Efficient processing and analysis of large-scale light-sheet microscopy data

Nature Protocols

Volumn 10, Issue 11, 2015, Pages 1679-1696

  Amat, Fernando ^a   Höckendorf, Burkhard ^a   Wan, Yinan ^a   Lemon, William C ^a   McDole, Katie ^a   Keller, Philipp J ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; CELL LINEAGE; CELL TRACKING; COMPUTER; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; IMAGE PROCESSING; IMAGE RECONSTRUCTION; INFORMATION PROCESSING; LIGHT SHEET MICROSCOPY; MICROSCOPY; PRIORITY JOURNAL; ALGORITHM; ANIMAL; COMPUTER PROGRAM; EMBRYO DEVELOPMENT; FLUORESCENCE IMAGING; PROCEDURES; SPATIOTEMPORAL ANALYSIS;

ALGORITHMS; ANIMALS; EMBRYONIC DEVELOPMENT; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY; OPTICAL IMAGING; SOFTWARE; SPATIO-TEMPORAL ANALYSIS;

EID: 84944386016     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2015.111     Document Type: Article

References (65)

1. Voie, A.H., Burns, D.H. & Spelman, F.A. Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens. J. Microsc. 170, 229-236 (1993).
2. Fuchs, E., Jaffe, J., Long, R. & Azam, F. Thin laser light sheet microscope for microbial oceanography. Opt. Express 10, 145-154 (2002).
3. 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).
4. Keller, P.J., Schmidt, A.D., Wittbrodt, J. & Stelzer, E.H. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322, 1065-1069 (2008).
5. Ahrens, M.B., Orger, M.B., Robson, D.N., Li, J.M. & Keller, P.J. Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Nat. Methods 10, 413-420 (2013).
6. Wu, Y. et al. Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nat. Biotechnol. 31, 1032-1038 (2013).
7. Krzic, U., Gunther, S., Saunders, T.E., Streichan, S.J. & Hufnagel, L. Multiview light-sheet microscope for rapid in toto imaging. Nat. Methods 9, 730-733 (2012).
8. 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 9, 755-763 (2012).
9. Schmid, B. et al. High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics. Nat. Commun. 4, 2207 (2013).
10. Holekamp, T.F., Turaga, D. & Holy, T.E. Fast three-dimensional fluorescence imaging of activity in neural populations by objective-coupled planar illumination microscopy. Neuron 57, 661-672 (2008).
11. 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).
12. Gao, L. et al. Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens. Cell 151, 1370-1385 (2012).
13. Chen, B.C. et al. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346, 1257998 (2014).
14. 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).
15. 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).
16. Keller, P.J. Imaging morphogenesis: technological advances and biological insights. Science 340, 1234168 (2013).
17. Pantazis, P. & Supatto, W. Advances in whole-embryo imaging: a quantitative transition is underway. Nat. Rev. Mol. Cell Biol. 15, 327-339 (2014).
18. Stelzer, E.H. Light-sheet fluorescence microscopy for quantitative biology. Nat. Methods 12, 23-26 (2014).
19. Huisken, J. Slicing embryos gently with laser light sheets. Bioessays 34, 406-411 (2012).
20. Pampaloni, F., Reynaud, E.G. & Stelzer, E.H. The third dimension bridges the gap between cell culture and live tissue. Nat. Rev. Mol. Cell Biol. 8, 839-845 (2007).
21. Keller, P.J., Ahrens, M.B. & Freeman, J. Light-sheet imaging for systems neuroscience. Nat. Methods 12, 27-29 (2014).
22. Keller, P.J. & Ahrens, M.B. Visualizing whole-brain activity and development at the single-cell level using light-sheet microscopy. Neuron 85, 462-483 (2015).
23. Lemon, W.C. & Keller, P.J. Live imaging of nervous system development and function using light-sheet microscopy. Mol. Reprod. Dev. 82, 605-618 (2015).
24. Megason, S.G. & Fraser, S.E. Imaging in systems biology. Cell 130, 784-795 (2007).
25. Khairy, K. & Keller, P.J. Reconstructing embryonic development. Genesis 49, 488-513 (2011).
26. 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).
27. Fernandez, R. et al. Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nat. Methods 7, 547-553 (2010).
28. Bosveld, F. et al. Mechanical control of morphogenesis by Fat/Dachsous/Four-jointed planar cell polarity pathway. Science 336, 724-727 (2012).
29. Murray, J.I. et al. Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nat. Methods 5, 703-709 (2008).
30. Liu, X. et al. Analysis of cell fate from single-cell gene expression profiles in C. elegans. Cell 139, 623-633 (2009).
31. Trichas, G. et al. Multi-cellular rosettes in the mouse visceral endoderm facilitate the ordered migration of anterior visceral endoderm cells. PLoS Biol. 10, e1001256 (2012).
32. Xiong, F. et al. Specified neural progenitors sort to form sharp domains after noisy Shh signaling. Cell 153, 550-561 (2013).
33. 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 156, 359-372 (2014).
34. Panier, T. et al. Fast functional imaging of multiple brain regions in intact zebrafish larvae using selective plane illumination microscopy. Front. Neural Circuits 7, 65 (2013).
35. Lemon, W. et al. Whole central nervous system functional imaging in larval Drosophila. Nat. Commun. 6, 7924 (2015).
36. Alivisatos, A.P. et al. The brain activity map project and the challenge of functional connectomics. Neuron 74, 970-974 (2012).
37. Saalfeld, S., Cardona, A., Hartenstein, V. & Tomančák, P CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics 25, 1984-1986 (2009).
38. Cardona, A. Collaborative annotation toolkit for massive amounts of image data (CATMAID) GitHub repository https://github.com/acardona/CATMAID (2015).
39. Amat, F. et al. Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data. Nat. Methods 11, 951-958 (2014).
40. Lauri, A. et al. Development of the annelid axochord: insights into notochord evolution. Science 345, 1365-1368 (2014).
41. 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).
42. Bao, Z. et al. Automated cell lineage tracing in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 103, 2707-2712 (2006).
43. Murray, J.I., Bao, Z., Boyle, T.J. & Waterston, R.H. The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree. Nat. Protoc. 1, 1468-1476 (2006).
44. Giurumescu, C.A. et al. Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos. Development 139, 4271-4279 (2012).
45. Olivier, N. et al. Cell lineage reconstruction of early zebrafish embryos using label-free nonlinear microscopy. Science 329, 967-971 (2010).
46. Kausler, B.X. et al. A discrete chain graph model for 3D+t cell tracking with high misdetection robustness. ECCV 7574, 144-157 (2012).
47. Stegmaier, J. et al. Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks. PLoS ONE 9, e90036 (2014).
48. Schiegg, M. et al. Graphical model for joint segmentation and tracking of multiple dividing cells. Bioinformatics 31, 948-956 (2014).
49. Allan, C. et al. OMERO: flexible, model-driven data management for experimental biology. Nat. Methods 9, 245-253 (2012).
50. Megason, S.G. In toto imaging of embryogenesis with confocal time-lapse microscopy. Methods Mol. Biol. 546, 317-332 (2009).
51. Schroeder, W., Martin, K. & Lorensen, B. The Visualization Toolkit: An Object-Oriented Approach to 3D Graphics. 4th edn. (Kitware, 2006).
52. Peng, H., Ruan, Z., Long, F., 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).
53. Bria, A., Iannello, G. & Peng, H. An open-source VAA3D plugin for real-time 3D visualization of terabyte-sized volumetric images. ISBI, 520-523 (2015).
54. Pietzsch, T., Saalfeld, S., Preibisch, S. & Tomancak, P. BigDataViewer: visualization and processing for large image data sets. Nat. Methods 12, 481-483 (2015).
55. Akerboom, J. et al. Optimization of a GCaMP calcium indicator for neural activity imaging. J. Neurosci. 32, 13819-13840 (2012).
56. Chen, T.W. et al. Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature 499, 295-300 (2013).
57. Kanodia, J.S. et al. A computational statistics approach for estimating the spatial range of morphogen gradients. Development 138, 4867-4874 (2011).
58. Pitrone, P.G. et al. OpenSPIM: an open-access light-sheet microscopy platform. Nat. Methods 10, 598-599 (2013).
59. Gualda, E.J. et al. OpenSpinMicroscopy: an open-source integrated microscopy platform. Nat. Methods 10, 599-600 (2013).
60. Bock, D.D. et al. Network anatomy and in vivo physiology of visual cortical neurons. Nature 471, 177-182 (2011).
61. Tomer, R., Ye, L., Hsueh, B. & Deisseroth, K. Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Nat. Protoc. 9, 1682-1697 (2014).
62. Susaki, E.A. et al. Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell 157, 726-739 (2014).
63. Dodt, H.U. et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods 4, 331-336 (2007).
64. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676-682 (2012).
65. Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. NIH image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671-675 (2012).