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Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant

  • Birgit Möller
  • Yvonne Poeschl
  • Sandra Klemm
  • Katharina BürstenbinderEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1992)

Abstract

Morphological analysis of cell shapes requires segmentation of cell contours from input images and subsequent extraction of meaningful shape descriptors that provide the basis for qualitative and quantitative assessment of shape characteristics. Here, we describe the publicly available ImageJ plugin PaCeQuant and its associated R package PaCeQuantAna, which provides a pipeline for fully automatic segmentation, feature extraction, statistical analysis, and graphical visualization of cell shape properties. PaCeQuant is specifically well suited for analysis of jigsaw puzzle-like leaf epidermis pavement cells from 2D input images and supports the quantification of global, contour-based, skeleton-based, and pavement cell-specific shape descriptors.

Key words

Epidermis Pavement cell shape Leaf morphogenesis Confocal laser scanning microscopy PaCeQuant R software ImageJ/Fiji 

Notes

Acknowledgments

This work was supported by the Deutsche Forschungsgemeinschaft (FZT 118, working group BIU, iDiv) and by IPB core funding (Leibniz Association) from the Federal Republic of Germany and the state of Saxony-Anhalt.

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Copyright information

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

Authors and Affiliations

  • Birgit Möller
    • 1
  • Yvonne Poeschl
    • 1
    • 2
  • Sandra Klemm
    • 3
  • Katharina Bürstenbinder
    • 3
    Email author
  1. 1.Institute of Computer ScienceMartin Luther University Halle-WittenbergHalle (Saale)Germany
  2. 2.iDiv, German Integrative Research Center for BiodiversityLeipzigGermany
  3. 3.Department of Molecular Signal ProcessingLeibniz Institute of Plant Biochemistry (IPB)Halle (Saale)Germany

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