View source for Applications/PaCeQuantToolset

== The PaCeQuant Plugin and Corresponding Tools ==
[[File:MiToBo_logo_PaCeQuant.png|border|150px|left|link=]]

The [[Applications/PaCeQuant|PaCeQuant plugin]] for fully automatic cell segmentation and shape feature extraction is part of MiToBo since release 1.8.6. 
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More details about the plugin and its usage can be found on the [[Applications/PaCeQuant|PaCeQuant's website]].

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Main publication:
* B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder,<br> '''''PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics'''''.<br> [http://www.plantphysiol.org/content/early/2017/09/20/pp.17.00961 Plant Physiology, 175(1), September 2017].

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Over the time the main plugin has been supplemented with several complementary tools to ease cell shape analysis and feature visualization:
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* the [[Applications/FeatureColorMapper|FeatureColorMapper]] plugin for creating heatmap visualizations of cell features
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* the [[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]] for handy manual post-processing of segmentation results
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* the R package [[Applications/PaCeQuantAna|PaCeQuantAna]] for statistical analysis of feature data and creation of publication-ready plots of feature distributions and statistical analysis results<br><br>

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Further references where PaCeQuant and the tools are documented or have been used:

* B. Möller, Y. Poeschl, S. Klemm, and K. Bürstenbinder,<br>'''''Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant'''''.<br>In F. Cvrčková and V. Žárský, editors, Plant Cell Morphogenesis: Methods and Protocols, chapter 22, pages 329-349, Springer New York, New York, NY, 2019.

* D. Mitra, S. Klemm, P. Kumari, J. Quegwer, B. Möller, Y. Poeschl, P. Pflug, G. Stamm, S. Abel, K. Bürstenbinder,<br>'''''Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana'''''.<br>In [https://academic.oup.com/jxb/article/70/2/529/5165408 Journal of Experimental Botany, 70(2):529-543, January 2019].