Review Article | Published:

Multiscale imaging of plant development by light-sheet fluorescence microscopy

Nature Plantsvolume 4pages639650 (2018) | Download Citation


Light-sheet fluorescence microscopy (LSFM) methods collectively represent the major breakthrough in developmental bio-imaging of living multicellular organisms. They are becoming a mainstream approach through the development of both commercial and custom-made LSFM platforms that are adjusted to diverse biological applications. Based on high-speed acquisition rates under conditions of low light exposure and minimal photo-damage of the biological sample, these methods provide ideal means for long-term and in-depth data acquisition during organ imaging at single-cell resolution. The introduction of LSFM methods into biology extended our understanding of pattern formation and developmental progress of multicellular organisms from embryogenesis to adult body. Moreover, LSFM imaging allowed the dynamic visualization of biological processes under almost natural conditions. Here, we review the most important, recent biological applications of LSFM methods in developmental studies of established and emerging plant model species, together with up-to-date methods of data editing and evaluation for modelling of complex biological processes. Recent applications in animal models push LSFM into the forefront of current bio-imaging approaches. Since LSFM is now the single most effective method for fast imaging of multicellular organisms, allowing quantitative analyses of their long-term development, its broader use in plant developmental biology will likely bring new insights.

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  1. 1.

    Gualda, E., Moreno, N., Tomancak, P. & Martins, G. G. Going “open” with Mesoscopy: a new dimension on multi-view imaging. Protoplasma 251, 363–372 (2014).

  2. 2.

    Reynaud, I. E., Peychl, J., Huisken, J. & Tomancak, P. Guide to light-sheet microscopy for adventurous biologists. Nat. Methods 12, 30–34 (2015).

  3. 3.

    Stelzer, E. H. K. Light-sheet fluorescence microscopy for quantitative biology. Nat. Methods 12, 23–26 (2015).

  4. 4.

    Weber, M. & Huisken, J. Light sheet microscopy for real-time developmental biology. Curr. Opin. Genet. Dev. 21, 566–572 (2011).

  5. 5.

    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).

  6. 6.

    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).

  7. 7.

    Berthet, B. & Maizel, A. Light sheet microscopy and live imaging of plants. J. Microsc. 263, 158–164 (2016).

  8. 8.

    Power, R. M. & Huisken, J. A guide to light-sheet fluorescence microscopy for multiscale imaging. Nat. Methods 14, 360–373 (2017).

  9. 9.

    Zagato, E. et al. Technical implementations of light sheet microscopy. Microsc. Res. Tech. (2018).

  10. 10.

    Girkin, J. M. & Carvalho, M. T. The light-sheet microscopy revolution. J. Opt. 20, 053002 (2018).

  11. 11.

    Keller, P. J. & Stelzer, E. H. K. Quantitative in vivo imaging of entire embryos with Digital Scanned Laser Light Sheet Fluorescence Microscopy. Curr. Opin. Neurobiol. 18, 624–632 (2008).

  12. 12.

    Icha, J., Weber, M., Waters, J. C. & Norden, C. Phototoxicity in live fluorescence microscopy, and how to avoid it. Bioessays 39, 1700003 (2017).

  13. 13.

    Laissue, P. P., Alghamdi, R. A., Tomancak, P., Reynaud, I. E. & Shroff, H. Assessing phototoxicity in live fluorescence imaging. Nat Methods 14, 657–661 (2017).

  14. 14.

    Capua, Y. & Eshed, Y. Coordination of auxin-triggered leaf initiation by tomato LEAFLESS. Proc. Natl Acad. Sci. USA 114, 3246–3251 (2017).

  15. 15.

    von Wangenheim, D. et al. Rules and self-organizing properties of post-embryonic plant organ cell division patterns. Curr. Biol. 26, 1–11 (2016).

  16. 16.

    Maizel, A., von Wangenheim, D., Federici, F., Haseloff, J. & Stelzer, E. H. K. High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy. Plant J. 68, 377–385 (2011).

  17. 17.

    Komis, G. et al. Dynamics and organization of cortical microtubules as revealed by superresolution structured illumination microscopy. Plant Physiol. 165, 129–148 (2014).

  18. 18.

    Rieckher, M. et al. A customized light sheet microscope to measure spatio-temporal protein dynamics in small model organisms. PLoS ONE 10, e0127869 (2015).

  19. 19.

    Maioli, V. et al. Time-lapse 3D measurements of a glucose biosensor in multicellular spheroids by light sheet fluorescence microscopy in commercial 96-well plates. Sci. Rep. 6, 37777 (2016).

  20. 20.

    Candeo, A., Doccula, F. G., Valentini, G., Bassi, A. & Costa, A. Light sheet fluorescence microscopy quantifies calcium oscillations in root hairs of Arabidopsis thaliana. Plant Cell Physiol. 58, 1161–1172 (2017).

  21. 21.

    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).

  22. 22.

    De Luis Balaguer, M. A. et al. Multi-sample Arabidopsis growth and imaging chamber (MAGIC) for long term imaging in the ZEISS Lightsheet Z.1. Dev. Biol. 419, 19–25 (2016).

  23. 23.

    Liu, L. et al. High-throughput imaging of zebrafish embryos using a linear-CCD-based flow imaging system. Biomed. Opt. Express 8, 5651–5662 (2017).

  24. 24.

    Berson, T. et al. Trans-Golgi network localized small GTPase RabA1d is involved in cell plate formation and oscillatory root hair growth. BMC Plant Biol. 14, 252 (2014).

  25. 25.

    Yamashita, N. et al. Three-dimensional tracking of plus-tips by lattice light-sheet microscopy permits the quantification of microtubule growth trajectories within the mitotic apparatus. J. Biomed. Opt. 20, 101206 (2015).

  26. 26.

    Aguet, F. et al. Membrane dynamics of dividing cells imaged by lattice light-sheet microscopy. Mol. Biol. Cell 27, 3418–3435 (2016).

  27. 27.

    Gustavsson, A. K., Petrov, P. N., Lee, M. Y., Shechtman, Y. & Moerner, W. E. 3D single-molecule super-resolution microscopy with a tilted light sheet. Nat. Commun. 9, 123 (2018).

  28. 28.

    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).

  29. 29.

    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).

  30. 30.

    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).

  31. 31.

    Chhetri, R. K., Amat, F., Wan, Y., Höckendorf, B., Lemon, W. C. & Keller, P. J. Whole-animal functional and developmental imaging with isotropic spatial resolution. Nat. Methods 12, 1171–1178 (2015).

  32. 32.

    Ejsmont, R. K., Sarov, M., Winkler, S., Lipinski, K. A. & Tomancak, P. A toolkit for high-throughput, cross-species gene engineering in Drosophila. Nat. Methods 6, 435–437 (2009).

  33. 33.

    Sarov, M. et al. A genome-wide resource for the analysis of protein localisation in Drosophila. eLife 5, e12068 (2016).

  34. 34.

    Schmied, C., Stamataki, E. & Tomancak, P. Open-source solutions for SPIMage processing. Methods Cell Biol. 123, 505–529 (2014).

  35. 35.

    Schmied, C. & Tomancak, P. Sample preparation and mounting of Drosophila embryos for multiview light sheet microscopy. Methods Mol. Biol. 1478, 189–202 (2016).

  36. 36.

    Pitrone, P. G. et al. OpenSPIM: an open-access light-sheet microscopy platform. Nat. Methods 10, 598–599 (2013).

  37. 37.

    Gualda, E. J. et al. OpenSpinMicroscopy: an open-source integrated microscopy platform. Nat. Methods 10, 599–600 (2013).

  38. 38.

    Lemon, W. C. et al. Whole-central nervous system functional imaging in larval Drosophila. Nat. Commun. 6, 7924 (2015).

  39. 39.

    Chen, B. C. et al. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346, 1257998 (2014).

  40. 40.

    Mir, M. et al. Dense Bicoid hubs accentuate binding along the morphogen gradient. Genes Dev. 31, 1784–1794 (2017).

  41. 41.

    Gao, L. et al. Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens. Cell 151, 1370–1385 (2012).

  42. 42.

    Amat, F. et al. Efficient processing and analysis of large-scale light-sheet microscopy data. Nat. Protoc. 10, 1679–1696 (2015).

  43. 43.

    Lye, C. M. et al. Mechanical coupling between endoderm invagination and axis extension in Drosophila. PLoS Biol. 13, e1002292 (2015).

  44. 44.

    Streichan, S. J., Lefebvre, M. F., Noll, N., Wieschaus, E. F. & Shraiman, B. I. Quantification of myosin distribution predicts global morphogenetic flow in the fly embryo. Preprint at (2017).

  45. 45.

    Strobl, F. & Stelzer, E. H. K. Non-invasive long-term fluorescence live imaging of Tribolium castaneum embryos. Development 141, 2331–2338 (2014).

  46. 46.

    Strobl, F., Schmitz, A. & Stelzer, E. H. K. Live imaging of Tribolium castaneum embryonic development using light-sheet-based fluorescence microscopy. Nat. Protoc. 10, 1486–1507 (2015).

  47. 47.

    Hilbrant, M., Horn, T., Koelzer, S. & Panfilio, K. A. The beetle amnion and serosa functionally interact as apposed epithelia. eLife 5, e13834 (2016).

  48. 48.

    Girstmair, J. et al. Light-sheet microscopy for everyone? experience of building an OpenSPIM to study flatworm development. BMC Dev. Biol. 16, 22 (2016).

  49. 49.

    Wolff, C. et al. Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb. eLife 7, e34410 (2018).

  50. 50.

    Wu, Y. et al. Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 108, 17708–17713 (2011).

  51. 51.

    Wu, Y. et al. Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nat. Biotechnol. 31, 1032–1038 (2013).

  52. 52.

    Kumar, A. et al. Dual-view plane illumination microscopy for rapid and spatially isotropic imaging. Nat. Protoc. 9, 2555–2573 (2014).

  53. 53.

    Rieckher, M. et al. A customized light sheet microscope to measure spatio-temporal protein dynamics in small model organisms. PLoS ONE 10, e0127869 (2015).

  54. 54.

    Kaufmann, A., Mickoleit, M., Weber, M. & Huisken, J. Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope. Development 139, 3242–3247 (2012).

  55. 55.

    Schmid, B. et al. High-speed panoramic light-sheet microscopy reveals global endodermal cell dynamics. Nat. Commun. 4, 2207 (2013).

  56. 56.

    Jahr, W., Schmid, B., Schmied, C., Fahrbach, F. & Huisken, J. Hyperspectral light sheet microscopy. Nat. Commun. 6, 7990 (2015).

  57. 57.

    Bassi, A., Schmid, B. & Huisken, J. Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development. Development 142, 1016–1020 (2015).

  58. 58.

    Lenard, A. et al. Endothelial cell self-fusion during vascular pruning. PLoS Biol. 13, e1002126 (2015).

  59. 59.

    Park, O. K. et al. 3D light-sheet fluorescence microscopy of cranial neurons and vasculature during sebrafish embryogenesis. Mol. Cells 38, 975–981 (2015).

  60. 60.

    Alvers, A. L., Ryan, S., Scherz, P. J., Huisken, J. & Bagnat, M. Single continuous lumen formation in the zebrafish gut is mediated by smoothened-dependent tissue remodeling. Development 141, 1110–1119 (2014).

  61. 61.

    Icha, J. et al. Using light sheet fluorescence microscopy to image zebrafish eye development. J. Vis. Exp. 110, e53966 (2016).

  62. 62.

    Beerman, R. W. et al. Direct in vivo manipulation and imaging of calcium transients in neutrophils identify a critical role for leading-edge calcium flux. Cell Rep. 13, 2107–2117 (2015).

  63. 63.

    Tomer, R. et al. SPED light sheet microscopy: fast mapping of biological system structure and function. Cell 163, 1796–1806 (2015).

  64. 64.

    Quirin, S. et al. Calcium imaging of neural circuits with extended depth-of-field light-sheet microscopy. Opt. Lett. 41, 855–858 (2016).

  65. 65.

    Arnaout, R. et al. Zebrafish model for human long QT syndrome. Proc. Natl Acad Sci. USA 104, 11316–11321 (2007).

  66. 66.

    Mickoleit, M. et al. High-resolution reconstruction of the beating zebrafish heart. Nat. Methods 11, 919–922 (2014).

  67. 67.

    Arrenberg, A. B., Stainier, D. Y., Baier, H. & Huisken, J. Optogenetic control of cardiac function. Science 330, 971–974 (2010).

  68. 68.

    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).

  69. 69.

    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).

  70. 70.

    Xiao, Y. et al. High-resolution live imaging reveals axon-glia interactions during peripheral nerve injury and repair in zebrafish. Dis. Model. Mech. 8, 553–564 (2015).

  71. 71.

    Icha, J., Kunath, C., Rocha-Martins, M. & Norden, C. Independent modes of ganglion cell translocation ensure correct lamination of the zebrafish retina. J. Cell Biol. 215, 259–275 (2016).

  72. 72.

    Sidhaye, J. & Norden, C. Concerted action of neuroepithelial basal shrinkage and active epithelial migration ensures efficient optic cup morphogenesis. eLife 6, e22689 (2017).

  73. 73.

    Ichikawa, T. et al. Live imaging of whole mouse embryos during gastrulation: migration analyses of epiblast and mesodermal cells. PLoS ONE 8, e64506 (2013).

  74. 74.

    Ichikawa, T. et al. Live imaging and quantitative analysis of gastrulation in mouse embryos using light-sheet microscopy and 3D tracking tools. Nat. Protoc. 9, 575–585 (2014).

  75. 75.

    Bouchard, M. B. et al. Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms. Nat. Photonics 9, 113–119 (2015).

  76. 76.

    Strnad, P. et al. Inverted light-sheet microscope for imaging mouse pre-implantation development. Nat. Methods 13, 139–142 (2016).

  77. 77.

    Ovečka, M. et al. Preparation of plants for developmental and cellular imaging by light-sheet microscopy. Nat. Protoc. 10, 1234–1247 (2015).

  78. 78.

    von Wangenheim, D., Hauschild, R. & Friml, J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. J. Vis. Exp. 119, e55044 (2017).

  79. 79.

    Rosquete, M. R. et al. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Curr. Biol. 23, 817–822 (2013).

  80. 80.

    Lucas, M. et al. Lateral root morphogenesis is dependent on the mechanical properties of the overlaying tissues. Proc. Natl Acad. Sci. USA 110, 5229–5234 (2013).

  81. 81.

    Vermeer, J. E. et al. A spatial accommodation by neighboring cells is required for organ initiation in Arabidopsis. Science 343, 178–183 (2014).

  82. 82.

    Sena, G., Frentz, Z., Birnbaum, K. D. & Leibler, S. Quantitation of cellular dynamics in growing Arabidopsis roots with light sheet microscopy. PLoS ONE 6, e21303 (2011).

  83. 83.

    Novák, D., Kuchařová, A., Ovečka, M., Komis, G. & Šamaj, J. Developmental nuclear localization and quantification of GFP-tagged EB1c in Arabidopsis root using light-sheet microscopy. Front. Plant Sci. 6, 1187 (2016).

  84. 84.

    Vyplelová, P., Ovečka, M. & Šamaj, J. Alfalfa root growth rate correlates with progression of microtubules during mitosis and cytokinesis as revealed by environmental light-sheet microscopy. Front. Plant Sci. 8, 1870 (2017).

  85. 85.

    Meinert, T., Tietz, O., Palme, K. J. & Rohrbach, A. Separation of ballistic and diffusive fluorescence photons in confocal light-sheet microscopy of Arabidopsis roots. Sci. Rep. 6, 30378 (2016).

  86. 86.

    Silverberg, J. L. et al. 3D imaging and mechanical modeling of helical buckling in Medicago truncatula plant roots. Proc. Natl Acad. Sci. USA 109, 16794–16799 (2012).

  87. 87.

    Slattery, R. A., Grennan, A. K., Sivaguru, M., Sozzani, R. & Ort, D. R. Light sheet microscopy reveals more gradual light attenuation in light-green versus dark-green soybean leaves. J. Exp. Bot. 67, 4697–4709 (2016).

  88. 88.

    Lichtenberg, M., Trampe, E. C. K., Vogelmann, T. C. & Kühl, M. Light Sheet Microscopy Imaging of Light Absorption and Photosynthesis Distribution in Plant Tissue. Plant Physiol. 175, 721–733 (2017).

  89. 89.

    von Wangenheim, D. Long-term observation of Arabidopsis thaliana root growth under close-to-natural conditions using light sheet-based fluorescence microscopy. PhD thesis, Johann Wolfgang Goethe-Universität (2015).

  90. 90.

    von Wangenheim, D. et al. Live imaging of Arabidopsis development. Methods Mol. Biol. 1062, 539–550 (2014).

  91. 91.

    Baesso, P., Randall, R. S. & Sena, G. Light sheet fluorescence microscopy optimized for long-term imaging of Arabidopsis root development. Methods Mol. Biol. 1761, 145–163 (2018).

  92. 92.

    Costa, A., Candeo, A., Fieramonti, L., Valentini, G. & Bassi, A. Calcium dynamics in root cells of Arabidopsis thaliana visualized with selective plane illumination microscopy. PLoS ONE 8, e75646 (2013).

  93. 93.

    De Col, V. et al. ATP sensing in living plant cells reveals tissue gradients and stress dynamics of energy physiology. eLife 6, e26770 (2017).

  94. 94.

    Smékalová, V. et al. Involvement of YODA and mitogen activated protein kinase 6 in Arabidopsis post-embryogenic root development through auxin up-regulation and cell division plane orientation. New Phytol. 203, 1175–1193 (2014).

  95. 95.

    Royer, L. A. et al. ClearVolume: open-source live 3D visualization for light-sheet microscopy. Nat. Methods 12, 480–481 (2015).

  96. 96.

    von Wangenheim, D. et al. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife 6, e26792 (2017).

  97. 97.

    Swoger, J., Verveer, P., Greger, K., Huisken, J. & Stelzer, E. H. K. Multi-view image fusion improves resolution in three-dimensional microscopy. Opt. Express 15, 8029–8042 (2007).

  98. 98.

    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).

  99. 99.

    Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

  100. 100.

    Preibisch, S. et al. Efficient Bayesian-based multiview deconvolution. Nat. Methods 11, 645–648 (2014).

  101. 101.

    Janes, G. et al. Cellular patterning of Arabidopsis roots under low phosphate conditions. Front. Plant Sci. 9, 735 (2018).

  102. 102.

    Barbier de Reuille, P. et al. MorphoGraphX: A platform for quantifying morphogenesis in 4D. eLife 4, e05864 (2015).

  103. 103.

    Heemskerk, I. & Streichan, S. J. Tissue cartography: compressing bio-image data by dimensional reduction. Nat. Methods 12, 1139–1142 (2015).

  104. 104.

    Schmied, C., Steinbach, P., Pietzsch, T., Preibisch, S. & Tomancak, P. An automated workflow for parallel processing of large multiview SPIM recordings. Bioinformatics 32, 1112–1114 (2016).

  105. 105.

    Pietzsch, T., Saalfeld, S., Preibisch, S. & Tomancak, P. BigDataViewer: visualization and processing for large image data sets. Nat. Methods 12, 481–483 (2015).

  106. 106.

    Jug, F., Pietzsch, T., Preibisch, S. & Tomancak, P. Bioimage Informatics in the context of Drosophila research. Methods 68, 60–73 (2014).

  107. 107.

    Planchon, T. A. et al. Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat. Methods 8, 417–423 (2011).

  108. 108.

    de Medeiros, G. et al. Confocal multiview light-sheet microscopy. Nat. Commun. 6, 8881 (2015).

  109. 109.

    Hu, Y. S., Zimmerley, M., Li, Y., Watters, R. & Cang, H. Single-molecule super-resolution light-sheet microscopy. Chem. Phys. Chem. 15, 577–586 (2014).

  110. 110.

    Hoyer, P. et al. Breaking the diffraction limit of light-sheet fluorescence microscopy by RESOLFT. Proc. Natl Acad. Sci. USA 113, 3442–3446 (2016).

  111. 111.

    Legant, W. R. et al. High-density three-dimensional localization microscopy across large volumes. Nat. Methods 13, 359–365 (2016).

  112. 112.

    Liu, T. L. et al. Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Science 360, eaaq1392 (2018).

  113. 113.

    Komis, G. et al. Superresolution live imaging of plant cells using structured illumination microscopy. Nat. Protoc. 10, 1248–1263 (2015).

  114. 114.

    Komis, G., Novák, D., Ovečka, M., Šamajová, O. & Šamaj, J. Advances in imaging plant cell dynamics. Plant Physiol. 176, 80–93 (2018).

  115. 115.

    Royer, L. A. et al. Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms. Nat. Biotechnol. 34, 1267–1278 (2016).

  116. 116.

    Novák, D. et al. Gene expression pattern and protein localization of Arabidopsis phospholipase D alpha 1 revealed by advanced light-sheet and super-resolution microscopy. Frontiers Plant Sci. 9, 371 (2018).

  117. 117.

    O’Callaghan, F. E., Braga, R. A., Neilson, R., MacFarlane, S. A. & Dupuy, L. X. New live-screening of plant-nematode interactions in the rhizosphere. Sci. Rep. 8, 1440 (2018).

  118. 118.

    Müllenbroich, M. C. et al. Comprehensive optical and data management infrastructure for high-throughput light-sheet microscopy of whole mouse brains. Neurophotonics 2, 041404 (2015).

  119. 119.

    Pampaloni, F., Richa, R., Ansari, N. & Stelzer, E. H. K. Live spheroid formation recorded with light sheet-based fluorescence microscopy. Methods Mol. Biol. 1251, 43–57 (2015).

  120. 120.

    Costantini, I. et al. A versatile clearing agent for multi-modal brain imaging. Sci. Rep. 5, 9808 (2015).

  121. 121.

    Fu, Q., Martin, B. L., Matus, D. Q. & Gao, L. Imaging multicellular specimens with real-time optimized tiling light-sheet selective plane illumination microscopy. Nat. Commun. 7, 11088 (2016).

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This work was supported from ERDF project ‘Plants as a tool for sustainable global development’ (CZ.02.1.01/0.0/0.0/16_019/0000827). D.v.W. was funded through the BBSRC grants BB/N018575/1 and BB/M001806/1. P.T. was supported by European Regional Development Fund in the IT4Innovations national supercomputing center - path to exascale project, project number CZ.02.1.01/0.0/0.0/16_013/0001791 within the Operational Programme Research, Development and Education.

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  1. These authors contributed equally to this work: Miroslav Ovečka, Daniel von Wangenheim, Pavel Tomančák.


  1. Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic

    • Miroslav Ovečka
    • , Olga Šamajová
    • , George Komis
    •  & Jozef Šamaj
  2. Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK

    • Daniel von Wangenheim
  3. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

    • Pavel Tomančák


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M.O. and D.W. prepared figures. All authors contributed to the writing of this article.

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The authors declare no competing interests.

Corresponding author

Correspondence to Jozef Šamaj.

Supplementary information

  1. Supplementary Information

    Supplementary Video legends

  2. Reporting Summary

  3. Supplementary Video 1

    Time-lapse imaging of Arabidopsis seed germination, early seedling growth and lateral root formation.

  4. Supplementary Video 2

    Growth of the primary root of Medicago sativa.

  5. Supplementary Video 3

    Adventitious root emergence from Oryza sativa stem nodes.

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