Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy
10.1038/nmeth.2062
Crossref journal-article
Springer Science and Business Media LLC
Nature Methods (297)
Bibliography

Tomer, R., Khairy, K., Amat, F., & Keller, P. J. (2012). Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nature Methods, 9(7), 755–763.

Authors 4
  1. Raju Tomer (first)
  2. Khaled Khairy (additional)
  3. Fernando Amat (additional)
  4. Philipp J Keller (additional)
References 45 Referenced 493
  1. McMahon, A., Supatto, W., Fraser, S.E. & Stathopoulos, A. Dynamic analyses of Drosophila gastrulation provide insights into collective cell migration. Science 322, 1546–1550 (2008). (10.1126/science.1167094) / Science by A McMahon (2008)
  2. Fernandez, R. et al. Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nat. Methods 7, 547–553 (2010). (10.1038/nmeth.1472) / Nat. Methods by R Fernandez (2010)
  3. Keller, P.J. et al. Fast, high-contrast imaging of animal development with scanned light sheet–based structured-illumination microscopy. Nat. Methods 7, 637–642 (2010). (10.1038/nmeth.1476) / Nat. Methods by PJ Keller (2010)
  4. Keller, P.J., Schmidt, A.D., Wittbrodt, J. & Stelzer, E.H.K. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322, 1065–1069 (2008). (10.1126/science.1162493) / Science by PJ Keller (2008)
  5. Fowlkes, C.C. et al. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell 133, 364–374 (2008). (10.1016/j.cell.2008.01.053) / Cell by CC Fowlkes (2008)
  6. Long, F., Peng, H., Liu, X., Kim, S.K. & Myers, E. A 3D digital atlas of C. elegans and its application to single-cell analyses. Nat. Methods 6, 667–672 (2009). (10.1038/nmeth.1366) / Nat. Methods by F Long (2009)
  7. Tomer, R., Denes, A.S., Tessmar-Raible, K. & Arendt, D. Profiling by image registration reveals common origin of annelid mushroom bodies and vertebrate pallium. Cell 142, 800–809 (2010). (10.1016/j.cell.2010.07.043) / Cell by R Tomer (2010)
  8. Gehrig, J. et al. Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos. Nat. Methods 6, 911–916 (2009). (10.1038/nmeth.1396) / Nat. Methods by J Gehrig (2009)
  9. Pardo-Martin, C. et al. High-throughput in vivo vertebrate screening. Nat. Methods 7, 634–636 (2010). (10.1038/nmeth.1481) / Nat. Methods by C Pardo-Martin (2010)
  10. Held, M. et al. CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. Nat. Methods 7, 747–754 (2010). (10.1038/nmeth.1486) / Nat. Methods by M Held (2010)
  11. Khairy, K. & Keller, P.J. Reconstructing embryonic development. Genesis 49, 488–513 (2011). (10.1002/dvg.20698) / Genesis by K Khairy (2011)
  12. Tomer, R., Khairy, K. & Keller, P.J. Shedding light on the system: studying embryonic development with light sheet microscopy. Curr. Opin. Genet. Dev. 21, 558–565 (2011). (10.1016/j.gde.2011.07.003) / Curr. Opin. Genet. Dev. by R Tomer (2011)
  13. Huisken, J. & Stainier, D.Y. Selective plane illumination microscopy techniques in developmental biology. Development 136, 1963–1975 (2009). (10.1242/dev.022426) / Development by J Huisken (2009)
  14. Keller, P.J. & Stelzer, E.H. Quantitative in vivo imaging of entire embryos with Digital Scanned Laser Light Sheet Fluorescence Microscopy. Curr. Opin. Neurobiol. 18, 624–632 (2008). (10.1016/j.conb.2009.03.008) / Curr. Opin. Neurobiol. by PJ Keller (2008)
  15. Planchon, T.A. et al. Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat. Methods 8, 417–423 (2011). (10.1038/nmeth.1586) / Nat. Methods by TA Planchon (2011)
  16. Capoulade, J., Wachsmuth, M., Hufnagel, L. & Knop, M. Quantitative fluorescence imaging of protein diffusion and interaction in living cells. Nat. Biotechnol. 29, 835–839 (2011). (10.1038/nbt.1928) / Nat. Biotechnol. by J Capoulade (2011)
  17. Ntziachristos, V. Going deeper than microscopy: the optical imaging frontier in biology. Nat. Methods 7, 603–614 (2010). (10.1038/nmeth.1483) / Nat. Methods by V Ntziachristos (2010)
  18. Palero, J., Santos, S.I., Artigas, D. & Loza-Alvarez, P. A simple scanless two-photon fluorescence microscope using selective plane illumination. Opt. Express 18, 8491–8498 (2010). (10.1364/OE.18.008491) / Opt. Express by J Palero (2010)
  19. Truong, T.V., Supatto, W., Koos, D.S., Choi, J.M. & Fraser, S.E. Deep and fast live imaging with two-photon scanned light-sheet microscopy. Nat. Methods 8, 757–760 (2011). (10.1038/nmeth.1652) / Nat. Methods by TV Truong (2011)
  20. Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J. & Stelzer, E.H.K. Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305, 1007–1009 (2004). (10.1126/science.1100035) / Science by J Huisken (2004)
  21. Swoger, J., Verveer, P., Greger, K., Huisken, J. & Stelzer, E.H. Multi-view image fusion improves resolution in three-dimensional microscopy. Opt. Express 15, 8029–8042 (2007). (10.1364/OE.15.008029) / Opt. Express by J Swoger (2007)
  22. Preibisch, S., Saalfeld, S., Schindelin, J. & Tomancak, P. Software for bead-based registration of selective plane illumination microscopy data. Nat. Methods 7, 418–419 (2010). (10.1038/nmeth0610-418) / Nat. Methods by S Preibisch (2010)
  23. Dodt, H.U. et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods 4, 331–336 (2007). (10.1038/nmeth1036) / Nat. Methods by HU Dodt (2007)
  24. Huisken, J. & Stainier, D.Y. Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM). Opt. Lett. 32, 2608–2610 (2007). (10.1364/OL.32.002608) / Opt. Lett. by J Huisken (2007)
  25. Xiong, G., Feng, C. & Ji, L. Dynamical Gaussian mixture model for tracking elliptical living objects. Pattern Recognit. Lett. 27, 838–842 (2006). (10.1016/j.patrec.2005.11.015) / Pattern Recognit. Lett. by G Xiong (2006)
  26. Xu, C. & Prince, J. Snakes, shapes, and gradient vector flow. IEEE Trans. Image Process 7, 359–369 (1998). (10.1109/83.661186) / IEEE Trans. Image Process by C Xu (1998)
  27. Pearson, B.J. & Doe, C.Q. Specification of temporal identity in the developing nervous system. Annu. Rev. Cell Dev. Biol. 20, 619–647 (2004). (10.1146/annurev.cellbio.19.111301.115142) / Annu. Rev. Cell Dev. Biol. by BJ Pearson (2004)
  28. Sánchez-Soriano, N., Tear, G., Whitington, P. & Prokop, A. Drosophila as a genetic and cellular model for studies on axonal growth. Neural Dev. 2, 9 (2007). (10.1186/1749-8104-2-9) / Neural Dev. by N Sánchez-Soriano (2007)
  29. Silies, M., Yuva-Aydemir, Y., Franzdottir, S.R. & Klambt, C. The eye imaginal disc as a model to study the coordination of neuronal and glial development. Fly 4, 71–79 (2010). (10.4161/fly.4.1.11312) / Fly by M Silies (2010)
  30. Yu, H.H. et al. A complete developmental sequence of a Drosophila neuronal lineage as revealed by twin-spot MARCM. PLoS Biol. 8, e1000461 (2010). (10.1371/journal.pbio.1000461) / PLoS Biol. by HH Yu (2010)
  31. Williams, D.W. & Truman, J.W. Mechanisms of dendritic elaboration of sensory neurons in Drosophila: insights from in vivo time lapse. J. Neurosci. 24, 1541–1550 (2004). (10.1523/JNEUROSCI.4521-03.2004) / J. Neurosci. by DW Williams (2004)
  32. Murray, M.J., Merritt, D.J., Brand, A.H. & Whitington, P.M. In vivo dynamics of axon pathfinding in the Drosophilia CNS: a time-lapse study of an identified motorneuron. J. Neurobiol. 37, 607–621 (1998). (10.1002/(SICI)1097-4695(199812)37:4<607::AID-NEU9>3.0.CO;2-Q) / J. Neurobiol. by MJ Murray (1998)
  33. Hiromi, Y., Kuroiwa, A. & Gehring, W.J. Control elements of the Drosophila segmentation gene fushi tarazu. Cell 43, 603–613 (1985). (10.1016/0092-8674(85)90232-6) / Cell by Y Hiromi (1985)
  34. Pfeiffer, B.D., Truman, J.W. & Rubin, G.M. Using translational enhancers to increase transgene expression in Drosophila. Proc. Natl. Acad. Sci. USA 109, 6626–6631 (2012). (10.1073/pnas.1204520109) / Proc. Natl. Acad. Sci. USA by BD Pfeiffer (2012)
  35. Arrenberg, A.B., Stainier, D.Y., Baier, H. & Huisken, J. Optogenetic control of cardiac function. Science 330, 971–974 (2010). (10.1126/science.1195929) / Science by AB Arrenberg (2010)
  36. Peng, H., Ruan, Z.C., Long, F.H., Simpson, J.H. & Myers, E.W. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat. Biotechnol. 28, 348–353 (2010). (10.1038/nbt.1612) / Nat. Biotechnol. by H Peng (2010)
  37. Abramoff, M.D., Magalhaes, P.J. & Ram, S.J. Image processing with ImageJ. Biophot. Internat. 11, 36–42 (2004). / Biophot. Internat. by MD Abramoff (2004)
  38. Li, G. et al. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biol. 8, 40 (2007). (10.1186/1471-2121-8-40) / BMC Cell Biol. by G Li (2007)
  39. Otsu, N. A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man. Cybern. 9, 62–66 (1979). (10.1109/TSMC.1979.4310076) / IEEE Trans. Syst. Man. Cybern. by N Otsu (1979)
  40. Gelas, A. et al. Variational level-set with Gaussian shape model for cell segmentation. in 2009 16th IEEE International Conference on Image Processing 1089–1092 (IEEE, 2009). (10.1109/ICIP.2009.5413463)
  41. Bishop, C.M. Pattern Recognition and Machine Learning (Springer, 2007).
  42. Dempster, A.P., Laird, N.M. & Rubin, D.B. Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. [Ser B] 39, 1–38 (1977). (10.1111/j.2517-6161.1977.tb01600.x) / J. R. Stat. Soc. [Ser B] by AP Dempster (1977)
  43. Kumar, N., Satoor, S. & Buck, I. Fast parallel expectation maximization for Gaussian mixture models on GPUs using CUDA. in 2009 11th IEEE International Conference on High Performance Computing and Communications 103–109 (IEEE, 2009). (10.1109/HPCC.2009.45)
  44. Nickolls, J., Buck, I., Garland, M. & Skadron, K. Scalable parallel programming with CUDA. Queue 6, 40–53 (2008). (10.1145/1365490.1365500) / Queue by J Nickolls (2008)
  45. Wilson, E.B. Probable inference, the law of succession, and statistical inference. J. Am. Stat. Assoc. 22, 209–212 (1927). (10.1080/01621459.1927.10502953) / J. Am. Stat. Assoc. by EB Wilson (1927)
Dates
Type When
Created 13 years, 2 months ago (June 4, 2012, 9:04 a.m.)
Deposited 1 year, 4 months ago (April 24, 2024, 6:46 p.m.)
Indexed 5 days ago (Aug. 26, 2025, 2:23 a.m.)
Issued 13 years, 2 months ago (June 3, 2012)
Published 13 years, 2 months ago (June 3, 2012)
Published Online 13 years, 2 months ago (June 3, 2012)
Published Print 13 years, 1 month ago (July 1, 2012)
Funders 0

None

@article{Tomer_2012, title={Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy}, volume={9}, ISSN={1548-7105}, url={http://dx.doi.org/10.1038/nmeth.2062}, DOI={10.1038/nmeth.2062}, number={7}, journal={Nature Methods}, publisher={Springer Science and Business Media LLC}, author={Tomer, Raju and Khairy, Khaled and Amat, Fernando and Keller, Philipp J}, year={2012}, month=jun, pages={755–763} }