Image-based phenotyping of the mature arabidopsis shoot system

The image-based phenotyping of mature plants faces severalchallenges from the image acquisition to the determination of quanti-tative characteristics describing their appearance. In this work a frame-work to extract geometrical and topological traits of 2D images of matureArabidopsis thalianais proposed. The phenotyping pipeline recovers therealistic branching architecture of dried and attened plants in two steps.In the rst step, a tracing approach is used for the extraction of centerlinesegments of the plant. In the second step, a hierarchical reconstructionis done to group the segments according to continuity principles. Thispaper covers an overview of the relevant processing steps along the pro-posed pipeline and provides an insight into the image acquisition as wellas into the most relevant results from the evaluation process.