ASSET: A robust algorithm for the automated segmentation and standardization of early Caenorhabditis elegans embryos

Developmental Dynamics

Volumn 239, Issue 12, 2010, Pages 3285-3296

  Blanchoud, Simon ^a   Budirahardja, Yemima ^a,b   Naef, Félix ^a   Gönczy, Pierre ^a  

^a EPFL   (Switzerland)

^b DUKE NUS MEDICAL SCHOOL   (Singapore)

Author keywords

Automation; C. elegans; DIC microscopy; Embryo; Image analysis; Quantification; Segmentation; Standardization

Indexed keywords

ALGORITHM; ARTICLE; AUTOMATION; CAENORHABDITIS ELEGANS; CELL STRUCTURE; CENTROSOME; EGG SHELL; EMBRYO; EMBRYO DEVELOPMENT; INVAGINATION; MICROSCOPY; NONHUMAN; PRIORITY JOURNAL; STANDARDIZATION;

ALGORITHMS; ANIMALS; CAENORHABDITIS ELEGANS; EMBRYO, NONMAMMALIAN; MICROSCOPY, FLUORESCENCE;

CAENORHABDITIS ELEGANS;

EID: 78649705038     PISSN: 10588388     EISSN: 10970177     Source Type: Journal    
DOI: 10.1002/dvdy.22486     Document Type: Article

References (37)

1. Afshar K, Werner ME, Tse YC, Glotzer M, Gönczy P. 2010. Regulation of cortical contractility and spindle positioning by the protein phosphatase 6 PPH-6 in one-cell stage C. elegans embryos. Development (Cambridge, England) 137: 237-247.
2. Baggett D, Nakaya M-a, McAuliffe M, Yamaguchi TP, Lockett S. 2005. Whole cell segmentation in solid tissue sections. Cytometry A 67: 137-143.
3. Bao Z, Murray JI, Boyle T, Ooi SL, Sandel MJ, Waterston RH. 2006. Automated cell lineage tracing in Caenorhabditis elegans. Proc Natl Acad Sci USA 103: 2707-2712.
4. Bellanger JM, Gönczy P. 2003. TAC-1 and ZYG-9 form a complex that promotes microtubule assembly in C. elegans embryos. Curr Biol 13: 1488-1498.
5. Bellman R. 1952. On the theory of dynamic programming. Proc Natl Acad Sci USA 38: 716-719.
6. Bischoff M, Schnabel R. 2006. Global cell sorting is mediated by local cell-cell interactions in the C. elegans embryo. Developmental biology 294: 432-444.
7. Brenner S. 1974. The genetics of Caenorhabditis elegans. Genetics 77: 71.
8. Castro C, Luengo-Oroz Ma, Desnoulez S, Duloquin L, Fernandez-de-Manuel L, Montagna S, Ledesma-Carbayo MJ, Bourgine P, Peyrieras N, Santos a. 2009. An automatic quantification and registration strategy to create a gene expression atlas of zebrafish embryogenesis. Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. 2009: 1469-1472.
9. Chen T, Alzahrani FM. 1997. A real-time edge detector: algorithm and VLSI architecture. Real-Time Imag 3: 363-378.
10. Dijkstra EW. 1959. A note on two problems in connexion with graphs. Numerische Mathematik 1: 269-271.
11. Durbin R, Eddy S, Krogh A, Mitchison G. 1998. Hidden Markov models. In: Biological sequence analysis. Cambridge: Cambridge University Press. p 52-62.
12. Fitzgibbon a, Pilu M, Fisher RB. 1999. Direct least square fitting of ellipses. IEEE Transact Pattern Anal Mach Intell 21: 476-480.
13. Fowlkes CC, Hendriks CLL, Keränen SVE, Weber GH, Rübel O, Huang M-Y, Chatoor S, DePace AH, Simirenko L, Henriquez C, Beaton A, Weiszmann R, Celniker S, Hamann B, Knowles DW, Biggin MD, Eisen MB, Malik J. 2008. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell 133: 364-374.
14. Geng W, Cosman P, Berry CC, Feng Z, Schafer WR. 2004. Automatic tracking, feature extraction and classification of C. elegans phenotypes. IEEE Transact Biomed Eng 51: 1811-1820.
15. Gönczy P. 2008. Mechanisms of asymmetric cell division: flies and worms pave the way. Nature reviews. Mol Cell Biol 9: 355-366.
16. Gönczy P, Schnabel H, Kaletta T, Kaletta T, Amores AD, Hyman T, Amores AD, Hyman AA, Schnabel R. 1999. Dissection of cell division processes in the one cell stage Caenorhabditis elegans embryo by mutational analysis. J Cell Biol 144: 927-946.
17. Goulding MB, Canman JC, Senning EN, Marcus AH, Bowerman B. 2007. Control of nuclear centration in the C. elegans zygote by receptor-independent Galpha signaling and myosin II. J Cell Biol 178: 1177-1191.
18. Halir R, Flusser J. 1998. Numerically stable direct least squares fitting of ellipses. The Sixth International Conference in Central Europe on Computer Graphics and Visualization (WSCG).
19. Hamahashi S, Onami S, Kitano H. 2005. Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking. BMC Bioinform 6: 125.
20. Hansen N, Ostermeier A. 2001. Completely derandomized self-adaptation in evolution strategies. Evol Comput 9: 159-195.
21. Jaensch S, Decker M, Hyman Aa, Myers EW. 2010. Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos. Bioinformatics (Oxford, England) 26: i13-i20.
22. Jaqaman K, Loerke D, Mettlen M, Kuwata H, Grinstein S, Danuser G. 2008. Robust single-particle tracking in live-cell time-lapse sequences. Nature Methods 5: 695-702.
23. Kachur TM, Audhya A, Pilgrim DB. 2008. UNC-45 is required for NMY-2 contractile function in early embryonic polarity establishment and germline cellularization in C. elegans. Dev Biol 314: 287-299.
24. Kass M, Witkin A, Terzopoulos D. 1988. Snakes: active contour models. Int J Comput Vis 1: 321-331.
25. Keller PJ, Schmidt AD, Santella A, Khairy K, Bao Z, Wittbrodt J, Stelzer EHK. 2010. Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nature Methods 7: 637-642.
26. Kennedy J, Eberhart R. 1995. Particle swarm optimization. Proceedings of IEEE International Conference on Neural Networks 4: 1942-1948.
27. Kimura A, Onami S. 2007. Local cortical pulling-force repression switches centrosomal centration and posterior displacement in C. elegans. J Cell Biol 179: 1347-1354.
28. Le Bot N, Tsai MC, Andrews RK, Ahringer J. 2003. TAC-1, a regulator of microtubule length in the C. elegans embryo. Curr Biol 13: 1499-1505.
29. Long F, Peng H, Liu X, Kim SK, Myers E. 2009. A 3D digital atlas of C. elegans and its application to single-cell analyses. Nature Methods 6: 667-672.
30. Ning F, Delhomme D, LeCun Y, Piano F, Bottou L, Barbano PE. 2005. Toward automatic phenotyping of developing embryos from videos. Proc IEEE 14: 1360-1371.
31. Oegema K, Hyman Aa. 2006. Cell division. WormBook: the online review of C. elegans biology. Available at: [Accessed 19 January 2010].
32. OlivoMarin J. 2002. Extraction of spots in biological images using multiscale products. Pattern Recog 35: 1989- 1996.
33. Otsu N. 1975. A threshold selection method from gray-level histograms. Automatica 11: 285-296.
34. Rabiner LR. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. Proc IEEE 77: 257-286.
35. Schnabel R, Priess JR. 1997. Specification of cell fates in the early embryo. In: Riddle DL, Blumenthal T, Meyer BJ, Priess JR. editors C. elegans II. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. p 361-382.
36. Shelton Ca, Bowerman B. 1996. Time-dependent responses to glp-1-mediated inductions in early C. elegans embryos. Development (Cambridge, England) 122: 2043-2050.
37. Srayko M, Quintin S, Schwager A, Hyman AA. 2003. Caenorhabditis elegans TAC-1 and ZYG-9 form a complex that is essential for long astral and spindle microtubules. Curr Biol 13: 1506-1511.