A framework for the extraction of quantitative traits from 2d images of mature Arabidopsis thaliana

In this work, we propose an image-based phenotyping framework for the determination of quantitative traits from mature Arabidopsis thaliana plants. Two-dimensional (2D) images taken from the dried and flattened plants are analyzed regarding their geometry as well as their branching topology. The realistic branching architecture is hereby reconstructed from a single 2D image using a tracing approach with a semi-circular search window. The centerline segments of the tracing procedure are subsequently merged and labeled based on a hierarchical approach combining continuity properties with geometrical and topological information determined during tracing. This paper covers a detailed description of the proposed plant phenotyping pipeline from the image acquisition process until the extraction of the quantitative traits. The framework is evaluated using a set of 106 images and compared to a manual phenotyping approach as well as a semi-automatic image-based approach. The most relevant results of this evaluation are presented.