A semi-local neighborhood-based framework for probabilistic cell lineage tracing

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Santella, Anthony ^a   Du, Zhuo ^a   Bao, Zhirong ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

Cell tracking; Developmental biology; Image processing; In vivo; Microscopy

Indexed keywords

BIFURCATION (MATHEMATICS); CELL PROLIFERATION; CYTOLOGY; ERRORS; GLOBAL OPTIMIZATION; IMAGE PROCESSING; MICROSCOPIC EXAMINATION;

CAENORHABDITIS ELEGANS; CELL TRACKING; COMPUTATIONAL EXPENSE; COMPUTATIONAL FRAMEWORK; DEVELOPMENTAL BIOLOGY; FLUORESCENCE LABELING; IN-VIVO; THREE-DIMENSIONAL ENVIRONMENT;

CELLS;

CAENORHABDITIS ELEGANS;

ANIMAL; ARTICLE; BAYES THEOREM; CAENORHABDITIS ELEGANS; CELL LINEAGE; CYTOLOGY; PRENATAL DEVELOPMENT; PROBABILITY;

ANIMALS; BAYES THEOREM; CAENORHABDITIS ELEGANS; CELL LINEAGE; PROBABILITY;

EID: 84902930332     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-217     Document Type: Article

References (25)

1. Bischoff M, Parfitt DE, Zernicka-Goetz M. Formation of the embryonic-abembryonic axis of the mouse blastocyst: relationships between orientation of early cleavage divisions and pattern of symmetric/asymmetric divisions. Development 2008, 135(5):953-962.
2. Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EH. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 2008, 322(5904):1065-1069.
3. Bao Z, Murray JI, Boyle T, Ooi SL, Sandel MJ, Waterston RH. Automated cell lineage tracing in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2006, 103(8):2707-2712.
4. Tomer R, Khairy K, Amat F, Keller PJ. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat Methods 2012, 9(7):755-763.
5. Krzic U, Gunther S, Saunders TE, Streichan SJ, Hufnagel L. Multiview light-sheet microscope for rapid in toto imaging. Nat Methods 2012, 9(7):730-733.
6. Truong TV, Supatto W, Koos DS, Choi JM, Fraser SE. Deep and fast live imaging with two-photon scanned light-sheet microscopy. Nat Methods 2011, 8(9):757-760.
7. Du Z, Santella A, He F, Tiongson M, Bao Z. De novo inference of systems-level mechanistic models of development from live-imaging-based phenotype analysis. Cell 2014, 156(1-2):359-372.
8. Kamentsky L, Jones TR, Fraser A, Bray MA, Logan DJ, Madden KL, Ljosa V, Rueden C, Eliceiri KW, Carpenter AE. Improved structure, function and compatibility for Cell Profiler: modular high-throughput image analysis software. Bioinformatics 2011, 27(8):1179-1180.
9. Al-Kofahi O, Radke RJ, Goderie SK, Shen Q, Temple S, Roysam B. Automated cell lineage construction: a rapid method to analyze clonal development established with murine neural progenitor cells. Cell Cycle 2006, 5(3):327-335.
10. Chen Y, Ladi E, Herzmark P, Robey E, Roysam B. Automated 5-D analysis of cell migration and interaction in the thymic cortex from time-lapse sequences of 3-D multi-channel multi-photon images. J Immunol Methods 2009, 340(1):65-80.
11. Jaqaman K, Loerke D, Mettlen M, Kuwata H, Grinstein S, Schmid SL, Danuser G. Robust single-particle tracking in live-cell time-lapse sequences. Nat Methods 2008, 5(8):695-702.
12. Jaensch S, Decker M, Hyman AA, Myers EW. Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos. Bioinformatics 2010, 26(12):i13-i20.
13. Lou X, Hamprecht FA. Structured Learning for Cell Tracking. NIPS 2011, 1296-1304.
14. Yang B, Chang H, Ram N. Learning affinities and dependencies for multi-target tracking using a CRF model. Computer Vision and Pattern Recognition (CVPR) 2011, 1233-1240.
15. Dzyubachyk O, Jelier R, Lehner B, Niessen W, Meijering E. Model-based approach for tracking embryogenesis in Caenorhabditis elegans fluorescence microscopy data. Conf Proc IEEE Eng Med Biol Soc 2009, 1:5356-5359.
16. Dufour A, Shinin V, Tajbakhsh S, Guillen-Aghion N, Olivo-Marin JC, Zimmer C. Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces. IEEE Trans Image Process 2005, 14(9):1396-1410.
17. Li K, Miller ED, Chen M, Kanade T, Weiss LE, Campbell PG. Cell population tracking and lineage construction with spatiotemporal context. Med Image Anal 2008, 12(5):546-566.
18. Smal I, Draegestein K, Galjart N, Niessen W, Meijering E. Rao-Blackwellized marginal particle filtering for multiple object tracking in molecular bioimaging. Inf Process Med Imaging 2007, 20:110-121.
19. Isard M, Blake A. CONDENSATION - Conditional density propagation for visual tracking. Int J Comput Vision 1998, 29(1):5-28.
20. Mace DL, Weisdepp P, Gevirtzman L, Boyle T, Waterston RH. A high-fidelity cell lineage tracing method for obtaining systematic spatiotemporal gene expression patterns in Caenorhabditis elegans. G3 (Bethesda) 2013, 3(5):851-863.
21. Amat F, Myers EW, Keller PJ. Fast and robust optical flow for time-lapse microscopy using super-voxels. Bioinformatics 2013, 29(3):373-380.
22. Santella A, Du Z, Nowotschin S, Hadjantonakis AK, Bao Z. A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D. BMC Bioinformatics 2010, 11:580.
23. Giurumescu CA, Kang S, Planchon TA, Betzig E, Bloomekatz J, Yelon D, Cosman P, Chisholm AD. Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos. Development 2012, 139(22):4271-4279.
24. Aydin Z, Murray JI, Waterston RH, Noble WS. Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo. BMC Bioinformatics 2010, 11:84.
25. Caruana R, Niculescu-Mizil A. An empirical comparison of supervised learning algorithms. Proceedings of the 23rd international conference on Machine learning; Pittsburgh, Pennsylvania 2006, 161-168. 1143865: ACM.