title: KymoRod: a method for automated kinematic analysis of rod-shaped plant organs.
abstract: A major challenge in plant systems biology is the development of robust, predictive multiscale models for organ growth. In this context it is important to bridge the gap between the, rather well-documented molecular scale and the organ scale by providing quantitative methods to study within-organ growth patterns. Here, we describe a simple method for the analysis of the evolution of growth patterns within rod-shaped organs that does not require adding markers at the organ surface. The method allows for the simultaneous analysis of root and hypocotyl growth, provides spatio-temporal information on curvature, growth anisotropy and relative elemental growth rate and can cope with complex organ movements. We demonstrate the performance of the method by documenting previously unsuspected complex growth patterns within the growing hypocotyl of the model species Arabidopsis thaliana during normal growth, after treatment with a growth-inhibiting drug or in a mechano-sensing mutant. The method is freely available as an intuitive and user-friendly Matlab application called KymoRod.
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.|Department of Collective Behaviour, Max Planck Institute for Ornithology and Department of Biology, University of Konstanz, Konstanz, Germany.
authors.forename: Renaud
authors.initials: R
authors.lastname: Bastien
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.|Biopolymères Interaction et Assemblages, INRA, UR1368, Nantes, F-44316, France.
authors.forename: David
authors.initials: D
authors.lastname: Legland
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
authors.forename: Marjolaine
authors.initials: M
authors.lastname: Martin
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
authors.forename: Lucien
authors.initials: L
authors.lastname: Fregosi
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Peaucelle
authors.affiliation: Matière et Systèmes Complexes, Université Paris-Diderot, Paris Cedex 13, 75025, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Douady
authors.affiliation: INRA, UMR 547 PIAF, Clermont-Ferrand, F-63100, France.|Clermont Université, Université Blaise Pascal, UMR 547 PIAF, Clermont-Ferrand, F-63100, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Moulia
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, Centre National pour la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
authors.forename: Herman
authors.initials: H
authors.lastname: Höfte
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D018546:Hypocotyl / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins
keywords: 
  Arabidopsis thaliana
  ; cellulose synthesis inhibitor; elongation growth; hypocotyl; image analysis; kinematics; mechano-sensing; root; technical advance