Automating Digital Leaf Measurement: The Tooth, the Whole Tooth, and Nothing but the Tooth
Open Access
- 1 August 2012
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 7 (8), e42112
- https://doi.org/10.1371/journal.pone.0042112
Abstract
Many species of plants produce leaves with distinct teeth around their margins. The presence and nature of these teeth can often help botanists to identify species. Moreover, it has long been known that more species native to colder regions have teeth than species native to warmer regions. It has therefore been suggested that fossilized remains of leaves can be used as a proxy for ancient climate reconstruction. Similar studies on living plants can help our understanding of the relationships. The required analysis of leaves typically involves considerable manual effort, which in practice limits the number of leaves that are analyzed, potentially reducing the power of the results. In this work, we describe a novel algorithm to automate the marginal tooth analysis of leaves found in digital images. We demonstrate our methods on a large set of images of whole herbarium specimens collected from Tilia trees (also known as lime, linden or basswood). We chose the genus Tilia as its constituent species have toothed leaves of varied size and shape. In a previous study we extracted leaves automatically from a set of images. Our new algorithm locates teeth on the margins of such leaves and extracts features such as each tooth’s area, perimeter and internal angles, as well as counting them. We evaluate an implementation of our algorithm’s performance against a manually analyzed subset of the images. We found that the algorithm achieves an accuracy of 85% for counting teeth and 75% for estimating tooth area. We also demonstrate that the automatically extracted features are sufficient to identify different species of Tilia using a simple linear discriminant analysis, and that the features relating to teeth are the most useful.This publication has 17 references indexed in Scilit:
- Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for BeginnersPLOS ONE, 2011
- Sensitivity of leaf size and shape to climate: global patterns and paleoclimatic applicationsNew Phytologist, 2011
- Phenotypic Plasticity of Leaf Shape along a Temperature Gradient in Acer rubrumPLOS ONE, 2009
- Neural networks and cluster analysis for unsupervised classification of cultivated species ofTilia(Malvaceae)Botanical Journal of the Linnean Society, 2009
- LAMINA: a tool for rapid quantification of leaf size and shape parametersBMC Plant Biology, 2008
- Why Do Toothed Leaves Correlate with Cold Climates? Gas Exchange at Leaf Margins Provides New Insights into a Classic Paleotemperature ProxyInternational Journal of Plant Sciences, 2006
- Correlations of climate and plant ecology to leaf size and shape: potential proxies for the fossil recordAmerican Journal of Botany, 2005
- How many species of seed plants are there?Taxon, 2003
- How many species of seed plants are there?Taxon, 2001
- A Botanical Index of Cretaceous and Tertiary ClimatesScience, 1915