title: Vascular Morphodynamics During Secondary Growth.
abstract: 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.
authors.affiliation: University of Bern, Altenbergrain 21, 3013, Bern, Switzerland.
authors.forename: Pierre Barbier
authors.initials: PB
authors.lastname: de Reuille
authors.affiliation: Center for Plant Molecular Biology-ZMBP, Developmental Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany. laura.ragni@zmbp.uni-tuebingen.de.
authors.forename: Laura
authors.initials: L
authors.lastname: Ragni
mesh_terms: D017360:Arabidopsis / Q000166:cytology / Q000254:growth & development; D007090:Image Interpretation, Computer-Assisted; D007091:Image Processing, Computer-Assisted; D008853:Microscopy / Q000379:methods; D063245:Plant Development; D058526:Plant Vascular Bundle / Q000166:cytology* / Q000254:growth & development*; D012984:Software
keywords: Arabidopsis hypocotyl; Cell segmentation; LithoGraphX; Quantitative histology