title: Landmark-free statistical analysis of the shape of plant leaves.
abstract: The shapes of plant leaves are important features to biologists, as they can help in distinguishing plant species, measuring their health, analyzing their growth patterns, and understanding relations between various species. Most of the methods that have been developed in the past focus on comparing the shape of individual leaves using either descriptors or finite sets of landmarks. However, descriptor-based representations are not invertible and thus it is often hard to map descriptor variability into shape variability. On the other hand, landmark-based techniques require automatic detection and registration of the landmarks, which is very challenging in the case of plant leaves that exhibit high variability within and across species. In this paper, we propose a statistical model based on the Squared Root Velocity Function (SRVF) representation and the Riemannian elastic metric of Srivastava et al. (2011) to model the observed continuous variability in the shape of plant leaves. We treat plant species as random variables on a non-linear shape manifold and thus statistical summaries, such as means and covariances, can be computed. One can then study the principal modes of variations and characterize the observed shapes using probability density models, such as Gaussians or Mixture of Gaussians. We demonstrate the usage of such statistical model for (1) efficient classification of individual leaves, (2) the exploration of the space of plant leaf shapes, which is important in the study of population-specific variations, and (3) comparing entire plant species, which is fundamental to the study of evolutionary relationships in plants. Our approach does not require descriptors or landmarks but automatically solves for the optimal registration that aligns a pair of shapes. We evaluate the performance of the proposed framework on publicly available benchmarks such as the Flavia, the Swedish, and the ImageCLEF2011 plant leaf datasets.
authors.affiliation: Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes SA5095, Australia; Australian Centre for Plant Functional Genomics, Pty Ltd, Australia. Electronic address: hamid.laga@unisa.edu.au.
authors.forename: Hamid
authors.initials: H
authors.lastname: Laga
authors.affiliation: Department of Statistics, The Ohio State University, United States.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kurtek
authors.affiliation: Department of Statistics, Florida State University, United States.
authors.forename: Anuj
authors.initials: A
authors.lastname: Srivastava
authors.affiliation: Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes SA5095, Australia; Australian Centre for Plant Functional Genomics, Pty Ltd, Australia.
authors.forename: Stanley J
authors.initials: SJ
authors.lastname: Miklavcic
mesh_terms: D002965:Classification / Q000379:methods*; D015233:Models, Statistical; D018515:Plant Leaves / Q000033:anatomy & histology*; D011336:Probability; D013045:Species Specificity
keywords: Elastic shape analysis; Leaf shape alignment; Plant development; Principal Component Analysis; Species comparison