Applications/PaCeQuantToolset: Difference between revisions
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The [[Applications/PaCeQuant|PaCeQuant plugin]] for fully automatic cell segmentation and shape feature extraction is part of MiToBo since release 1.8.6. | 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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In MiToBo version 2.0 released in May 2020 it got an update which added the largest empty circle as shape criterion to PaCeQuant's feature set. | |||
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Further references where PaCeQuant and the tools are documented or have been used: | 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. | * Y. Poeschl, B. Möller, L. Müller, and K. Bürstenbinder,<br>'''''User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools'''''.<br>In [https://www.sciencedirect.com/science/article/pii/S0091679X20300741?via%3Dihub Methods in Cell Biology], Academic Press, 2020. | ||
* 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, [https://link.springer.com/protocol/10.1007%2F978-1-4939-9469-4_22 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].<br><br> | |||
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PaCeQuant and the different tools have been developed in close collaboration with... | |||
* the group of [https://www.ipb-halle.de/en/employee/katharina-buerstenbinder/ Dr. Katharina Bürstenbinder], [https://www.ipb-halle.de/en/research/molecular-signal-processing/ Department of Molecular Signal Processing], [https://www.ipb-halle.de/en/ Leibniz Institute of Plant Biochemistry], Halle (Saale), Germany.<br/> | |||
* | * [https://www.idiv.de/de/gruppen_und_personen/mitarbeiterinnen/mitarbeiterdetails/eshow/poeschl_yvonne.html Dr. Yvonne Pöschl-Grau], member of the [https://www.idiv.de/en/groups_and_people/central_management/bioinformatics_unit_biu.html Bioinformatics Unit (BIU)] of the [https://www.idiv.de/en.html German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig]<br/><br/> | ||
Latest revision as of 17:13, 16 May 2020
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.
In MiToBo version 2.0 released in May 2020 it got an update which added the largest empty circle as shape criterion to PaCeQuant's feature set.
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:
- Y. Poeschl, B. Möller, L. Müller, and K. Bürstenbinder,
User-friendly assessment of pavement cell shape features with PaCeQuant: Novel functions and tools.
In Methods in Cell Biology, Academic Press, 2020.
- 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.
PaCeQuant and the different tools have been developed in close collaboration with...
- the group of Dr. Katharina Bürstenbinder, Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany.
