Jonathan Y. Clark

Review: Plant species identification using digital morphometrics: A review

Plants are of fundamental importance to life on Earth. The shapes of leaves, petals and whole plants are of great significance to plant science, as they can help to distinguish between different species, to measure plant health, and even to model climate change. The growing interest in biodiversity and the increasing availability of digital images combine to make this topic timely. The global shortage of expert taxonomists further increases the demand for software tools that can recognize and characterize plants from images. A robust automated species identification system would allow people with only limited botanical training and expertise to carry out valuable field work. We review the main computational, morphometric and image processing methods that have been used in recent years to analyze images of plants, introducing readers to relevant botanical concepts along the way. We discuss the measurement of leaf outlines, flower shape, vein structures and leaf textures, and describe a wide range of analytical methods in use. We also discuss a number of systems that apply this research, including prototypes of hand-held digital field guides and various robotic systems used in agriculture. We conclude with a discussion of ongoing work and outstanding problems in the area.

Artificial neural networks for species identification by taxonomists

This paper is a study of the value of applying artificial neural networks (ANNs), specifically a multilayer perceptron (MLP), to identification of higher plants using morphological characters collected by conventional means. A practical methodology is thus demonstrated to enable botanical or zoological taxonomists to use ANNs as advisory tools for identification purposes. A comparison is made between the ability of the neural network and that of traditional methods for plant identification by means of a case study in the flowering plant genus Lithops N.E. Brown (Aizoaceae). In particular, a comparison is made with taxonomic keys generated by means of the DELTA system. The ANN is found to perform better than the DELTA key generator, for conditions where the available data is limited, and species relatively difficult to distinguish.

Automating Digital Leaf Measurement: The Tooth, the Whole Tooth, and Nothing but the Tooth

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.

Identification of botanical specimens using artificial neural networks

This work describes a method of training an artificial neural network, specifically a multilayer perceptron (MLP), to identify plants using morphological characters collected from herbarium specimens. A practical methodology is presented to enable taxonomists to use neural networks as advisory tools for identification purposes, by collating results from a population of neural networks. A comparison is made between the ability of the neural network and that of other methods for identification by means of a case study in the ornamental tree genus Tilia L. (Tiliaceae). In particular, a comparison is made with taxonomic keys generated by means of the DELTA system, a suite of programs commonly used by botanists for that purpose. In this study, the MLP was found to perform better than the DELTA key generator.

A Bayesian Network Model for the Diagnosis of the Caring Procedure for Wheelchair Users with Spinal Injury

This paper describes a probabilistic causal model for the caring procedure to be followed on wheelchair users with spinal injury. Uncertainty in the caring procedure arises mostly from incomplete information about patient findings (i.e. the signs and symptoms) due to loss of sensation and movement caused by the spinal cord injury. As a result, it may not be easy to assess the extent of a condition -- and, thus, make an accurate diagnosis. Bayesian networks are used for diagnostic reasoning because they offer a way of conducting probabilistic inference about the conditions associated with the caring procedure in the face of uncertainty. The network structure and numerical parameters are based on data elicited from the qualified staff nurses and literature of the National Spinal Injury Centre, Stoke Mandeville Hospital, Aylesbury, UK. We also present the model and report the results of the diagnostic performance tests using the AgenaRisk Bayesian network package.

Automated plant identification using artificial neural networks

This paper describes a method of training an artificial neural network, specifically a multilayer perceptron (MLP), to act as a tool to help identify plants using morphological characters collected automatically from images of botanical herbarium specimens. A methodology is presented here to provide a practical way for taxonomists to use neural networks as automated identification tools, by collating results from a population of neural networks. A case study is provided using data extracted from specimens of the genus Tilia in the Herbarium of the Royal Botanic Gardens, Kew, UK. A classification accuracy of 44% was achieved on this challenging multiclass problem.

A Bayesian network model for the diagnosis of the caring procedure for wheelchair users with spinal injury

This paper describes a probabilistic causal model for the caring procedure to be followed on wheelchair users with spinal injury. Uncertainty in the caring procedure arises mostly from incomplete information about patient findings (i.e. the signs and symptoms) due to loss of sensation and movement caused by the spinal cord injury. As a result, it may not be easy to assess the extent of a condition -- and, thus, make an accurate diagnosis. Bayesian networks are used for diagnostic reasoning because they offer a way of conducting probabilistic inference about the conditions associated with the caring procedure in the face of uncertainty. The network structure and numerical parameters are based on data elicited from the qualified staff nurses and literature of the National Spinal Injury Centre, Stoke Mandeville Hospital, Aylesbury, UK. We also present the model and report the results of the diagnostic performance tests using the AgenaRisk Bayesian network package.

DIMITRA: An online expert system for carers of paraplegics and quadriplegics

During the last three decades, the area of expert systems has attracted enormous research interest, and a multitude of systems, tackling all kinds of applications, have been designed and implemented. An area where expert systems have been extensively applied is medical care; however, despite the very large number of systems implemented, no system for the special care required for wheelchair users with spinal injury has been developed. The purpose of this report is to present the design and implementation methodology of the DIMITRA expert system, an online consultation system under development for the special caring procedure of such patients. This system is considered to be of value for virtual healthcare in the home, because it is designed for remote access by carers and their patients.