Stuart Phinn

The University of Queensland | UQ · School of Earth and Environmental Sciences

Data pre-processing for developing a generalised land use and land cover (LULC) deep learning model using earth observation data is important for the classification of a different date and/or sensor. However, it is unclear how to approach deep learning segmentation problems in earth observation data. In this paper, we trialled different methods of...

In this paper, we trialled different methods of data preparation for Convolutional Neural Network (CNN) training and semantic segmentation of land use land cover (LULC) features within aerial photography over the Wet Tropics and Atherton Tablelands, Queensland, Australia. This was conducted through trialling and ranking various training patch selec...

Landscape rehabilitation following mining is required to be resilient to disturbance impacts such as fire, drought and disease. As mining companies undergo the process of rehabilitation certification and mine closure, there are notable knowledge gaps on the ecological risks associated with mature rehabilitated landscapes, based largely on the assum...

Convolutional Neural Networks (CNN) consist of various hyper-parameters which need to be specified or can be altered when defining a deep learning architecture. There are numerous studies which have tested different types of networks (e.g. U-Net, DeepLabv3+) or created new architectures, benchmarked against well-known test datasets. However, there...

The determination of key phenological growth stages of banana plantations, such as flower emergence and plant establishment, is difficult due to the asynchronous growth habit of banana plants. Identifying phenological events assists growers in determining plant maturity, and harvest timing and guides the application of time-specific crop inputs. Cu...

This research investigates the capability of field-based spectroscopy (350–2500 nm) for discriminating banana plants (Cavendish subgroup Williams) infested with spider mites from those unaffected. Spider mites are considered a major threat to agricultural production, as they occur on over 1000 plant species, including banana plant varieties. Plants...

In the Australian summer season of 2022, exceptional rainfall events occurred in Southeast Queensland and parts of New South Wales, leading to extensive flooding of rural and urban areas. Here, we map the extent of flooding in the city of Brisbane and evaluate the change in electricity usage as a proxy for flood impact using VIIRS nighttime brightn...

The Great Barrier Reef is generally considered a passive tectonic setting, however the effect of antecedent topography and local geological structures on Holocene reef development is poorly understood. Offshore reefs along the central shelf were recently hypothesized to have grown continuously through a possible small Holocene sea level fall, in re...

The commencement of the United Nations Decade on Ecosystem Restoration has highlighted the urgent need to improve restoration science and fast‐track ecological outcomes. The application of remote sensing for monitoring purposes has increased over the past two decades providing a variety of image datasets and derived products suitable to map and mea...

Improved development of remote sensing approaches to deliver timely and accurate measurements for environmental monitoring, particularly with respect to marine and estuarine environments is a priority. We describe a machine learning, cloud processing protocol for simultaneous mapping seagrass meadows in waters of variable quality across Moreton Bay...

Most of the worlds’ population relies on the processes and ecosystems in the coastal zone. Understanding the long-term change of coastlines is critical for the effective management of these complex, and heavily utilised regions. There has been a recent increase of studies focused on large-scale shoreline change mapping. However, most current method...

The aim of this research is to expand recent developments in the mapping of pasture yield with remotely piloted aircraft systems to that of satellite-borne imagery. To date, spatially explicit and accurate information of the pasture resource base is needed for improved climate-adapted livestock rangeland grazing. This study developed deep learning...

In the summer of 2019-2020, Australia experienced its most severe season of wildfires. In our paper, (Levin, N., Yebra, M., Phinn, S. (2021) Unveiling the factors responsible for Australia’s Black Summer fires of 2019/2020. Fire, 4(3):58. https://doi.org/10.3390/fire4030058 ), we analyzed the largest wildfires of Australia's Black Summer (> 100 sq....

The summer season of 2019-2020 has been named Australia's Black Summer because of the large forest fires that burnt for months in southeast Australia, affecting millions of Australia's citizens and hundreds of millions of animals and capturing global media attention. This extensive fire season has been attributed to the global climate crisis, a lon...

The aim of this research is to expand recent developments in the mapping of pasture yield with remotely piloted aircraft systems to that of satellite-borne imagery. Up to date, spatially explicit and accurate information of the pasture resource base is needed for improved climate-adapted livestock rangeland grazing. This study developed deep learni...

Remote sensing has been applied to map the extent and biophysical properties of mangroves. However, the impact of several critical factors, such as the fractional cover and leaf-to-total area ratio of mangroves, on their canopy reflectance have rarely been reported. In this study, a systematic global sensitivity analysis was performed for mangroves...

Evaluating shoreline retreat rate (SRR) on different spatial‐temporal scales is critical for effective coastal management. Large‐scale evaluations typically rely on data‐driven methods such as Discrete Bayesian networks (BNs). However, these BNs require discretization of continuous variables which can lead to information loss. Here, we propose a ne...

Unoccupied aerial vehicles (UAVs) have become increasingly commonplace in aiding planning and management decisions in agricultural and horticultural crop production. The ability of UAV-based sensing technologies to provide high spatial (<1 m) and temporal (on-demand) resolution data facilitates monitoring of individual plants over time and can prov...

Global shallow water bathymetry maps offer critical information to inform activities such as scientific research, environment protection, and marine transportation. Methods that employ satellite-based bathymetric modeling provide an alternative to conventional shipborne measurements, offering high spatial resolution combined with extensive coverage...

Big data reveals new, stark pictures of the state of our environments. It also reveals ‘bright spots’ amongst the broad pattern of decline and—crucially—the key conditions for these cases. Big data analyses could benefit the planet if tightly coupled with ongoing sustainability efforts.

Coral reef research and management efforts can be improved when supported by reef maps providing local-scale details across global extents. However, such maps are difficult to generate due to the broad geographic range of coral reefs, the complexities of relating satellite imagery to geomorphic or ecological realities, and other challenges. However...

The aim of this research was to test recent developments in the use of Remotely Piloted Aircraft Systems or Unmanned Aerial Vehicles (UAV)/drones to map both pasture quantity as biomass yield and pasture quality as the proportions of key pasture nutrients, across a selected range of field sites throughout the rangelands of Queensland. Improved past...

The mining industry has been operating across the globe for millennia, but it is only in the last 50 years that remote sensing technology has enabled the visualization, mapping and assessment of mining impacts and landscape recovery. Our review of published literature (1970–2019) found that the number of ecologically focused remote sensing studies...

The aim of this research was to test recent developments in the use of Remotely Piloted Aircraft Systems or Unmanned Aerial Vehicles (UAV) to map pasture biomass yield and nutrient status, across a selected range of field sites throughout the rangelands of Queensland. Improved pasture management begins with an understanding of the state of the reso...

Coral reef management and conservation stand to benefit from improved high-resolution global mapping. Yet classifications employed in large-scale reef mapping to date are typically poorly defined, not shared or region-specific. Here we present Reef Cover , a new coral reef geomorphic zone classification, developed to support global-scale coral reef...

Machine learning has been employed for various mapping and modeling tasks using input variables from different sources of remote sensing data. For feature selection involving high-spatial and spectral dimensionality data, various methods have been developed and incorporated into the machine learning framework to ensure an efficient and optimal comp...

Ecosystem monitoring is fundamental to our understanding of how ecosystem change is impacting our natural resources and is vital for developing evidence‐based policy and management. However, the different types of ecosystem monitoring, along with their recommended applications, are often poorly understood and contentious. Varying definitions and st...

To support the adoption of precision agricultural practices in horticultural tree crops, prior research has investigated the relationship between crop vigour (height, canopy density, health) as measured by remote sensing technologies, to fruit quality, yield and pruning requirements. However, few studies have compared the accuracy of different remo...

Australia is one of the world’s largest producers of macadamia nuts. As macadamia trees can take up to 15 years to mature and produce maximum yield, it is important to optimize tree condition. Field based assessment of macadamia tree condition is time-consuming and often inconsistent. Using remotely sensed imagery may allow for faster, more extensi...

Airborne Laser Scanning (ALS) and Terrestrial Laser Scanning (TLS) systems are useful tools for deriving horticultural tree structure estimates. However, there are limited studies to guide growers and agronomists on different applications of the two technologies for horticultural tree crops, despite the importance of measuring tree structure for pr...

Sentinel-2 data provided the opportunity for complementary data to existing missions including Landsat and SPOT. In this study, multitemporal cloud masking (MCM) used to detect cloud and cloud shadow masking for Landsat 8 was improved to detect cloud and cloud shadow for Sentinel-2 data. This improvement takes advantages of the spectral similarity...

In recent times, multi-spectral drone imagery has proved to be a useful tool for measuring tree crop canopy structure. In this context, establishing the most appropriate flight planning variable settings is an essential consideration due to their controls on the quality of the imagery and derived maps of tree and crop biophysical properties. During...

Restoring degraded landscapes for conservation purposes can involve transaction costs to acquire the land in the first place. Zunyi and colleagues propose a framework for prioritizing uncontested lands that can provide ecosystem services without those costs.

Great Barrier Reef catchments are under pressure from the effects of climate change, landscape modifications, and hydrology alterations. With the use of remote sensing datasets covering large areas, conventional methods of change detection can expose broad transitions, whereas workflows that excerpt data for time-series trends divulge more subtle t...

Forests and coral reefs are structurally complex ecosystems threatened by climate change. In situ 3D imaging measurements provide unprecedented, quantitative and detailed structural information that allows testing of hypotheses relating form to function. This affords new insights into both individual organisms and their relationship to their surrou...

Following over 20 years of manned airborne LiDAR in the remote sensing of geomorphological change in coastal environments, rapid advancements in unmanned aerial vehicle (UAV) technologies have expanded the possibilities of acquiring very high-resolution data efficiently over spatial-temporal scales not previously feasible. This study employed a new...

Environmental monitoring data is fundamental to our understanding of environmental change and is vital to evidence-based policy and management. However, different types of ecological monitoring, along with their different applications, are often poorly understood and contentious. Varying definitions and strict adherence to a specific monitoring typ...

Knowledge of the extent and degree of wooded vegetation cover in the arid parts of Australia is essential for land-holders and management agencies. The balance between wooded and ground-cover vegetation is important to livestock production and landscape health. Adequate mapping of changes in wooded vegetation cover allows the assessment of its expa...

Policies aiming to preserve vegetated coastal ecosystems (VCE; tidal marshes, mangroves and seagrasses) to mitigate greenhouse gas emissions require national assessments of blue carbon resources. Here, we present organic carbon (C) storage in VCE across Australian climate regions and estimate potential annual CO2 emission benefits of VCE conservati...

Landsat 8 images have been widely used for many applications, but cloud and cloud-shadow cover issues remain. In this study, multitemporal cloud masking (MCM), designed to detect cloud and cloud-shadow for Landsat 8 in tropical environments, was improved for application in sub-tropical environments, with the greatest improvement in cloud masking. W...

Forest structure is an important driver of ecosystem dynamics, including the exchange of carbon, water and energy between canopies and the atmosphere. Structural descriptors are also used in numerous studies of ecological processes and ecosystem services. Over the last 20+ years, lidar technology has fundamentally changed the way we observe and des...

Accurate bathymetric mapping of shallow waters (above 15 m) is essential for a wide range of scientific research, government, transport, and industry globally. Satellite-based bathymetry estimation approaches offer an alternative to traditional shipborne measurements, especially given advancements in their spatial and temporal resolution of satelli...

Globally, the area of agricultural land is shrinking in part due to environmental degradation. Acquisition and restoration of degraded lands no longer used for agriculture may present a major conservation opportunity with minimal social and political opposition. The ability to efficiently and accurately identify these lands from regional to global...

The capabilities and utility of UAV LiDAR and surface from motion photogrammetry have been of wide discussion in the remote sensing community and assumptions made, often speculative, about the potential strengths and limitations of these systems. Here, we employ a side-by-side test of the CSIRO Hovermap LiDAR and Micasense RedEdge multispectral cam...

Savannas comprise a major component of the Earth system and contribute ecosystem services and functions essential to human livelihoods. Monitoring spatial and temporal trends in savanna vegetation and understanding change drivers is therefore crucial. Widespread greening has been identified across southern Africa; yet its drivers and manifestations...

Utilised globally across a wide range of applications, the ability to assess and understand LiDAR system capabilities represents an essential component in developing informed decisions on instrument selection and the logistical planning processes associated with site-specific limitations, project objectives and UAV operations. This study employed t...

Woody vegetation is an integral component of savannas. Here, two main change processes alter woody vegetation, namely shrub encroachment and deforestation. Both impact a range of ecosystem services and functions across scales. Accurate estimates of change, including spatial extent, rate and drivers are lacking. This is primarily due to savanna vege...

Mammals can serve as an indicator of global climate change impacts on species’ distributions due to the wide range of ecological niches they utilize. Tropical Asia encompasses several biodiversity hotspots, is the largest reservoir of mammalian diversity on earth, and has already experienced the extinction of several mammal species either regionall...

Tree condition, pruning and orchard management practices within intensive horticultural tree crop systems can be determined via measurements of tree structure. Multi-spectral imagery acquired from an unmanned aerial system (UAS) has been demonstrated as an accurate and efficient platform for measuring various tree structural attributes, but researc...

Increasing human populations around the global coastline have caused extensive loss, degradation and fragmentation of coastal ecosystems, threatening the delivery of important ecosystem services¹. As a result, alarming losses of mangrove, coral reef, seagrass, kelp forest and coastal marsh ecosystems have occurred1–6. However, owing to the difficul...

Tree condition, pruning and orchard management practices within intensive horticultural tree crop systems can be determined via measurements of tree structure. Multi-spectral imagery acquired from an unmanned aerial system (UAS) has been demonstrated as an accurate and efficient platform for measuring various tree structural attributes, but researc...

Vegetation metrics, such as leaf area (LA), leaf area density (LAD), and vertical leaf area profile, are essential measures of tree-scale biophysical processes associated with photosynthetic capacity, and canopy geometry. However, there are limited published investigations of their use for horticultural tree crops. This study evaluated the ability...

Multi-spectral imagery captured from unmanned aerial systems (UAS) is becoming increasingly popular for the improved monitoring and managing of various horticultural crops. However, for UAS-based data to be used as an industry standard for assessing tree structure and condition as well as production parameters, it is imperative that the appropriate...

The Sentinel-2A and 2B Multi-Spectral Instrument (MSI) offers a specification of potential value toward a number of objectives in remote sensing of coral reefs. Coral reefs represent a unique challenge for remote sensing, being highly heterogeneous at metre scales and occurring at variable depths and water clarity regimes. However, conservation ini...

UAS-based multi-spectral imagery is becoming increasingly popular for the improved monitoring and managing of various horticultural crops. However, for UAS data to be used as an industry standard for assessing tree structure and condition as well as production parameters, it is imperative that the appropriate data collection and pre-processing prot...

This chapter explains the types of information on the biophysical properties of seagrass and its surrounding environments, which are able to be measured, mapped, monitored and/or modelled using remote sensing techniques. This includes specifying the environmental conditions where these approaches do not work. “Remote sensing” refers to the use of a...

Seagrass seascapes are 100s m² to 1000s of km² coastal regions in nearshore, sandy to muddy benthic environments that are characterized by the presence of seagrasses. Here we explore the development of seagrass seascape research in Australia. Determining the distribution of seagrasses started with mapping their extent, but improvements in remote se...