope. In Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. In press.

2. Choe, Y., Mayerich, D., Kwon, J., Miller, D. E., Chung, J. R., Sung, C., Keyser, J., and Abbott, L. C. (2011). Knife-edge scanning microscopy for connectomics research. In Proceedings of the International Joint Conference on Neural Networks, 2258–2265. Piscataway, NJ: IEEE Press.

3. Chung, J. R., Sung, C., Mayerich, D., Kwon, J., Miller, D. E., Huffman, T., Abbott, L. C., Keyser, J., and Choe, Y. (2011). Multiscale exploration of mouse brain microstructures using the knife-edge scanning microscope brain atlas. Frontiers in Neuroinformatics, 5:29.

4. Mayerich, D., Kwon, J., Sung, C., Abbott, L. C., Keyser, J., and Choe, Y. (2011). Fast macro-scale transmission imaging of microvascular networks using KESM. Biomedical Optics Express, 2:2888–2896.

5. Sung, C., Chung, J. R., Mayerich, D., Kwon, J., Miller, D. E., Huffman, T., Keyser, J., Abbott, L. C., and Choe, Y. (2011). Knife-edge scanning microscope brain atlas: A submicrometer-resolution web-based mouse brain atlas. In Neuroscience Meeting Planner, Washington, DC: Society for Neuroscience. Program No. 328.05. Online.

6. Choe, Y., Abbott, L. C., Miller, D. E., Han, D., Yang, H.-F., Chung, J. R., Sung, C., Mayerich, D., Kwon, J., Micheva, K., and Smith, S. J. (2010). Multiscale imaging, analysis, and integration of mouse brain networks. In Neuroscience Meeting Planner, San Diego, CA: Society for Neuroscience. Program No. 516.3. Online.

7. Choe, Y., Abbott, L. C., Han, D., Huang, P.-S., Keyser, J., Kwon, J., Mayerich, D., Melek, Z., and McCormick, B. H. (2009a). Knife-edge scanning microscopy: High-throughput imaging and analysis of massive volumes of biological microstructures. In Rao, A. R., and Cecchi, G., editors, High-Throughput Image Reconstruction and Analysis: Intelligent Microscopy Applications, 11–37. Boston, MA: Artech House.

8. Choe, Y., Han, D., Huang, P.-S., Keyser, J., Kwon, J., Mayerich, D., and Abbott, L. C. (2009b). Complete submicrometer scans of mouse brain microstructure: Neurons and vasculatures. In Neuroscience Meeting Planner, Chicago, IL: Society for Neuroscience. Program No. 389.10. Online.

9. Eng, D. C.-Y., and Choe, Y. (2008). Stereo pseudo 3D rendering for web-based display of scientific volumetric data. In Proceedings of the IEEE/EG International Symposium on Volume Graphics.

Total of 9 entries.

Publications related to KESM (selected):

1. Lim, S., Nowak, M., and Choe, Y. (2016). Automated neurovascular tracing and analysis of the knife-edge scanning microscope rat nissl data set using a computing cluster. In Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. In press.

2. Miller, D. E., Shah, R., Zhang, W., Yoo, J., Kwon, J., Mayerich, D., Keyser, J., Abbott, L. C., and Choe, Y. (2016). Fast submicrometer-scale imaging of whole zebrafish using the knife-edge scanning microscope. In Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. In press.

3. Nowak, M., and Choe, Y. (2016). Learning to distinguish cerebral vasculature data from mechanical chatter in india-ink images acquired using knife-edge scanning microscopy. In Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. In press.

4. Nowak, M., Lozovskiy, A., Dobroskok, D., and Choe, Y. (2016). Knife-edge scanning microscopy for in silico study of cerebral blood flow: from biological imaging data to flow simulations. In Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. In press.

5. Choe, Y. (2015a). Brain atlases. In Jaeger, D., and Jung, R., editors, Encyclopedia of Computational Neuroscience, 434. New York: Springer. First edition.

6. Choe, Y. (2015b). Computational neuroanatomy: Overview. In Jaeger, D., and Jung, R., editors, Encyclopedia of Computational Neuroscience, 24–26. New York: Springer. First edition.

7. Choe, Y. (2015c). Connectome, general. In Jaeger, D., and Jung, R., editors, Encyclopedia of Computational Neuroscience, 798–806. New York: Springer. First edition.

8. Choe, Y. (2015d). Physical sectioning microscopy. In Jaeger, D., and Jung, R., editors, Encyclopedia of Computational Neuroscience, 2376–2379. New York: Springer. First edition.

9. Choe, Y., Kwon, J., Mayerich, D., and Abbott, L. C. (2015). Connectome, mouse. In Jaeger, D., and Jung, R., editors, Encyclopedia of Computational Neuroscience, 807–810. New York: Springer. First edition.

10. Lal Das, S., Keyser, J., and Choe, Y. (2015). Random-forest-based automated cell detection in knife-edge scanning microscope rat nissl data. In Proceedings of the International Joint Conference on Neural Networks. DOI: 10.1109/IJCNN.2015.7280852.

11. Mayerich, D., Choe, Y., and Keyser, J. (2015). Reconstruction, techniques and validation. In Jaeger, D., and Jung, R., editors, Encyclopedia of Computational Neuroscience, 2591–2593. New York: Springer. First edition.

12. Zhang, W., Yoo, J., Keyser, J., Abbott, L. C., and Choe, Y. (2015). Real-time detection of imaging errors in the knife-edge scanning microscope through change detection. In Proceedings of the 2015 IEEE 12th International Symposium on Biomedical Imaging, 177–181.

13. Sung, C., Woo, J., Goodman, M., Huffman, T., and Choe, Y. (2013). biblinkScalable, incremental learning with MapReduce parallelization for cell detection in high-resolution 3D microscopy data http://faculty.cs.tamu.edu/choe/ftp/publications/sung-ijcnn13.pdf. In Proceedings of the International Joint Conference on Neural Networks, 434–440.

14. Choe, Y., Mayerich, D., Kwon, J., Miller, D. E., Chung, J. R., Sung, C., Keyser, J., and Abbott, L. C. (2011a). Knife-edge scanning microscopy for connectomics research. In Proceedings of the International Joint Conference on Neural Networks, 2258–2265. Piscataway, NJ: IEEE Press.

15. Choe, Y., Mayerich, D., Kwon, J., Miller, D. E., Sung, C., Chung, J. R., Huffman, T., Keyser, J., and Abbott, L. C. (2011b). Specimen preparation, imaging, and analysis protocols for knife-edge scanning microscopy. Journal of Visualized Experiments, 58:e3248. Doi: 10.3791/3248.

16. Choe, Y., Abbott, L. C., Han, D., Huang, P.-S., Keyser, J., Kwon, J., Mayerich, D., Melek, Z., and McCormick, B. H. (2009). Knife-edge scanning microscopy: High-throughput imaging and analysis of massive volumes of biological microstructures. In Rao, A. R., and Cecchi, G., editors, High-Throughput Image Reconstruction and Analysis: Intelligent Microscopy Applications, 11–37. Boston, MA: Artech House.

17. Mayerich, D., and Keyser, J. (2009). Hardware accelerated segmentation of complex volumetric filament networks. IEEE Transactions on Visualization and Computer Graphics, 15:670–681.

18. Mayerich, D., Abbott, L. C., and Keyser, J. (2008a). Visualization of cellular and microvessel relationship. IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization), 14:1611–1618.

19. Mayerich, D., Abbott, L. C., and McCormick, B. H. (2008b). Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain. Journal of Microscopy, 231:134–143.

20. McCormick, B. H., Abbott, L. C., Mayerich, D., Keyser, J., Kwon, J., and Choe, Y. (2007). Concurrent serial sectioning and microimaging of whole small animal brain at submicron resolution. In CSHL Meeting Abstracts, March 22-25, 2007: Imaging Neurons & Neural Activity: New Methods, New Results.

21. McCormick, B. H. (2006). KESM 1.5 optics and cameras. Technical Report TR2006-10-1, Department of Computer Science, Texas A&M University, College Station, TX.

22. McCormick, B. H., Busse, B. L., Mayerich, D. M., Abbott, L. C., Choe, Y., Keyser, J., Smith, S. J., and Denk, W. (2005a). Biologically accurate modeling of mouse brain requires biologically accurate networks. Microscopy and Microanalysis, 11 (Supplement 2):66–67.

23. McCormick, B. H., Mayerich, D. M., Busse, B. L., Melek, Z., Koh, W., Abbott, L. C., Choe, Y., and Kim, E.-J. (2005b). The whole mouse brain: The spatial distribution and morphology of its neurons. Microscopy and Microanalysis, 11 (Supplement 2):640–641.

24. McCormick, B. H. (2004). System and method for imaging an object. USPTO patent #US 6,744,572 (for Knife-Edge Scanning; 13 claims).

25. McCormick, B. H., Choe, Y., Koh, W., Abbott, L. C., Keyser, J., Melek, Z., Doddapaneni, P., and Mayerich, D. (2004). Construction of anatomically correct models of mouse brain networks. Neurocomputing, 58–60:379–386.

26. McCormick, B. H., and Mayerich, D. M. (2004). Three-dimensional imaging using Knife-Edge Scanning Microscope. Microscopy and Microanalysis, 10 (Suppl. 2):1466–1467.

27. McCormick, B. H. (2003). The knife-edge scanning microscope. Technical report, Department of Computer Science, Texas A&M University. http://research.cs.tamu.edu/bnl/.

28. McCormick, B. H. (2002). Development of the brain tissue scanner. Technical report, Department of Computer Science, Texas A&M University.

29. McCormick, B. H. (1999). Design of a brain tissue scanner. Neurocomputing, 26–27:1025–1032.

30. McCormick, B. H., DeFanti, T. A., and Brown, M. D. (1987). Scientific and engineering research opportunities: Visualization in scientific computing. ACM SIGGRAPH Computer Graphics, 21:A–1–A–17.

Total of 30 entries.