title: A practical introduction to skeletons for the plant sciences.
abstract: Before the availability of digital photography resulting from the invention of charged couple devices in 1969, the measurement of plant architecture was a manual process either on the plant itself or on traditional photographs. The introduction of cheap digital imaging devices for the consumer market enabled the wide use of digital images to capture the shape of plant networks such as roots, tree crowns, or leaf venation. Plant networks contain geometric traits that can establish links to genetic or physiological characteristics, support plant breeding efforts, drive evolutionary studies, or serve as input to plant growth simulations. Typically, traits are encoded in shape descriptors that are computed from imaging data. Skeletons are one class of shape descriptors that are used to describe the hierarchies and extent of branching and looping plant networks. While the mathematical understanding of skeletons is well developed, their application within the plant sciences remains challenging because the quality of the measurement depends partly on the interpretation of the skeleton. This article is meant to bridge the skeletonization literature in the plant sciences and related technical fields by discussing best practices for deriving diameters and approximating branching hierarchies in a plant network.
authors.affiliation: School of Biology and School of Interactive Computing, Georgia Institute of Technology, Atlanta, Georgia 30332 USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Bucksch
keywords: Reeb graph; branching structure; leaf venation; medial axis; plant network; root; skeletonization; tree crown