PloidyQuantX: A quantitative microscopy imaging tool for ploidy quantification at cell and organ level in arabidopsis root

Xavier Sevillano; Marc Ferrer; Mary Paz González-García; Irina Pavelescu; Ana I. Caño-Delgado

doi:10.1007/978-3-319-16483-0_21

PloidyQuantX: A quantitative microscopy imaging tool for ploidy quantification at cell and organ level in arabidopsis root

Xavier Sevillano, Marc Ferrer, Mary Paz González-García, Irina Pavelescu, Ana I. Caño-Delgado

La Salle International School of Commerce and Digital Economy

Research output: Book chapter › Conference contribution › peer-review

Abstract

Mapping centromere distribution in complete organs is a key step towards establishing how this couples to organ development and cell functions. In this context, quantitative microscopy tools play a key role, as they allow a precise measurement of centromere presence at both individual cell and whole organ levels. This work introduces PloidyQuantX, an imaging tool that operates on confocal microscopy image stacks. Tested on imagery obtained from wholemount centromere Q-FISH of the Arabidopsis thaliana primary root, Ploidy- QuantX incorporates interactive segmentation and image analysis modules that allow quantifying the number of centromeres present in each cell nucleus, thus creating maps of centromere distribution in cells across the whole organ. Moreover, the presented tool also allows rendering three-dimensional models of each individual root cell, which makes it possible to relate their internal topology to specific cell functions.

Original language	English
Title of host publication	Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings
Editors	Francisco Ortuño, Ignacio Rojas
Publisher	Springer Verlag
Pages	210-215
Number of pages	6
ISBN (Print)	9783319164823
DOIs	https://doi.org/10.1007/978-3-319-16483-0_21
Publication status	Published - 2015
Event	3rd International Work Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015 - Granada, Spain Duration: 15 Apr 2015 → 17 Apr 2015

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9043
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	3rd International Work Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015
Country/Territory	Spain
City	Granada
Period	15/04/15 → 17/04/15

Keywords

Biomedical imaging
Centromere quantification
Image processing
Quantitative microscopy

Access to Document

10.1007/978-3-319-16483-0_21

Cite this

Sevillano, X., Ferrer, M., González-García, M. P., Pavelescu, I., & Caño-Delgado, A. I. (2015). PloidyQuantX: A quantitative microscopy imaging tool for ploidy quantification at cell and organ level in arabidopsis root. In F. Ortuño, & I. Rojas (Eds.), Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings (pp. 210-215). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9043). Springer Verlag. https://doi.org/10.1007/978-3-319-16483-0_21

Sevillano, Xavier ; Ferrer, Marc ; González-García, Mary Paz et al. / PloidyQuantX : A quantitative microscopy imaging tool for ploidy quantification at cell and organ level in arabidopsis root. Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. editor / Francisco Ortuño ; Ignacio Rojas. Springer Verlag, 2015. pp. 210-215 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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title = "PloidyQuantX: A quantitative microscopy imaging tool for ploidy quantification at cell and organ level in arabidopsis root",

abstract = "Mapping centromere distribution in complete organs is a key step towards establishing how this couples to organ development and cell functions. In this context, quantitative microscopy tools play a key role, as they allow a precise measurement of centromere presence at both individual cell and whole organ levels. This work introduces PloidyQuantX, an imaging tool that operates on confocal microscopy image stacks. Tested on imagery obtained from wholemount centromere Q-FISH of the Arabidopsis thaliana primary root, Ploidy- QuantX incorporates interactive segmentation and image analysis modules that allow quantifying the number of centromeres present in each cell nucleus, thus creating maps of centromere distribution in cells across the whole organ. Moreover, the presented tool also allows rendering three-dimensional models of each individual root cell, which makes it possible to relate their internal topology to specific cell functions.",

keywords = "Biomedical imaging, Centromere quantification, Image processing, Quantitative microscopy",

author = "Xavier Sevillano and Marc Ferrer and Gonz{\'a}lez-Garc{\'i}a, {Mary Paz} and Irina Pavelescu and Ca{\~n}o-Delgado, {Ana I.}",

note = "Publisher Copyright: {\textcopyright} Springer International Publishing Switzerland 2015.; 3rd International Work Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015 ; Conference date: 15-04-2015 Through 17-04-2015",

year = "2015",

doi = "10.1007/978-3-319-16483-0_21",

language = "English",

isbn = "9783319164823",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

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booktitle = "Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings",

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Sevillano, X, Ferrer, M, González-García, MP, Pavelescu, I & Caño-Delgado, AI 2015, PloidyQuantX: A quantitative microscopy imaging tool for ploidy quantification at cell and organ level in arabidopsis root. in F Ortuño & I Rojas (eds), Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9043, Springer Verlag, pp. 210-215, 3rd International Work Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, Granada, Spain, 15/04/15. https://doi.org/10.1007/978-3-319-16483-0_21

PloidyQuantX: A quantitative microscopy imaging tool for ploidy quantification at cell and organ level in arabidopsis root. / Sevillano, Xavier; Ferrer, Marc; González-García, Mary Paz et al.
Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. ed. / Francisco Ortuño; Ignacio Rojas. Springer Verlag, 2015. p. 210-215 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9043).

Research output: Book chapter › Conference contribution › peer-review

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T2 - 3rd International Work Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015

AU - Sevillano, Xavier

AU - Ferrer, Marc

AU - González-García, Mary Paz

AU - Pavelescu, Irina

AU - Caño-Delgado, Ana I.

N1 - Publisher Copyright: © Springer International Publishing Switzerland 2015.

PY - 2015

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N2 - Mapping centromere distribution in complete organs is a key step towards establishing how this couples to organ development and cell functions. In this context, quantitative microscopy tools play a key role, as they allow a precise measurement of centromere presence at both individual cell and whole organ levels. This work introduces PloidyQuantX, an imaging tool that operates on confocal microscopy image stacks. Tested on imagery obtained from wholemount centromere Q-FISH of the Arabidopsis thaliana primary root, Ploidy- QuantX incorporates interactive segmentation and image analysis modules that allow quantifying the number of centromeres present in each cell nucleus, thus creating maps of centromere distribution in cells across the whole organ. Moreover, the presented tool also allows rendering three-dimensional models of each individual root cell, which makes it possible to relate their internal topology to specific cell functions.

AB - Mapping centromere distribution in complete organs is a key step towards establishing how this couples to organ development and cell functions. In this context, quantitative microscopy tools play a key role, as they allow a precise measurement of centromere presence at both individual cell and whole organ levels. This work introduces PloidyQuantX, an imaging tool that operates on confocal microscopy image stacks. Tested on imagery obtained from wholemount centromere Q-FISH of the Arabidopsis thaliana primary root, Ploidy- QuantX incorporates interactive segmentation and image analysis modules that allow quantifying the number of centromeres present in each cell nucleus, thus creating maps of centromere distribution in cells across the whole organ. Moreover, the presented tool also allows rendering three-dimensional models of each individual root cell, which makes it possible to relate their internal topology to specific cell functions.

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SN - 9783319164823

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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BT - Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings

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A2 - Rojas, Ignacio

PB - Springer Verlag

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ER -

Sevillano X, Ferrer M, González-García MP, Pavelescu I, Caño-Delgado AI. PloidyQuantX: A quantitative microscopy imaging tool for ploidy quantification at cell and organ level in arabidopsis root. In Ortuño F, Rojas I, editors, Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Springer Verlag. 2015. p. 210-215. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-16483-0_21

PloidyQuantX: A quantitative microscopy imaging tool for ploidy quantification at cell and organ level in arabidopsis root

Abstract

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Keywords

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