title: Extracting Metrics for Three-dimensional Root Systems: Volume and Surface Analysis from In-soil X-ray Computed Tomography Data.
abstract: Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to climate change and crop management. Quantitative size information on roots in their native environment is invaluable for studying root growth and environmental processes involving plants. X-ray computed tomography (XCT) has been demonstrated to be an effective tool for in situ root scanning and analysis. We aimed to develop a costless and efficient tool that approximates the surface and volume of the root regardless of its shape from three-dimensional (3D) tomography data. The root structure of a Prairie dropseed (Sporobolus heterolepis) specimen was imaged using XCT. The root was reconstructed, and the primary root structure was extracted from the data using a combination of licensed and open-source software. An isosurface polygonal mesh was then created for ease of analysis. We have developed the standalone application imeshJ, generated in MATLAB(1), to calculate root volume and surface area from the mesh. The outputs of imeshJ are surface area (in mm(2)) and the volume (in mm(3)). The process, utilizing a unique combination of tools from imaging to quantitative root analysis, is described. A combination of XCT and open-source software proved to be a powerful combination to noninvasively image plant root samples, segment root data, and extract quantitative information from the 3D data. This methodology of processing 3D data should be applicable to other material/sample systems where there is connectivity between components of similar X-ray attenuation and difficulties arise with segmentation.
authors.affiliation: Environmental Molecular Sciences Laboratory.
authors.forename: Niraj
authors.initials: N
authors.lastname: Suresh
authors.affiliation: Environmental Molecular Sciences Laboratory.
authors.forename: Sean A
authors.initials: SA
authors.lastname: Stephens
authors.affiliation: Environmental Molecular Sciences Laboratory.
authors.forename: Lexor
authors.initials: L
authors.lastname: Adams
authors.affiliation: Environmental Molecular Sciences Laboratory.
authors.forename: Anthon N
authors.initials: AN
authors.lastname: Beck
authors.affiliation: Environmental Molecular Sciences Laboratory.
authors.forename: Adriana L
authors.initials: AL
authors.lastname: McKinney
authors.affiliation: Environmental Molecular Sciences Laboratory; Tamas.Varga@pnnl.gov.
authors.forename: Tamas
authors.initials: T
authors.lastname: Varga
mesh_terms: D004777:Environment; D007091:Image Processing, Computer-Assisted / Q000379:methods; D021621:Imaging, Three-Dimensional / Q000379:methods; D018517:Plant Roots / Q000033:anatomy & histology*; D006109:Poaceae / Q000033:anatomy & histology; D012984:Software; D012987:Soil; D014057:Tomography, X-Ray Computed / Q000379:methods*
chemical_list: D012987:Soil