Pollen image classification using the classifynder system: Algorithm comparison and a case study on New Zealand honey

We describe an investigation into how Massey University’s Pollen Classifynder can accelerate the understanding of pollen and its role in nature. The Classifynder is an imaging microscopy system that can locate, image and classify slide based pollen samples. Given the laboriousness of purely manual image acquisition and identification it is vital to exploit assistive technologies like the Classifynder to enable acquisition and analysis of pollen samples. It is also vital that we understand the strengths and limitations of automated systems so that they can be used (and improved) to compliment the strengths and weaknesses of human analysts to the greatest extent possible. This article reviews some of our experiences with the Classifynder system and our exploration of alternative classifier models to enhance both accuracy and interpretability. Our experiments in the pollen analysis problem domain have been based on samples from the Australian National University’s pollen reference collection (2,890 grains, 15 species) and images bundled with the Classifynder system (400 grains, 4 species). These samples have been represented using the Classifynder image feature set.We additionally work through a real world case study where we assess the ability of the system to determine the pollen make-up of samples of New Zealand honey. In addition to the Classifynder’s native neural network classifier, we have evaluated linear discriminant, support vector machine, decision tree and random forest classifiers on these data with encouraging results. Our hope is that our findings will help enhance the performance of future releases of the Classifynder and other systems for accelerating the acquisition and analysis of pollen samples.

A comparison of classification algorithms within the Classifynder pollen imaging system

We describe an investigation into how Massey University's Pollen Classifynder can accelerate the understanding of pollen and its role in nature. The Classifynder is an imaging microscopy system that can locate, image and classify slide based pollen samples. Given the laboriousness of purely manual image acquisition and identification it is vital to exploit assistive technologies like the Classifynder to enable acquisition and analysis of pollen samples. It is also vital that we understand the strengths and limitations of automated systems so that they can be used (and improved) to compliment the strengths and weaknesses of human analysts to the greatest extent possible. This article reviews some of our experiences with the Classifynder system and our exploration of alternative classifier models to enhance both accuracy and interpretability. Our experiments in the pollen analysis problem domain have been based on samples from the Australian National University's pollen reference collection (2890 grains, 15 species) and images bundled with the Classifynder system (400 grains, 4 species). These samples have been represented using the Classifynder image feature set. In addition to the Classifynder's native neural network classifier, we have evaluated linear discriminant, support vector machine, decision tree and random forest classifiers on these data with encouraging results. Our hope is that our findings will help enhance the performance of future releases of the Classifynder and other systems for accelerating the acquisition and analysis of pollen samples. © 2013 AIP Publishing LLC.

The Macroecology of Airborne Pollen in Australian and New Zealand Urban Areas

he composition and relative abundance of airborne pollen in urban areas of Australia and New Zealand are strongly influenced by geographical location, climate and land use. There is mounting evidence that the diversity and quality of airborne pollen is substantially modified by climate change and land-use yet there are insufficient data to project the future nature of these changes. Our study highlights the need for long-term aerobiological monitoring in Australian and New Zealand urban areas in a systematic, standardised, and sustained way, and provides a framework for targeting the most clinically significant taxa in terms of abundance, allergenic effects and public health burden.

New evidence of the reproductive organs of Glossopteris based on permineralized fossils from Queensland, Australia. II: pollen-bearing organ Ediea gen. nov

Ediea homevalensis H. Nishida, Kudo, Pigg & Rigby gen. et sp. nov. is proposed for permineralized pollen-bearing structures from the Late Permian Homevale Station locality of the Bowen Basin, Queensland, Australia. The taxon represents unisexual fertile shoots bearing helically arranged leaves on a central axis. The more apical leaves are fertile microsporophylls bearing a pair of multi-branched stalks on their adaxial surfaces that each supports a cluster of terminally borne pollen sacs. Proximal to the fertile leaves there are several rows of sterile scale-like leaves. The pollen sacs (microsporangia) have thickened and dark, striate walls that are typical of the Arberiella type found in most pollen organs presumed to be of glossopterid affinity. An examination of pollen organs at several developmental stages, including those containing in situ pollen of the Protohaploxypinus type, provides the basis for a detailed analysis of these types of structures, which bear similarities to both compression/impression Eretmonia-type glossopterid microsporangiate organs and permineralized Eretmonia macloughlinii from Antarctica. These fossils demonstrate that at least some Late Permian pollen organs were simple microsporophyll-bearing shoot systems and not borne directly on Glossopteris leaves.

Structural, physiological and molecular characterisation of the Australian native resurrection grass Tripogon loliiformis (F.Meull) C.E.Hubb during dehydration and rehydration

There is an urgent need to develop crops that can withstand future climates. Results from this thesis demonstrated that a native Australian resurrection grass exhibits structural, physiological and metabolic strategies to tolerate drying. These strategies may be utilized for the generation of stress tolerant crops.

Establishing turf grass increases soil greenhouse gas emissions in peri-urban environments

Urbanization is becoming increasingly important in terms of climate change and ecosystem functionality worldwide. We are only beginning to understand how the processes of urbanization influence ecosystem dynamics and how peri-urban environments contribute to climate change. Brisbane in South East Queensland (SEQ) currently has the most extensive urban sprawl of all Australian cities. This leads to substantial land use changes in urban and peri-urban environments and the subsequent gaseous emissions from soils are to date neglected for IPCC climate change estimations. This research examines how land use change effects methane (CH4) and nitrous oxide (N2O) fluxes from peri-urban soils and consequently influences the Global Warming Potential (GWP) of rural ecosystems in agricultural use undergoing urbanization. Therefore, manual and fully automated static chamber measurements determined soil gas fluxes over a full year and an intensive sampling campaign of 80 days after land use change. Turf grass, as the major peri-urban land cover, increased the GWP by 415 kg CO2-e ha 1 over the first 80 days after conversion from a well-established pasture. This results principally from increased daily average N2O emissions of 0.5 g N2O ha-1 d-1 from the pasture to 18.3 g N2O ha-1 d-1 from the turf grass due to fertilizer application during conversion. Compared to the native dry sclerophyll eucalypt forest, turf grass establishment increases the GWP by another 30 kg CO2-e ha 1. The results presented in this study clearly indicate the substantial impact of urbanization on soil-atmosphere gas exchange in form of non-CO2 greenhouse gas emissions particularly after turf grass establishment.

The biology and natural history of Tripogon loliiformis (Poaceae, Chloridoideae), an Australian resurrection grass

Tripogon loliiformis is a desiccation-tolerant grass that occurs throughout mainland Australia. There has been recent interest in this species as a model system for understanding desiccation tolerance in a native grass at the structural, molecular and physiological levels. However, not much is known about the biology and natural history of this species, despite its widespread geographic distribution and remarkable capability of withstanding prolonged drying. We provide an overview of the genus by consolidating information from a wide variety of sources. We report a variety of new and interesting observations on the general biology, ecology and desiccation response of T. loliiformis and conclude by highlighting areas for future research.