Quantifying Plant Growth and Cell Proliferation with MorphoGraphX

  • Soeren Strauss
  • Aleksandra Sapala
  • Daniel Kierzkowski
  • Richard S. SmithEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1992)


Confocal microscopy is widely used to live-image plant tissue. Cell outlines can be visualized using fluorescent probes that mark the cell wall or plasma membrane, enabling the confocal microscope to be used as a 3D scanner with submicron precision. After imaging, the data needs to be analyzed by specialized software to quantify the features of interest, such as cell size and shape, growth rates and anisotropy, and gene expression. Here we present a protocol for the 3D image processing software MorphoGraphX ( using time-lapse images of an Arabidopsis thaliana sepal and the shoot apex of tomato.

Key words

Confocal microscopy Image analysis 3D visualization Time lapse Cell proliferation Growth analysis Lineage tracking 



We gratefully acknowledge all those involved in the development of the MorphoGraphX, with special thanks to Anne-Lise Routier-Kierzkowska. We acknowledge Pierre Barbier de Reuille and Sarah Robinson who contributed to a previous version of this chapter [7]. We would also like to thank the Tsiantis’s department of the Max Planck Institute for Plant Breeding Research for support.


  1. 1.
    de Reuille PB, Routier-Kierzkowska AL, Kierzkowski D, Bassel GW, Schüpbach T et al (2015) MorphoGraphX: a platform for quantifying morphogenesis in 4D. Elife 4:e05864CrossRefGoogle Scholar
  2. 2.
    Hervieux N, Dumond M, Sapala A, Routier-Kierzkowska AL, Kierzkowski D et al (2016) A mechanical feedback restricts sepal growth and shape in Arabidopsis. Curr Biol 26:1019–1028CrossRefGoogle Scholar
  3. 3.
    Kierzkowski D, Nakayama N, Routier-Kierzkowska AL, Weber A, Bayer E et al (2012) Elastic domains regulate growth and organogenesis in the plant shoot apical meristem. Science 335:1096–1099CrossRefGoogle Scholar
  4. 4.
    Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M et al (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676–682CrossRefGoogle Scholar
  5. 5.
    Abramoff M, Magalhaes P, Ram S (2004) Image processing with ImageJ. Biophoton Int 11:36–42Google Scholar
  6. 6.
    Lorensen WE, Cline HE (1987) Marching cubes: a high resolution 3d surface construction algorithm. Comput Graph 21:163–169CrossRefGoogle Scholar
  7. 7.
    de Reuille PB, Robinson S, Smith RS (2014) Quantifying cell shape and gene expression in the shoot apical meristem using MorphoGraphX. Methods Mol Biol 1080:121–134CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Soeren Strauss
    • 1
  • Aleksandra Sapala
    • 2
    • 1
  • Daniel Kierzkowski
    • 1
    • 3
  • Richard S. Smith
    • 1
    Email author
  1. 1.Max Planck Institute for Plant Breeding ResearchCologneGermany
  2. 2.Department of Biosystems Science and EngineeringETH ZurichSwitzerland
  3. 3.Institut de Recherche en Biologie VégétaleUniversity of MontréalMontrealCanada

Personalised recommendations