Abstract
The development of high-resolution microscopy makes possible the high-throughput screening of cellular information, such as gene expression at single cell resolution. One of the critical enabling techniques yet to be developed is the automatic recognition or annotation of specific cells in a 3D image stack. In this paper, we present a novel graph-based algorithm, ARC, that determines cell identities in a 3D confocal image of C. elegans based on their highly stereotyped arrangement. This is an essential step in our work on gene expression analysis of C. elegans at the resolution of single cells. Our ARC method integrates both the absolute and relative spatial locations of cells in a C. elegans body. It uses a marker-guided, spatially-constrained, two-stage bipartite matching to find the optimal match between cells in a subject image and cells in 15 template images that have been manually annotated and vetted. We applied ARC to the recognition of cells in 3D confocal images of the first larval stage (L1) of C. elegans hermaphrodites, and achieved an average accuracy of 94.91%.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Riddle, D., Blumenhal, T., Meyer, B., Priess, J.R.: C. Elegans II. Cold Spring Harbor Laboratory Press, New York (1997)
Long, F., Peng, H., Liu, X., Kim, S., Myers, E.W.: A 3D digital cell atlas for the first larval stage of C. elegans hermaphrodite, HHMI JFRC Technical Report (2007), (Also Appear on 2007 Int. Conference of C. elegans)
Peng, H., Long, F., Liu, X., Kim, S., Myers, E.: Straightening C.elegans Images. Bioinformatics 24(2), 234-242 (2008)
Conte, D., Foggia, P., Sansone, C., Vento, M.: Thirty Years of Graph Matching in Pattern Recognition. International Journal of Pattern Recognition and Artificial Intelligence 18(3), 265–298 (2004)
Ullman, J.R.: An Algorithm for Subgraph Isomorphism. J. Assoc. Comput. Mach. 23, 31–42 (1976)
Llados, J., Marti, E., Villanueva, J.J.: Symbol Recognition by Error-Tolerant Sub-Graph Matching Between Region Adjacency Graphs. IEEE Trans. Patt. Anal. Mach. Intell. 23, 1137–1143 (2001)
Gold, S., Rangarajan, A.: A Graduated Assignment Algorithm for Graph Matching. IEEE Trans Patt. Anal. Mach. Intell. 18, 377–388 (1996)
Christmas, W.J., Kittler, J., Petrou, M.: Structural Matching in Computer Vision Using Probabilistic Relaxation. IEEE Trans. Patt. Anal. Mach. Intell. 17(8), 749–764 (1995)
Umeyama, S.: An Eigendecomposition Approach to Weighted Graph Matching Problems. IEEE Trans. Patt. Anal. Mach. Intell. 10, 695–703 (1988)
Wilson, R.C., Hancock, E.R.: Structural Matching by Discrete Relaxation. IEEE Trans. Patt. Anal. Mach. Intell. 19, 634–648 (1997)
Kotropoulos, C., Tefas, A., Pitas, I.: Frontal Face Authentication Using Morphological Elastic Graph Matching. IEEE Trans. Imag. Process. 9, 555–560 (2000)
Chen, H.T., Lin, H., Liu, T.L.: Multi-object Tracking Using Dynamical Graph Matching. In: Proc. 2001 IEEE Computer Soc. Conf. Computer Vision and Pattern Recognition, pp. 210–217 (2001)
Berretti, S., Del Bimbo, A., Vicario, E.: Efficient Matching and Indexing of Graph Models in Content-based Retrieval. IEEE Trans. Patt. Anal. Mach. Intell. 23, 1089–1105 (2001)
Ton, J., Jain, A.K.: Registering Landsat Images by Point Matching. IEEE Trans. Geoscience and Remote Sensing 27(5), 642–651 (1989)
Munkres, J.: Algorithms for the Assignment and Transportation Problems. Journal of the Society of Industrial and Applied Mathematics 5(1), 32–38 (1957)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Long, F., Peng, H., Liu, X., Kim, S., Myers, G. (2008). Automatic Recognition of Cells (ARC) for 3D Images of C. elegans . In: Vingron, M., Wong, L. (eds) Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science(), vol 4955. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-78839-3_12
Download citation
DOI: https://doi.org/10.1007/978-3-540-78839-3_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-78838-6
Online ISBN: 978-3-540-78839-3
eBook Packages: Computer ScienceComputer Science (R0)