Applications/PaCeQuantToolset - Revision history

Moeller: /* The PaCeQuant Plugin and Corresponding Tools */

2020-05-16T16:13:35Z

The PaCeQuant Plugin and Corresponding Tools

← Older revision		Revision as of 18:13, 16 May 2020
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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.
			<br>
			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.
	<br>		<br>

Moeller: /* The PaCeQuant Plugin and Corresponding Tools */

2020-05-16T16:10:50Z

The PaCeQuant Plugin and Corresponding Tools

← Older revision		Revision as of 18:10, 16 May 2020
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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>		* 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>

Moeller at 15:34, 28 January 2020

2020-01-28T15:34:08Z

← Older revision		Revision as of 17:34, 28 January 2020
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	* 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.		* 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].		* 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>

			<p>
			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/>

Moeller at 15:28, 28 January 2020

2020-01-28T15:28:51Z

← Older revision		Revision as of 17:28, 28 January 2020
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	[[File:MiToBo_logo_PaCeQuant.png\|border\|150px\|left\|link=]]		[[File:MiToBo_logo_PaCeQuant.png\|border\|150px\|left\|link=]]

	The 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.
	<br>		<br>

Moeller at 15:28, 28 January 2020

2020-01-28T15:28:20Z

← Older revision		Revision as of 17:28, 28 January 2020
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	* the [[Operators/Tools/Interactive/LabelImageEditor\|LabelImageEditor]] for handy manual post-processing of segmentation results		* the [[Operators/Tools/Interactive/LabelImageEditor\|LabelImageEditor]] for handy manual post-processing of segmentation results
	<p><p>		<p><p>
	* 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		* 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>

			<p>
			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].

Moeller: Created page with "== The PaCeQuant Plugin and Corresponding Tools == link= The PaCeQuant plugin for fully automatic cell segmentation and s..."

2020-01-28T15:08:04Z

Created page with "== The PaCeQuant Plugin and Corresponding Tools == border|150px|left|link= The PaCeQuant plugin for fully automatic cell segmentation and s..."

New page

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

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 [[Applications/PaCeQuant|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'''''. [http://www.plantphysiol.org/content/early/2017/09/20/pp.17.00961 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 [[Applications/FeatureColorMapper|FeatureColorMapper]] plugin for creating heatmap visualizations of cell features

* the [[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]] for handy manual post-processing of segmentation results

* 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