Topological Image Analysis and (Normalised) Representations for Plant Phenotyping

This paper discusses the use of topological image analysis to derive characteristics needed in plant phenotyping. Due to certain features of root systems (deformation over time, overlaps of branches in a 2D image of the root system) a topological analysis is needed to correctly derive these characteristics. The advantages of such a topological analysis are highlighted in this paper and root phenotyping is presented as a new application for computational topology. Characteristics used in plant phenotyping that can be derived from root images using methods of topological image analysis are further presented. A Reeb graph based representation of root images is shown as an example for such a topological analysis. Based on a graph representation a new, normalised representation of root images is introduced.