A new tool for analysis of root growth in the spatio‐temporal continuum

Abstract

Summary• Quantification of overall growth and local growth zones in root system development is key to understanding the biology of plant growth, and thus to exploring the effects of environmental, genotypic and mutational variations on plant development and productivity.• We introduce a methodology for analyzing growth patterns of plant roots from twodimensional time series images, treating them as a spatio-temporal three-dimensional (3D) image volume. The roots are segmented from the images and then two types of analysis are performed: 3D spatio-temporal reconstruction analysis for simultaneous assessment of initiation and growth of multiple roots; and spatio-temporal pixel intensity analysis along root midlines for quantification of the growth zones.• The test measurements show simultaneous emergence of basal roots but sequential emergence of lateral roots in Phaseolus vulgaris, while lateral roots of Cicer arietinum emerge in a rhythmic pattern. Local growth analysis reveals multimodal transient growth zone in basal roots. At the initial stages after emergence, the roots oscillate rapidly, which slows down with time.• The methodology presented here allows detailed characterization of the phenomenology of roots, providing valuable information of spatio-temporal development, with applications in a wide range of growing plant organs.

KymoRod: a method for automated kinematic analysis of rod‐shaped plant organs

“…Some of them only measure part of the process, focusing on apical hook angle (Geng et al, 2013;Russino et al, 2013;Slovak et al, 2014), while others only measure length and length variation (French et al, 2009;Wang et al, 2009;Geng et al, 2013), the relative elemental growth rate (REGR; van der Weele et al, 2003;Walter et al, 2002) or curvature (French et al, 2009;Wang et al, 2009). Recent advances have been made in measurement of the full kinematics, mainly in roots (Basu et al, 2007;Chavarria-Krauser et al, 2008;Basu and Pal, 2012), inflorescence stems (Hall and Ellis, 2013) or a variety of organs (Barbier de Reuille et al, 2015). One method relies on a structure tensor and optical flow to track the speed of each pixel (Chavarria-Krauser et al, 2008).…”

High‐throughput two‐dimensional root system phenotyping platform facilitates genetic analysis of root growth and development

“…With the development of both general purpose and custom root analysis systems, many unique quantitative studies of root system growth are now possible (Zeng, Birchfield & Wells 2008;Le Bot et al 2010). In recent years, root analysis system designs have focused on combining imaging methods with automated algorithms that enable root system features to be measured or tracked (Armengaud et al 2009;French et al 2009;Basu & Pal 2012;Galkovskyi et al 2012).…”

Recovering Root System Traits Using Image Analysis Exemplified by Two-Dimensional Neutron Radiography Images of Lupine

“…Analysis of such sequences may lead to better insight into the development of the root system (e.g. DART, SmartRoot) or even reveal growth zones and their local growth velocities (Basu and Pal, 2012).…”

“…RootReader2D, GiA Roots, SmartRoot, EZ-Rhizo; Stingaciu et al [2013]). Other methods include the livewire algorithm (Basu and Pal, 2012) or the levelset method (RootTrak; Mairhofer et al, 2012) that determine the borders of each root. The creation of a root system skeleton is either done manually (e.g.…”