Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant

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


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 



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.


  1. 1.
    Tsukaya H (2013) Leaf development. Arabidopsis Book 11:e0163CrossRefGoogle Scholar
  2. 2.
    Tsukaya H (1995) Developmental genetics of leaf morphogenesis in dicotyledonous plants. J Plant Res 108:407–416CrossRefGoogle Scholar
  3. 3.
    Glover BJ (2000) Differentiation in plant epidermal cells. J Exp Bot 51:497–505CrossRefGoogle Scholar
  4. 4.
    Qian PP, Hou SW, Guo GQ (2009) Molecular mechanisms controlling pavement cell shape in Arabidopsis leaves. Plant Cell Rep 28:1147–1157CrossRefGoogle Scholar
  5. 5.
    Guimil S, Dunand C (2007) Cell growth and differentiation in Arabidopsis epidermal cells. J Exp Bot 58:3829–3840CrossRefGoogle Scholar
  6. 6.
    Jacques E, Verbelen JP, Vissenberg K (2014) Review on shape formation in epidermal pavement cells of the Arabidopsis leaf. Funct Plant Biol 41:914–921CrossRefGoogle Scholar
  7. 7.
    Armour WJ, Barton DA, Law AM, Overall RL (2015) Differential growth in periclinal and anticlinal walls during lobe formation in Arabidopsis cotyledon pavement cells. Plant Cell 27:2484–2500CrossRefGoogle Scholar
  8. 8.
    Fu Y, Gu Y, Zheng ZL, Wasteneys G, Yang ZB (2005) Arabidopsis interdigitating cell growth requires two antagonistic pathways with opposing action on cell morphogenesis. Cell 120:687–700CrossRefGoogle Scholar
  9. 9.
    Kotzer AM, Wasteneys GO (2006) Mechanisms behind the puzzle: microtubule-microfilament cross-talk in pavement cell formation. Can J Bot 84:594–603CrossRefGoogle Scholar
  10. 10.
    Zhang CH, Halsey LE, Szymanski DB (2011) The development and geometry of shape change in Arabidopsis thaliana cotyledon pavement cells. BMC Plant Biol 11:27CrossRefGoogle Scholar
  11. 11.
    Ivakov A, Persson S (2013) Plant cell shape: modulators and measurements. Front Plant Sci 4:439CrossRefGoogle Scholar
  12. 12.
    Gao Y, Zhang Y, Zhang D, Dai X, Estelle M et al (2015) Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development. Proc Natl Acad Sci U S A 112:2275–2280CrossRefGoogle Scholar
  13. 13.
    Li S, Blanchoin L, Yang Z, Lord EM (2003) The putative Arabidopsis Arp2/3 complex controls leaf cell morphogenesis. Plant Physiol 132:2034–2044CrossRefGoogle Scholar
  14. 14.
    Bannigan A, Baskin TI (2005) Directional cell expansion—turning toward actin. Curr Opin Plant Biol 8:619–624CrossRefGoogle Scholar
  15. 15.
    Xu TD, Wen MZ, Nagawa S, Fu Y, Chen JG et al (2010) Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis. Cell 143:99–110CrossRefGoogle Scholar
  16. 16.
    Wu TC, Belteton S, Pack J, Szymanski DB, Umulis D (2016) LobeFinder: a convex hull-based method for quantitative boundary analyses of lobed plant cells. Plant Physiol 171:2331–2342PubMedPubMedCentralGoogle Scholar
  17. 17.
    Sanchez-Corrales YE, Hartley M, van Rooij J, Maree AFM, Grieneisen VA (2018) Morphometrics of complex cell shapes: lobe contribution elliptic Fourier analysis (LOCO-EFA). Development 145:dev156778CrossRefGoogle Scholar
  18. 18.
    Möller B, Poeschl Y, Plötner R, Bürstenbinder K (2017) PaCeQuant: A tool for high-throughput quantification of pavement cell shape characteristics. Plant Physiol 175:998–1017CrossRefGoogle Scholar
  19. 19.
    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
  20. 20.
    Vanhaeren H, Gonzales NR, Inzé D (2015) A journey through a leaf: Phenomics analysis of leaf growth in Arabidopsis thaliana. Arabidopsis Book 13:e0181CrossRefGoogle Scholar
  21. 21.
    Mitra D, Kumari P, Quegwer J, Klemm S, Möller B et al (2018) Microtubule-associated protein IQ67 DOMAIN5 regulates interdigitation of leaf pavement cells in Arabidopsis thaliana. J Exp Bot ery39522.
  22. 22.
    Liang H, Zhang Y, Martinez P, Rasmussen C, Xu T et al (2018) The microtubule-associated protein IQ67 DOMAIN5 modulates microtubule dynamics and pavement cell shape. Plant Physiol 177:1555–1568PubMedGoogle Scholar
  23. 23.
    Möller B, Glaß M, Misiak D, Posch S (2016) MiToBo - A toolbox for image processing and analysis. J Open Res Softw 4:e17CrossRefGoogle Scholar
  24. 24.
    Wu HM, Hazak O, Cheung AY, Yalovsky S (2011) RAC/ROP GTPases and auxin signaling. Plant Cell 23:1208–1218CrossRefGoogle Scholar
  25. 25.
    Guo X, Qin Q, Yan J, Niu Y, Huang B et al (2015) TYPE-ONE PROTEIN PHOSPHATASE4 regulates pavement cell interdigitation by modulating PIN-FORMED1 polarity and trafficking in Arabidopsis. Plant Physiol 167:1058–1075CrossRefGoogle Scholar

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© 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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