Similarity analysis of cell movements in video microscopy

IEEE Symposium on Biological Data Visualization 2012, BioVis 2012 - Proceedings

Volumn , Issue , 2012, Pages 69-76

  Fangerau, Jens ^a   Höckendorf, Burkhard ^a   Wittbrodt, Joachim ^a   Leitte, Heike ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

Computer Graphics I.3.6 : Methodology Techniques Interaction techniques; Pattern Recognition I.5.3 : Clustering Similarity measures

Indexed keywords

2D PROJECTIONS; CELL DIVISIONS; CELL MIGRATION; CELL MOVEMENT; CLUSTER ALGORITHMS; COMPUTATIONAL TECHNIQUE; DATA SETS; INDIVIDUAL CELLS; INTERACTION TECHNIQUES; LIVING ORGANISMS; REAL DATA SETS; SIMILAR PATTERN; SIMILARITY ANALYSIS; SIMILARITY MEASURE; VIDEO MICROSCOPY; ZEBRAFISH;

ALGORITHMS; CELL PROLIFERATION; CYTOLOGY; DATA VISUALIZATION; PATTERN RECOGNITION; THREE DIMENSIONAL COMPUTER GRAPHICS;

CELLS;

EID: 84872222024     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BioVis.2012.6378595     Document Type: Conference Paper

References (33)

1. R. Agrawal, C. Faloutsos, and A. Swami. Efficient similarity search in sequence databases. In Proceedings of the 4th International Conference on Foundations of Data Organization and Algorithms, pages 69-84, London, UK, 1993. Springer Verlag.
2. H. Alt. The computational geometry of comparing shapes. In S. Albers, H. Alt, and S. Naher, editors, Efficient Algorithms, pages 235-248. Springer Verlag, Berlin Heidelberg, 2009.
3. H. Alt and M. Godau. Computing the frechct distance between two polygonal curves. International Journal of Computational Geometry and Applications, 5:75-91, 1995.
4. H. Alt and L. J. Guibas. Discrete geometric shapes: Matching, interpolation, and approximation. In Handbook of Computational Geometry, pages 121-153. Elsevier S. P. B.V. North-Holland, 2000.
5. D. J. Berndt and J. Clifford. Using dynamic time warping to find patterns in time series. In AAAI Workshop on Knowledge Proceedings of KDD-94, pages 359-370, Seattle, Washington, July 1994.
6. T. J. Boyle, Z. Bao, J. I. Murray, C. L. Araya, and R. H. Waterston. AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. BMC Bioinformatics. 7(275), 2006.
7. A. Cedilnik, J. Baumes, L. Ibanez, S. Megason, and B. Wylie. Integration of information and volume visualization for analysis of cell lineage and gene expression during embryogenesis. In Proceedings of SPIE, volume 6809, 2007.
8. L. Chen, M. T. Özsu, and V. Oria. Robust and fast similarity search for moving object trajectories. In In SIGMOD, pages 491-502, 2005.
9. H. Ding, G. Trajcevski, P. Scheuermann, X. Wang, and E. Keogh. Querying and mining of time series data: experimental comparison of representations and distance measures. Proc. VLDB Endow., 1(2):1542-1552, August 2008.
10. S. Dodge. Exploring Movement Using Similarity Analysis. PhD thesis, University of zurich, 2011.
11. T. Eiter and H. Mannila. Computing discrete frechct distance. Technical report, Technische Universitat Wien, 1994.
12. M. T. Goodrich, J. S. B. Mitchell, and M. W. Orletsky. Approximate geometric pattern matching under rigid motions. PAMI, IEEE Transactions, 21(4):371-379, April 1999.
13. T. H. Group. Hierarchical data format version 5. http://www.hdfgroup.org/ HDF5, 2000-2010.
14. J. Huisken, J. Swoger, D. F, J. Wittbrodt, and E. Stelzer. Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science, 305(5686):1007-1009, 2004.
15. G. F. Jenks. Geographic logic in line generalization. Cartographica: The Int. J.for Geograph. Info. and Geovis., 26(1):27-42, 1989.
16. J. Joe H. Ward. Hierarchical grouping to optimize an objective function. J. of the American Statistical Association, 58:236-244, 1963.
17. T. Jones, I. Kang, D. Wheeler, R. Lindquist, A. Papallo, D. Sabatini, P. Golland, and A. Carpenter. Cellprofiler analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics, 9(1):482, 2008.
18. D. F. Keefe, M. Ewert, W. Ribarsky, and R. Chang. Interactive coordinated multiple-view visualization of biomechanical motion data. IEEE Transactions on Visualization and Computer Graphics (IEEE Visualization 2009), 15:1383-1390, 2009.
19. P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science, 322(5904):1065-1069, 2008.
20. K. Khairy and P. J. Keller. Reconstructing embryonic development. Genesis, 49(7):488-513, July 2011.
21. S. Kotsiantis and P. Pintelas. Recent advances in clustering: A brief survey. WSEAS Transactions on Information Science and Applications, 1:73-81, 2004.
22. G. N. Lance and W. T. Williams. A general theory of classificatory sorting strategies 1. hierarchical systems. The Computer Journal, 9(4):373-380, 1967.
23. H. Leitte, J. Fangerau, X. Lou, B. Hockendorf, S. Lemke, A. Maizel, and J. Wittbrodt. Visualization software for 3d video microscopy: A design study. In Eurographics Conference on Visualization (EuroVis Short Papers), 2012.
24. X. Lou, F. O. Kaster, M. S. Lindner, B. X. Kausler, U. Kothe, B. Hockendorf, J. Wittbrodt, H. Janicke, and F. A. Hamprecht. Deltr: Digital embryo lineage tree reconstructor. In Biomedical Imaging: From Nano to Macro, pages 1557-1560. IEEE, April 2011.
25. S. D. Martinelli, C. G. Brown, and R. Durbin. Gene expression and development databases for C. elegans. Seminars in Cell and Developmental Biology, 8(5):459-467, -1997.
26. S. I. O'Donoghue, A.-C. C. Gavin, N. Gehlenborg, D. S. Goodsell, J.-K. K. Heriche, C. B. Nielsen, C. North, A. J. Olson, J. B. Procter, D. W. Shattuck, T. Walter, and B. Wong. Visualizing biological data-now and in the future. Nature methods, 7(3 Suppl):S2-S4, 2010.
27. N. Olivier, M. A. Luengo-Oroz, L. Duloquin, E. Faure, T. Savy, I. Veilleux, X. Solinas, D. Debarre, P. Bourgine, A. Santos, N. Peyriéras, and E. Beaurepaire. Cell lineage reconstruction of early zebrafish embryos using label-free nonlinear microscopy. Science, 329(5994):967-971, August 2010.
28. N. Pelekis, I. Kopanakis, G. Marketos, I. Ntoutsi, G. Andrienko, and Y. Theodoridis. Similarity search in trajectory databases. In Proceedings of the 14th Int. Symp. on Temp. Repres. and Reas., pages 129-140, Washington, DC, USA, 2007. IEEE Computer Society.
29. H. Pengo Bioimage informatics: a new area of engineering biology. Bioinformatics. 24(17):1827-1836, September 2008.
30. R. Schnabel, H. Hutter, D. Moerman, and H. Schnabel. Assessing normal embryogenesis in Caenorhabditis elegans using a 4d microscope: Variability of development and regional specification. Developmental Biology, 184(2):234-265, 1997.
31. M. Vlachos, G. Kollios, and D. Gunopulos. Discovering similar multidimensional trajectories. In Proceedings of the 18th International Conference on Data Engineering, ICDE '02, pages 673-684, Washington, DC, USA, 2002. IEEE Computer Society.
32. T. Walter, D. Shattuck, R. Baldock, M. Bastin, A. Carpenter, S. Duce, J. Ellenberg, A. Fraser, N. Hamilton, S. Pieper, M. Ragan, J. Schneider' P. Tomancak, and J.-K. Heriche. Visualization of image data from cells to organisms. Nature methods, 7(3):S26-S41, 2010.
33. R. Xu and D. W. II. Survey of clustering algorithms. Neural Networks, IEEE Transactions on, 16(3):645-678, May 2005.