title: Automated recovery of three-dimensional models of plant shoots from multiple color images.
abstract: Increased adoption of the systems approach to biological research has focused attention on the use of quantitative models of biological objects. This includes a need for realistic three-dimensional (3D) representations of plant shoots for quantification and modeling. Previous limitations in single-view or multiple-view stereo algorithms have led to a reliance on volumetric methods or expensive hardware to record plant structure. We present a fully automatic approach to image-based 3D plant reconstruction that can be achieved using a single low-cost camera. The reconstructed plants are represented as a series of small planar sections that together model the more complex architecture of the leaf surfaces. The boundary of each leaf patch is refined using the level-set method, optimizing the model based on image information, curvature constraints, and the position of neighboring surfaces. The reconstruction process makes few assumptions about the nature of the plant material being reconstructed and, as such, 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 data sets of wheat (Triticum aestivum) and rice (Oryza sativa) plants as well as a unique virtual data set that allows us to compute quantitative measures of reconstruction accuracy. The output is a 3D mesh structure that is suitable for modeling applications in a format that can be imported in the majority of 3D graphics and software packages.
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P., A.P.F., E.H.M., T.P.P.); andSchool of Computer Science, University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, United Kingdom (A.P.F., T.P.P.).
authors.forename: Michael P
authors.initials: MP
authors.lastname: Pound
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P., A.P.F., E.H.M., T.P.P.); andSchool of Computer Science, University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, United Kingdom (A.P.F., T.P.P.).
authors.forename: Andrew P
authors.initials: AP
authors.lastname: French
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P., A.P.F., E.H.M., T.P.P.); andSchool of Computer Science, University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, United Kingdom (A.P.F., T.P.P.).
authors.forename: Erik H
authors.initials: EH
authors.lastname: Murchie
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (M.P.P., A.P.F., E.H.M., T.P.P.); andSchool of Computer Science, University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, United Kingdom (A.P.F., T.P.P.) tony.pridmore@nottingham.ac.uk.
authors.forename: Tony P
authors.initials: TP
authors.lastname: Pridmore
mesh_terms: D000465:Algorithms; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008962:Models, Theoretical; D012275:Oryza / Q000166:cytology* / Q000254:growth & development; D018515:Plant Leaves / Q000166:cytology / Q000254:growth & development; D018520:Plant Shoots / Q000166:cytology / Q000254:growth & development; D012984:Software; D014908:Triticum / Q000166:cytology* / Q000254:growth & development