Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos

Developmental Cell

Volumn 36, Issue 2, 2016, Pages 225-240

  Stegmaier, Johannes ^a,b   Amat, Fernando ^a   Lemon, William C ^a   McDole, Katie ^a   Wan, Yinan ^a   Teodoro, George ^c   Mikut, Ralf ^b   Keller, Philipp J ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^c UNIVERSITY OF BRASILIA   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ANIMAL EXPERIMENT; ANISOTROPY; ARTICLE; AUTOANALYSIS; CELL LINEAGE; CELL SHAPE; CELL STRUCTURE; CELL TRACKING; CONFOCAL MICROSCOPE; CONFOCAL MICROSCOPY; DROSOPHILA; EMBRYO; EMBRYO DEVELOPMENT; EMBRYO SEGMENTATION; FEMALE; GENERAL DEVICE; MALE; MOUSE; MOUSE EMBRYO; NONHUMAN; PRIORITY JOURNAL; REAL TIME ACCURATE CELL SHAPE EXTRACTOR; THREE DIMENSIONAL IMAGING; ZEBRA FISH; ALGORITHM; ANIMAL; COMPUTER PROGRAM; FLUORESCENCE MICROSCOPY; PHYSIOLOGY; PROCEDURES;

ALGORITHMS; ANIMALS; CELL SHAPE; CELL TRACKING; DROSOPHILA; EMBRYONIC DEVELOPMENT; IMAGING, THREE-DIMENSIONAL; MICE; MICROSCOPY, FLUORESCENCE; SOFTWARE; ZEBRAFISH;

EID: 84975726385     PISSN: 15345807     EISSN: 18781551     Source Type: Journal    
DOI: 10.1016/j.devcel.2015.12.028     Document Type: Article

References (32)

1. Amat F., Lemon W., Mossing D.P., McDole K., Wan Y., Branson K., Myers E.W., Keller P.J. Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data. Nat. Methods 2014, 11:951-958.
2. Amat F., Hockendorf B., Wan Y., Lemon W.C., McDole K., Keller P.J. Efficient processing and analysis of large-scale light-sheet microscopy data. Nat. Protoc. 2015, 10:1679-1696.
3. Antiga L. Generalizing vesselness with respect to dimensionality and shape. Insight J. 2007, 3. http://hdl.handle.net/1926/576.
4. Blankenship J.T., Wieschaus E. Two new roles for the Drosophila AP patterning system in early morphogenesis. Development 2001, 128:5129-5138.
5. Bosveld F., Bonnet I., Guirao B., Tlili S., Wang Z., Petitalot A., Marchand R., Bardet P.L., Marcq P., Graner F., et al. Mechanical control of morphogenesis by Fat/Dachsous/Four-jointed planar cell polarity pathway. Science 2012, 336:724-727.
6. Cardona A., Saalfeld S., Schindelin J., Arganda-Carreras I., Preibisch S., Longair M., Tomancak P., Hartenstein V., Douglas R.J. TrakEM2 software for neural circuit reconstruction. PLoS One 2012, 7:e38011.
7. Chhetri R.K., Amat F., Wan Y., Hockendorf B., Lemon W.C., Keller P.J. Whole-animal functional and developmental imaging with isotropic spatial resolution. Nat. Methods 2015, 12:1171-1178.
8. Coelho L.P., Shariff A., Murphy R.F. Nuclear segmentation in microscope cell images: a hand-segmented dataset and comparison of algorithms. IEEE International Symposium on Biomedical Imaging: from Nano to Macro (ISBI) 2009, 518-521. IEEE.
9. Fernandez R., Das P., Mirabet V., Moscardi E., Traas J., Verdeil J.L., Malandain G., Godin C. Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nat. Methods 2010, 7:547-553.
10. Frangi A.F., Niessen W.J., Vincken K.L., Viergever M.A. Multiscale vessel enhancement filtering. Medical Image Computing and Computer-Assisted Interventions (MICCAI) 1998, 130-137. Springer.
11. Funke J., Andres B., Hamprecht F.A., Cardona A., Cook M. Efficient automatic 3D-reconstruction of branching neurons from EM data. IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 2012, 1004-1011. IEEE.
12. He B., Doubrovinski K., Polyakov O., Wieschaus E. Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation. Nature 2014, 508:392-396.
13. Keller P.J. Imaging morphogenesis: technological advances and biological insights. Science 2013, 340:1234168.
14. Khan Z., Wang Y.C., Wieschaus E.F., Kaschube M. Quantitative 4D analyses of epithelial folding during Drosophila gastrulation. Development 2014, 141:2895-2900.
15. Lecuit T., Le Goff L. Orchestrating size and shape during morphogenesis. Nature 2007, 450:189-192.
16. Liu T., Jones C., Seyedhosseini M., Tasdizen T. A modular hierarchical approach to 3D electron microscopy image segmentation. J. Neurosci. Methods 2014, 226:88-102.
17. Maurer C.R., Qi R., Raghavan V. A linear time algorithm for computing exact Euclidean distance transforms of binary images in arbitrary dimensions. IEEE Trans. Pattern Anal. Mach. Intell. 2003, 25:265-270.
18. Mosaliganti K.R., Noche R.R., Xiong F., Swinburne I.A., Megason S.G. ACME: automated cell morphology extractor for comprehensive reconstruction of cell membranes. PLoS Comp. Biol. 2012, 8:e1002780.
19. Nüsslein-Volhard C., Frohnhofer H.G., Lehmann R. Determination of anteroposterior polarity in Drosophila. Science 1987, 238:1675-1681.
20. Oates A.C., Gorfinkiel N., Gonzalez-Gaitan M., Heisenberg C.P. Quantitative approaches in developmental biology. Nat. Rev. Genet. 2009, 10:517-530.
21. Osterfield M., Du X., Schupbach T., Wieschaus E., Shvartsman S.Y. Three-dimensional epithelial morphogenesis in the developing Drosophila egg. Dev. Cell 2013, 24:400-410.
22. Pantazis P., Supatto W. Advances in whole-embryo imaging: a quantitative transition is underway. Nat. Rev. Mol. Cell Biol. 2014, 15:327-339.
23. Pare A.C., Vichas A., Fincher C.T., Mirman Z., Farrell D.L., Mainieri A., Zallen J.A. A positional Toll receptor code directs convergent extension in Drosophila. Nature 2014, 515:523-527.
24. Saalfeld S., Cardona A., Hartenstein V., Tomančák P. CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics 2009, 25:1984-1986.
25. Stegmaier J., Otte J.C., Kobitski A., Bartschat A., Garcia A., Nienhaus G.U., Strähle U., Mikut R. Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks. PLoS One 2014, 9:e90036.
26. Sweeton D., Parks S., Costa M., Wieschaus E. Gastrulation in Drosophila: the formation of the ventral furrow and posterior midgut invaginations. Development 1991, 112:775-789.
27. Tamada M., Farrell D.L., Zallen J.A. Abl regulates planar polarized junctional dynamics through beta-catenin tyrosine phosphorylation. Dev. Cell 2012, 22:309-319.
28. Teodoro G., Pan T., Kurc T.M., Kong J., Cooper L.A., Podhorszki N., Klasky S., Saltz J.H. High-throughput analysis of large microscopy image datasets on CPU-GPU cluster platforms. IPDPS 2013, 2013:103-114.
29. Tomer R., Khairy K., Amat F., Keller P.J. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat. Methods 2012, 9:755-763.
30. Trichas G., Begbie J., Srinivas S. Use of the viral 2A peptide for bicistronic expression in transgenic mice. BMC Biol. 2008, 6:40.
31. Vachier C., Meyer F. The viscous watershed transform. J. Math. Imaging Vis. 2005, 22:251-267.
32. Wang Y.C., Khan Z., Kaschube M., Wieschaus E.F. Differential positioning of adherens junctions is associated with initiation of epithelial folding. Nature 2012, 484:390-393.