Pound, Michael P. and French, Andrew P. and Fozard, John A. and Murchie, Erik H. and Pridmore, Tony P. (2016) A patch-based approach to 3D plant shoot phenotyping. Machine Vision and Applications . ISSN 1432-1769

The emerging discipline of plant phenomics aims to measure key plant characteristics, or traits, though as yet the set of plant traits that should be measured by automated systems is not well defined. Methods capable of recovering generic representations of the 3D structure of plant shoots from images would provide a key technology underpinning quantification of a wide range of current and future physiological and morphological traits. We present a fully automatic approach to image-based 3D plant reconstruction which represents plants as series of small planar sections that together model the complex architecture of leaf surfaces. The initial boundary of each leaf patch is refined using a level set method, optimising the model based on image information, curvature constraints and the position of neighbouring surfaces. The reconstruction process makes few assumptions about the nature of the plant material being reconstructed. As such it is applicable to a wide variety of plant species and topologies, and can be extended to canopy-scale imaging. We demonstrate the effectiveness of our approach on real images of wheat and rice plants, an artificial plant with challenging architecture, as well as a novel virtual dataset that allows us to compute distance measures of reconstruction accuracy. We also illustrate the method’s potential to support the identifiB Tony P. Pridmore tony.pridmore@nottingham.ac.uk Michael P. Pound michael.pound@nottingham.ac.uk 1 School of Computer Science, University of Nottingham, Nottingham NG8 1BB, UK 2 Centre for Plant Integrative Biology, University of Nottingham, Nottingham, UK 3 School of Biosciences, University of Nottingham, Nottingham, UK cation of individual leaves, and so the phenotyping of plant shoots, using a spectral clustering approach.