Vascular Morphodynamics During Secondary Growth

Barbier de Reuille, Pierre; Ragni, Laura (2017). Vascular Morphodynamics During Secondary Growth. In: de Lucas, Miguel; Etchells, John Peter (eds.) Xylem - Methods and Protocols. Methods in Molecular Biology: Vol. 1544 (pp. 103-125). New York, NY: Humana Press 10.1007/978-1-4939-6722-3_10

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Quantification of vascular morphodynamics during secondary growth has been hampered by the scale of the process. Even in the tiny model plant Arabidopsis thaliana, the xylem can include more than 2000 cells in a single cross section, rendering manual counting impractical. Moreover, due to its deep location, xylem is an inaccessible tissue, limiting live imaging. A novel method to visualize and measure secondary growth progression has been proposed: “the Quantitative Histology” approach. This method is based on a detailed anatomical atlas, and image segmentation coupled with machine learning to automatically extract cell shapes and identify cell type. Here we present a new version of this approach, with a user-friendly interface implemented in the open source software LithoGraphX.

Item Type:

Book Section (Book Chapter)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS) > Plant Development
08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS)

UniBE Contributor:

Barbier de Reuille, Pierre

Subjects:

500 Science > 580 Plants (Botany)

ISSN:

1064-3745

ISBN:

978-1-4939-6720-9

Series:

Methods in Molecular Biology

Publisher:

Humana Press

Language:

English

Submitter:

Peter Alfred von Ballmoos-Haas

Date Deposited:

06 Apr 2017 16:41

Last Modified:

06 Apr 2017 16:41

Publisher DOI:

10.1007/978-1-4939-6722-3_10

PubMed ID:

28050833

Uncontrolled Keywords:

Arabidopsis hypocotyl, Cell segmentation, LithoGraphX, Quantitative histology

BORIS DOI:

10.7892/boris.92610

URI:

https://boris.unibe.ch/id/eprint/92610

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