Centerline extraction based three-dimensional architecture parameter measurement method for plant roots

Abstract

The detection of architecture was one of the essential questions of plant root phenotyping research. The classical root architecture detection method was carried out by manual measurement. It is not only tedious, but also has a poor reliability, and the roots are damaged easily. This paper described a three-dimensional architecture measurement method based on XCT and centerline extraction method. The method includes the following steps: (1) obtaining the root CT images through the XCT system; (2) obtaining a root three-dimensional model after image segmentation and reconstruction. To solve the problem of model fracture, the quality of the reconstruction model was improved by a series of pre-processing methods; (3) extracting the root's centerline based on the mesh contraction, and the high-quality centerline was obtained after the post-processing methods; (4) calculating the architecture parameters. Different root samples were tested to validate the method for centerline extraction, and the root architecture was calculated by the centerline. The results were compared with the manual measurements, and the mean absolute percentage error of root length and root angle were 1.74% and 4.51, respectively. The entire algorithm runs for less than 30 seconds. The study may provide an effective method for root architecture detection.

A Low-Cost 3D Phenotype Measurement Method of Leafy Vegetables Using Video Recordings from Smartphones

“…The point cloud model not only has a large number of data and high amount of redundancy, but it is also difficult to directly obtain effective plant phenotypic parameters [34]. The skeleton can not only reflect the topological information of a shape, but can also describe the geometric information of said shape [35]. Therefore, in this study, the point cloud model was segmented and skeletonized, and the phenotypic information was obtained from them.…”