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Quantifying Cell Shape and Gene Expression in the Shoot Apical Meristem Using MorphoGraphX

Part of the Methods in Molecular Biology book series (MIMB,volume 1080)

Abstract

Confocal microscopy is a technique widely used to live-image plant tissue. Cells can be visualized by using fluorescent probes that mark the cell wall or plasma membrane. This enables the confocal microscope to be used as a 3D scanner with submicron precision. Here we present a protocol using the 3D image processing software MorphoGraphX (http://www.MorphoGraphX.org) to extract the surface geometry and cell shapes in the shoot apex. By segmenting cells over consecutive time points, precise growth maps of the shoot apex can be produced. It is also possible to tag a protein of interest with a fluorescent marker and quantify protein expression at the cellular level.

Key words

  • Shoot apex
  • Confocal microscopy
  • Image analysis
  • Segmentation
  • Watershed
  • Shape analysis
  • Expression pattern
  • 3D visualization

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  • DOI: 10.1007/978-1-62703-643-6_10
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References

  1. Kierzkowski D, Nakayama N, Routier-Kierzkowska A-L et al (2012) Elastic domains regulate growth and organogenesis in the plant shoot apical meristem. Science 335:1096–1099

    PubMed  CrossRef  CAS  Google Scholar 

  2. Nakayama N, Smith RS, Mandel T et al (2012) Mechanical regulation of auxin-mediated growth. Curr Biol 22:1468–1476

    PubMed  CrossRef  CAS  Google Scholar 

  3. Santuari L, Scacchi E, Rodriguez-Villalon A et al (2011) Positional information by differential endocytosis splits auxin response to drive arabidopsis root meristem growth. Curr Biol 21:1918–1923

    PubMed  CrossRef  CAS  Google Scholar 

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

    PubMed  CrossRef  CAS  Google Scholar 

  5. Abramoff M, Magalhaes P, Ram S (2004) Image processing with imagej. Biophoton Int 11:36–42

    Google Scholar 

  6. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH image to imagej: 25 years of image analysis. Nat Methods 9:671–675

    PubMed  CrossRef  CAS  Google Scholar 

  7. Linkert M, Rueden CT, Allan C et al (2010) Metadata matters: access to image data in the real world. J Cell Biol 189:777–782

    PubMed  CrossRef  CAS  Google Scholar 

  8. Lorensen WE, Cline HE (1987) Marching cubes: a high resolution 3d surface construction algorithm. Comput Graph 21:163–169

    CrossRef  Google Scholar 

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Acknowledgments

We gratefully acknowledge all those involved in the development of the MorphoGraphX—Naomi Nakayama, Thierry Schuepbach, Alain Weber, Anne-Lise Routier-Kierzkowska, and Micha Hersch. We thank Daniel Kierzkowski for time series images and Cris Kuhlemeier for discussions. This work was supported by SystemX.ch, the Swiss National Science Foundation, EMBO Long-Term Fellowship to S.R., and the University of Bern.

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de Reuille, P.B., Robinson, S., Smith, R.S. (2014). Quantifying Cell Shape and Gene Expression in the Shoot Apical Meristem Using MorphoGraphX. In: Žárský, V., Cvrčková, F. (eds) Plant Cell Morphogenesis. Methods in Molecular Biology, vol 1080. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-643-6_10

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  • DOI: https://doi.org/10.1007/978-1-62703-643-6_10

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-642-9

  • Online ISBN: 978-1-62703-643-6

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