Applications/PaCeQuantToolset

The PaCeQuant Plugin and Corresponding Tools

The PaCeQuant plugin for fully automatic cell segmentation and shape feature extraction is part of MiToBo since release 1.8.6.

More details about the plugin and its usage can be found on the PaCeQuant's website.

Main publication:

• B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder,
  PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics.
  Plant Physiology, 175(1), September 2017.

Over the time the main plugin has been supplemented with several complementary tools to ease cell shape analysis and feature visualization:

• the FeatureColorMapper plugin for creating heatmap visualizations of cell features

• the LabelImageEditor for handy manual post-processing of segmentation results

• the R package PaCeQuantAna for statistical analysis of feature data and creation of publication-ready plots of feature distributions and statistical analysis results
  
  

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

• B. Möller, Y. Poeschl, S. Klemm, and K. Bürstenbinder,
  Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant.
  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,
  Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana.
  In Journal of Experimental Botany, 70(2):529-543, January 2019.