Acute pseudo-landmarking and Constellation homologies: A generalized workflow to identify and track segmented structures in plant time series images

Assessing plant phenotypes throughout the lifecycle is integral to exploring the development, genetics, and evolution of morphology, and can be critical for agronomic and basic research studies. Although various automated or semi-automated phenomic approaches have been developed, it has been challenging to analyze differential growth because of difficulties in segmenting and annotating specific structures or positions in the plant body and maintaining their identities throughout time-series data. To address this gap, we have developed a generalized workflow linking our previously published function, Acute, with a companion homology workflow, Constellation, in the PlantCV environment. Acute identifies acute shapes (pseudo-landmarks) in the plant body, most often corresponding to leaf tips and ligular regions. Constellation uses a strategy of dimensionality reduction via starscape followed by hierarchical clustering through constella to identify ‘constellations’ of segments in eigenspace ...