Image-based phenotyping of the mature arabidopsis shoot system

Abstract

The image-based phenotyping of mature plants faces several challenges from the image acquisition to the determination of quantitative characteristics describing their appearance. In this work a framework to extract geometrical and topological traits of 2D images of mature Arabidopsis thaliana is proposed. The phenotyping pipeline recovers the realistic branching architecture of dried and flattened plants in two steps. In the first step, a tracing approach is used for the extraction of centerline segments of the plant. In the second step, a hierarchical reconstruction is done to group the segments according to continuity principles. This paper covers an overview of the relevant processing steps along the proposed pipeline and provides an insight into the image acquisition as well as into the most relevant results from the evaluation process.