In Situ Root System Architecture Extraction from Magnetic Resonance Imaging for Water Uptake Modeling

An automated method for root system architecture reconstruction from three-dimensional volume data sets obtained from magnetic resonance imaging (MRI) was developed and validated with a three-dimensional semimanual reconstruction using virtual reality and a two-dimensional reconstruction using SmartRoot. It was tested on the basis of an MRI image of a 25-d-old lupin (Lupinus albus L.) grown in natural sand with a resolution of 0.39 by 0.39 by 1.1 mm. The automated reconstruction algorithm was inspired by methods for blood vessel detection in MRI images. It describes the root system by a hierarchical network of nodes, which are connected by segments of defi ned length and thickness, and also allows the calculation of root parameter profi les such as root length, surface, and apex density The obtained root system architecture (RSA) varied in number of branches, segments, and connectivity of the segments but did not vary in the average diameter of the segments(0.137 cm for semimanual and 0.143 cm for automatic RSA), total root surface (127 cm2 for semimanual and 124 cm2 for automatic RSA), total root length (293 cm for semimanual and 282 cm for automatic RSA), and total root volume (4.7 cm3 for semimanual and 4.7 cm3 for automatic RSA). The difference in performance of the automated and semimanual reconstructions was checked by using the root system as input for water uptake modeling with the Doussan model. Both systems worked well and allowed for continuous water flow. Slight diff erences in the connectivity appeared to be leading to locally different water flow velocities, which were 30% smaller for the semimanual method.

[1]  S. Tyerman,et al.  Comparison between gradient-dependent hydraulic conductivities of roots using the root pressure probe: the role of pressure propagations and implications for the relative roles of parallel radial pathways. , 2007, Plant, cell & environment.

[2]  N. Shah,et al.  Comparing 1H‐NMR imaging and relaxation mapping of German white asparagus from five different cultivation sites , 2007 .

[3]  Loïc Pagès,et al.  A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture1[W][OA] , 2011, Plant Physiology.

[4]  Hanno Scharr,et al.  3d Reconstruction of Plant Roots from Mri Images , 2012 .

[5]  Lore Kutschera,et al.  Wurzelatlas mitteleuropäischer Ackerunkräuter und Kulturpflanzen , 1960 .

[6]  Jan Vanderborght,et al.  Use of a Three‐Dimensional Detailed Modeling Approach for Predicting Root Water Uptake , 2008 .

[7]  Jan Vanderborght,et al.  Parameterizing a Dynamic Architectural Model of the Root System of Spring Barley from Minirhizotron Data , 2012 .

[8]  Mark L. Rivers,et al.  Using X-ray computed tomography in hydrology: systems, resolutions, and limitations , 2002 .

[9]  Eberhard Lehmann,et al.  Neutron radiography and tomography of water distribution in the root zone. , 2010 .

[10]  P. Benfey,et al.  Imaging and Analysis Platform for Automatic Phenotyping and Trait Ranking of Plant Root Systems1[W][OA] , 2010, Plant Physiology.

[11]  Ernst Steudle,et al.  Water uptake by plant roots , 2003 .

[12]  Guido Gerig,et al.  Three-dimensional multi-scale line filter for segmentation and visualization of curvilinear structures in medical images , 1998, Medical Image Anal..

[13]  Stefan Mairhofer,et al.  RooTrak: Automated Recovery of Three-Dimensional Plant Root Architecture in Soil from X-Ray Microcomputed Tomography Images Using Visual Tracking1[W] , 2011, Plant Physiology.

[14]  H. As,et al.  MRI in Soils: Determination of Water Content Changes Due to Root Water Uptake by Means of a Multi-Slice-Multi-Echo Sequence (MSME) , 2010 .

[15]  Claude Doussan,et al.  Water Uptake by Plant Roots: I – Formation and Propagation of a Water Extraction Front in Mature Root Systems as Evidenced by 2D Light Transmission Imaging , 2006, Plant and Soil.

[16]  P J White,et al.  The dynamics of root meristem distribution in the soil. , 2010, Plant, cell & environment.

[17]  Alejandro F. Frangi,et al.  Muliscale Vessel Enhancement Filtering , 1998, MICCAI.

[18]  M. R. Thorpe,et al.  Non-invasive approaches for phenotyping of enhanced performance traits in bean. , 2011, Functional plant biology : FPB.

[19]  Loïc Pagès,et al.  Water Uptake by Plant Roots: II – Modelling of Water Transfer in the Soil Root-system with Explicit Account of Flow within the Root System – Comparison with Experiments , 2006, Plant and Soil.

[20]  Edsger W. Dijkstra,et al.  A note on two problems in connexion with graphs , 1959, Numerische Mathematik.

[21]  Mathieu Javaux,et al.  Model-assisted integration of physiological and environmental constraints affecting the dynamic and spatial patterns of root water uptake from soils. , 2010, Journal of experimental botany.

[22]  Jan Vanderborght,et al.  Changes in Soil Water Content Resulting from Ricinus Root Uptake Monitored by Magnetic Resonance Imaging , 2008 .

[23]  Loïc Pagès,et al.  MODELLING OF THE HYDRAULIC ARCHITECTURE OF ROOT SYSTEMS : AN INTEGRATED APPROACH TO WATER ABSORPTION : MODEL DESCRIPTION , 1998 .

[24]  A. Diggle,et al.  Modelling the interactions between water and nutrient uptake and root growth , 2002, Plant and Soil.

[25]  R. MacCurdy,et al.  Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform1[C][W][OA] , 2011, Plant Physiology.