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.
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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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Möller, B., Poeschl, Y., Klemm, S., Bürstenbinder, K. (2019). Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant. In: Cvrčková, F., Žárský, V. (eds) Plant Cell Morphogenesis. Methods in Molecular Biology, vol 1992. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9469-4_22
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DOI: https://doi.org/10.1007/978-1-4939-9469-4_22
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