Abstract

The production of crops capable of efficient nutrient use is essential for addressing the problem of global food security. The ability of a plant's root system to interact with the soil micro-environment determines how effectively it can extract water and nutrients. In order to assess this ability and develop the fast and cost effective phenotyping techniques which are needed to establish efficient root systems, in situ imaging in soil is required. To date this has not been possible due to the high density of scatterers and absorbers in soil or because other growth substrates do not sufficiently model the heterogeneity of a soil's microenvironment. We present here a new form of light sheet imaging with novel transparent soil containing refractive index matched particles. This imaging method does not rely on fluorescence, but relies solely on scattering from root material. We term this form of imaging Light Sheet Tomography (LST). We have tested LST on a range of materials and plant roots in transparent soil and gel. Due to the low density of root structures, i.e. relatively large spaces between adjacent roots, long-term monitoring of lettuce root development in situ with subsequent quantitative analysis was achieved.

© 2013 OSA

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    [CrossRef]
  13. L. Dolan, K. Janmaat, V. Willemsen, P. Linstead, S. Poethig, K. Roberts, and B. Scheres, “Cellular organisation of the Arabidopsis thaliana root,” Development119(1), 71–84 (1993).
    [PubMed]
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    [CrossRef] [PubMed]

2013 (1)

D. B. Dresbøll, K. Thorup-Kristensen, B. M. McKenzie, L. X. Dupuy, and A. G. Bengough, “Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging,” Plant Soil, 1–11 (2013).

2012 (3)

F. Fiorani, U. Rascher, S. Jahnke, and U. Schurr, “Imaging plants dynamics in heterogenic environments,” Curr. Opin. Biotechnol.23(2), 227–235 (2012).
[CrossRef] [PubMed]

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

H. Downie, N. Holden, W. Otten, A. J. Spiers, T. A. Valentine, and L. X. Dupuy, “Transparent soil for imaging the rhizosphere,” PLoS ONE7(9), e44276 (2012).
[CrossRef] [PubMed]

2008 (1)

E. G. Reynaud, U. Krzic, K. Greger, and E. H. K. Stelzer, “Light sheet-based fluorescence microscopy: more dimensions, more photons, and less photodamage,” HFSP J2(5), 266–275 (2008).
[CrossRef] [PubMed]

2004 (1)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

2001 (1)

G. Gbur and E. Wolf, “The Rayleigh range of Gaussian Schell-model beams,” J. Mod. Opt.48, 1735–1741 (2001).

1998 (1)

S. Declerck, D. G. Strullu, and C. Plenchette, “Monoxenic culture of the intraradical forms of SP isolated from a tropical ecosystem: A proposed methodology for germplasm collection,” Mycologia90(4), 579–585 (1998).
[CrossRef]

1995 (1)

J. Lynch, “Root Architecture and Plant Productivity,” Plant Physiol.109(1), 7–13 (1995).
[PubMed]

1993 (1)

L. Dolan, K. Janmaat, V. Willemsen, P. Linstead, S. Poethig, K. Roberts, and B. Scheres, “Cellular organisation of the Arabidopsis thaliana root,” Development119(1), 71–84 (1993).
[PubMed]

1989 (1)

D. M. Shotton, “Confocal scanning optical microscopy and its applications for biological specimens,” J. Cell Sci.94, 175–206 (1989).

1988 (1)

1982 (1)

W. J. Alford, R. D. VanderNeut, and V. J. Zaleckas, “Laser scanning microscopy,” Proc. IEEE70(6), 641–651 (1982).
[CrossRef]

Alford, W. J.

W. J. Alford, R. D. VanderNeut, and V. J. Zaleckas, “Laser scanning microscopy,” Proc. IEEE70(6), 641–651 (1982).
[CrossRef]

Beeckman, T.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Benfey, P.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Bengough, A. G.

D. B. Dresbøll, K. Thorup-Kristensen, B. M. McKenzie, L. X. Dupuy, and A. G. Bengough, “Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging,” Plant Soil, 1–11 (2013).

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Bennett, M.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Broadley, M. R.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Casimiro, I.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

De Smet, I.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Declerck, S.

S. Declerck, D. G. Strullu, and C. Plenchette, “Monoxenic culture of the intraradical forms of SP isolated from a tropical ecosystem: A proposed methodology for germplasm collection,” Mycologia90(4), 579–585 (1998).
[CrossRef]

Del Bene, F.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

Dolan, L.

L. Dolan, K. Janmaat, V. Willemsen, P. Linstead, S. Poethig, K. Roberts, and B. Scheres, “Cellular organisation of the Arabidopsis thaliana root,” Development119(1), 71–84 (1993).
[PubMed]

Downie, H.

H. Downie, N. Holden, W. Otten, A. J. Spiers, T. A. Valentine, and L. X. Dupuy, “Transparent soil for imaging the rhizosphere,” PLoS ONE7(9), e44276 (2012).
[CrossRef] [PubMed]

Draye, X.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Dresbøll, D. B.

D. B. Dresbøll, K. Thorup-Kristensen, B. M. McKenzie, L. X. Dupuy, and A. G. Bengough, “Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging,” Plant Soil, 1–11 (2013).

Dupuy, L.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Dupuy, L. X.

D. B. Dresbøll, K. Thorup-Kristensen, B. M. McKenzie, L. X. Dupuy, and A. G. Bengough, “Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging,” Plant Soil, 1–11 (2013).

H. Downie, N. Holden, W. Otten, A. J. Spiers, T. A. Valentine, and L. X. Dupuy, “Transparent soil for imaging the rhizosphere,” PLoS ONE7(9), e44276 (2012).
[CrossRef] [PubMed]

Fiorani, F.

F. Fiorani, U. Rascher, S. Jahnke, and U. Schurr, “Imaging plants dynamics in heterogenic environments,” Curr. Opin. Biotechnol.23(2), 227–235 (2012).
[CrossRef] [PubMed]

Fukaki, H.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Gbur, G.

G. Gbur and E. Wolf, “The Rayleigh range of Gaussian Schell-model beams,” J. Mod. Opt.48, 1735–1741 (2001).

Greger, K.

E. G. Reynaud, U. Krzic, K. Greger, and E. H. K. Stelzer, “Light sheet-based fluorescence microscopy: more dimensions, more photons, and less photodamage,” HFSP J2(5), 266–275 (2008).
[CrossRef] [PubMed]

Hammond, J. P.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Häusler, G.

Heckel, W.

Heidstra, R.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Hochholdinger, F.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Holden, N.

H. Downie, N. Holden, W. Otten, A. J. Spiers, T. A. Valentine, and L. X. Dupuy, “Transparent soil for imaging the rhizosphere,” PLoS ONE7(9), e44276 (2012).
[CrossRef] [PubMed]

Huisken, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

Jahnke, S.

F. Fiorani, U. Rascher, S. Jahnke, and U. Schurr, “Imaging plants dynamics in heterogenic environments,” Curr. Opin. Biotechnol.23(2), 227–235 (2012).
[CrossRef] [PubMed]

Janmaat, K.

L. Dolan, K. Janmaat, V. Willemsen, P. Linstead, S. Poethig, K. Roberts, and B. Scheres, “Cellular organisation of the Arabidopsis thaliana root,” Development119(1), 71–84 (1993).
[PubMed]

Krzic, U.

E. G. Reynaud, U. Krzic, K. Greger, and E. H. K. Stelzer, “Light sheet-based fluorescence microscopy: more dimensions, more photons, and less photodamage,” HFSP J2(5), 266–275 (2008).
[CrossRef] [PubMed]

Laplaze, L.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Laskowski, M.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Lepetit, M.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Linstead, P.

L. Dolan, K. Janmaat, V. Willemsen, P. Linstead, S. Poethig, K. Roberts, and B. Scheres, “Cellular organisation of the Arabidopsis thaliana root,” Development119(1), 71–84 (1993).
[PubMed]

Lynch, J.

J. Lynch, “Root Architecture and Plant Productivity,” Plant Physiol.109(1), 7–13 (1995).
[PubMed]

Lynch, J. P.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

McKenzie, B. M.

D. B. Dresbøll, K. Thorup-Kristensen, B. M. McKenzie, L. X. Dupuy, and A. G. Bengough, “Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging,” Plant Soil, 1–11 (2013).

Mooney, S.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Nacry, P.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Otten, W.

H. Downie, N. Holden, W. Otten, A. J. Spiers, T. A. Valentine, and L. X. Dupuy, “Transparent soil for imaging the rhizosphere,” PLoS ONE7(9), e44276 (2012).
[CrossRef] [PubMed]

Parizot, B.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Péret, B.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Plenchette, C.

S. Declerck, D. G. Strullu, and C. Plenchette, “Monoxenic culture of the intraradical forms of SP isolated from a tropical ecosystem: A proposed methodology for germplasm collection,” Mycologia90(4), 579–585 (1998).
[CrossRef]

Poethig, S.

L. Dolan, K. Janmaat, V. Willemsen, P. Linstead, S. Poethig, K. Roberts, and B. Scheres, “Cellular organisation of the Arabidopsis thaliana root,” Development119(1), 71–84 (1993).
[PubMed]

Rascher, U.

F. Fiorani, U. Rascher, S. Jahnke, and U. Schurr, “Imaging plants dynamics in heterogenic environments,” Curr. Opin. Biotechnol.23(2), 227–235 (2012).
[CrossRef] [PubMed]

Reynaud, E. G.

E. G. Reynaud, U. Krzic, K. Greger, and E. H. K. Stelzer, “Light sheet-based fluorescence microscopy: more dimensions, more photons, and less photodamage,” HFSP J2(5), 266–275 (2008).
[CrossRef] [PubMed]

Roberts, K.

L. Dolan, K. Janmaat, V. Willemsen, P. Linstead, S. Poethig, K. Roberts, and B. Scheres, “Cellular organisation of the Arabidopsis thaliana root,” Development119(1), 71–84 (1993).
[PubMed]

Scheres, B.

L. Dolan, K. Janmaat, V. Willemsen, P. Linstead, S. Poethig, K. Roberts, and B. Scheres, “Cellular organisation of the Arabidopsis thaliana root,” Development119(1), 71–84 (1993).
[PubMed]

Schurr, U.

F. Fiorani, U. Rascher, S. Jahnke, and U. Schurr, “Imaging plants dynamics in heterogenic environments,” Curr. Opin. Biotechnol.23(2), 227–235 (2012).
[CrossRef] [PubMed]

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Shotton, D. M.

D. M. Shotton, “Confocal scanning optical microscopy and its applications for biological specimens,” J. Cell Sci.94, 175–206 (1989).

Spiers, A. J.

H. Downie, N. Holden, W. Otten, A. J. Spiers, T. A. Valentine, and L. X. Dupuy, “Transparent soil for imaging the rhizosphere,” PLoS ONE7(9), e44276 (2012).
[CrossRef] [PubMed]

Stelzer, E. H. K.

E. G. Reynaud, U. Krzic, K. Greger, and E. H. K. Stelzer, “Light sheet-based fluorescence microscopy: more dimensions, more photons, and less photodamage,” HFSP J2(5), 266–275 (2008).
[CrossRef] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

Strullu, D. G.

S. Declerck, D. G. Strullu, and C. Plenchette, “Monoxenic culture of the intraradical forms of SP isolated from a tropical ecosystem: A proposed methodology for germplasm collection,” Mycologia90(4), 579–585 (1998).
[CrossRef]

Swoger, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

Thorup-Kristensen, K.

D. B. Dresbøll, K. Thorup-Kristensen, B. M. McKenzie, L. X. Dupuy, and A. G. Bengough, “Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging,” Plant Soil, 1–11 (2013).

Valentine, T. A.

H. Downie, N. Holden, W. Otten, A. J. Spiers, T. A. Valentine, and L. X. Dupuy, “Transparent soil for imaging the rhizosphere,” PLoS ONE7(9), e44276 (2012).
[CrossRef] [PubMed]

VanderNeut, R. D.

W. J. Alford, R. D. VanderNeut, and V. J. Zaleckas, “Laser scanning microscopy,” Proc. IEEE70(6), 641–651 (1982).
[CrossRef]

White, P. J.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Willemsen, V.

L. Dolan, K. Janmaat, V. Willemsen, P. Linstead, S. Poethig, K. Roberts, and B. Scheres, “Cellular organisation of the Arabidopsis thaliana root,” Development119(1), 71–84 (1993).
[PubMed]

Wittbrodt, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

Wolf, E.

G. Gbur and E. Wolf, “The Rayleigh range of Gaussian Schell-model beams,” J. Mod. Opt.48, 1735–1741 (2001).

Zaleckas, V. J.

W. J. Alford, R. D. VanderNeut, and V. J. Zaleckas, “Laser scanning microscopy,” Proc. IEEE70(6), 641–651 (1982).
[CrossRef]

Zhang, H.

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Appl. Opt. (1)

Curr. Opin. Biotechnol. (1)

F. Fiorani, U. Rascher, S. Jahnke, and U. Schurr, “Imaging plants dynamics in heterogenic environments,” Curr. Opin. Biotechnol.23(2), 227–235 (2012).
[CrossRef] [PubMed]

Development (1)

L. Dolan, K. Janmaat, V. Willemsen, P. Linstead, S. Poethig, K. Roberts, and B. Scheres, “Cellular organisation of the Arabidopsis thaliana root,” Development119(1), 71–84 (1993).
[PubMed]

HFSP J (1)

E. G. Reynaud, U. Krzic, K. Greger, and E. H. K. Stelzer, “Light sheet-based fluorescence microscopy: more dimensions, more photons, and less photodamage,” HFSP J2(5), 266–275 (2008).
[CrossRef] [PubMed]

J. Cell Sci. (1)

D. M. Shotton, “Confocal scanning optical microscopy and its applications for biological specimens,” J. Cell Sci.94, 175–206 (1989).

J. Mod. Opt. (1)

G. Gbur and E. Wolf, “The Rayleigh range of Gaussian Schell-model beams,” J. Mod. Opt.48, 1735–1741 (2001).

Mycologia (1)

S. Declerck, D. G. Strullu, and C. Plenchette, “Monoxenic culture of the intraradical forms of SP isolated from a tropical ecosystem: A proposed methodology for germplasm collection,” Mycologia90(4), 579–585 (1998).
[CrossRef]

Plant Cell (1)

I. De Smet, P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, M. Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Péret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett, “Analyzing lateral root development: how to move forward,” Plant Cell24(1), 15–20 (2012).
[CrossRef] [PubMed]

Plant Physiol. (1)

J. Lynch, “Root Architecture and Plant Productivity,” Plant Physiol.109(1), 7–13 (1995).
[PubMed]

Plant Soil (1)

D. B. Dresbøll, K. Thorup-Kristensen, B. M. McKenzie, L. X. Dupuy, and A. G. Bengough, “Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging,” Plant Soil, 1–11 (2013).

PLoS ONE (1)

H. Downie, N. Holden, W. Otten, A. J. Spiers, T. A. Valentine, and L. X. Dupuy, “Transparent soil for imaging the rhizosphere,” PLoS ONE7(9), e44276 (2012).
[CrossRef] [PubMed]

Proc. IEEE (1)

W. J. Alford, R. D. VanderNeut, and V. J. Zaleckas, “Laser scanning microscopy,” Proc. IEEE70(6), 641–651 (1982).
[CrossRef]

Science (1)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science305(5686), 1007–1009 (2004).
[CrossRef] [PubMed]

Other (2)

R. Tomer, K. Khairy, and P. J. Keller, “Light sheet microscopy in cell biology,” in Cell Imaging Techniques (Humana Press 2013) ,123–137.

M. Minsky, “Microscopy Apparatus,” U.S. patent 3013467 (1961).

Supplementary Material (5)

» Media 1: AVI (4049 KB)     
» Media 2: AVI (3756 KB)     
» Media 3: AVI (3121 KB)     
» Media 4: AVI (3438 KB)     
» Media 5: AVI (1305 KB)     

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Figures (7)

Fig. 1
Fig. 1

Setup of the LST (top view).

Fig. 2
Fig. 2

(a) Image of 2 µm calibrated colloids in PAA under 10X objective. (b) Amplification of the image (a). (c) Profile of two spheres on the image.

Fig. 3
Fig. 3

Images of lens tissue. (a) Bright-field image of the paper under 10X magnification showing 2D structure of lens tissue. (b) Individual sections of the sample illuminated by the light sheet. The laser was incident from the “bottom” of the images. Images were cropped to 1280 × 300 pixels to highlight the details. Scale bars are 100 µm. (c) 3D image of the paper. (Media 1)

Fig. 4
Fig. 4

Images of dense foam. (a) Bright-field image of the dense foam under 10X magnifications. (b) Different stacks of the sample by laser-sheet section. Images were cropped to 1280×300 pixels. Scale bar 100 µm. (c) 3D image of the sample. (Media 2)

Fig. 5
Fig. 5

Root of a live A. thaliana. (a) Plant growing in transparent soil. (b) Sample after addition of RI matched solution. (c-f) Images slices at different depth obtained using LST demonstrate it allows detection of root hairs (e) and coarse anatomic features (c,d,f). LST is also suitable to image A. thaliana root 3D structure (g). (Media 3)

Fig. 6
Fig. 6

Projected images of lettuce root at different time point. (a)~(d) are images taken at respectively 0h, 6h,12h and 18h after the start of the experiment. The XY plane was obtained from Z projection of the image stacks whilst the XZ plane was reconstructed from 150-image sequences. Tracking of the root tip was achieved with the manual tracking plugin in ImageJ. (Media 4)

Fig. 7
Fig. 7

XY plane projected images of lettuce root at different time points. (a)-(d) are images taken at respectively 0h, 5h, 10h and 15h after the start of the experiment. (Media 5)

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