How Much Shallow Coral Habitat Is There on the Great Barrier Reef?

Australia’s Great Barrier Reef (GBR) is a globally unique and precious national resource; however, the geomorphic and benthic composition and the extent of coral habitat per reef are greatly understudied. However, this is critical to understand the spatial extent of disturbance impacts and recovery potential. This study characterizes and quantifies coral habitat based on depth, geomorphic and benthic composition maps of more than 2164 shallow offshore GBR reefs. The mapping approach combined a Sentinel-2 satellite surface reflectance image mosaic and derived depth, wave climate, reef slope and field data in a random-forest machine learning and object-based protocol. Area calculations, for the first time, incorporated the 3D characteristic of the reef surface above 20 m. Geomorphic zonation maps (0–20 m) provided a reef extent estimate of 28,261 km2 (a 31% increase to current estimates), while benthic composition maps (0–10 m) estimated that ~10,600 km2 of reef area (~57% of shallow offshore reef area) was covered by hard substrate suitable for coral growth, the first estimate of potential coral habitat based on substrate availability. Our high-resolution maps provide valuable information for future monitoring and ecological modeling studies and constitute key tools for supporting the management, conservation and restoration efforts of the GBR

Coral Reef Change Detection in Remote Pacific Islands Using Support Vector Machine Classifiers

Despite the abundance of research on coral reef change detection, few studies have been conducted to assess the spatial generalization principles of a live coral cover classifier trained using remote sensing data from multiple locations. The aim of this study is to develop a machine learning classifier for coral dominated benthic cover-type class (CDBCTC) based on ground truth observations and Landsat images, evaluate the performance of this classifier when tested against new data, then deploy the classifier to perform CDBCTC change analysis of multiple locations. The proposed framework includes image calibration, support vector machine (SVM) training and tuning, statistical assessment of model accuracy, and temporal pixel-based image dierencing. Validation of the methodology was performed by cross-validation and train/test split using ground truth observations of benthic cover from four dierent reefs. These four locations (Palmyra Atoll, Kingman Reef, Baker Island Atoll, and Howland Island) as well as two additional locations (Kiritimati Island and Tabuaeran Island) were then evaluated for CDBCTC change detection. The in-situ training accuracy against ground truth observations for Palmyra Atoll, Kingman Reef, Baker Island Atoll, and Howland Island were 87.9%, 85.7%, 69.2%, and 82.1% respectively. The classifier attained generalized accuracy scores of 78.8%, 81.0%, 65.4%, and 67.9% for the respective locations when trained using ground truth observations from neighboring reefs and tested against the local ground truth observations of each reef. The classifier was trained using the consolidated ground truth data of all four sites and attained a cross-validated accuracy of 75.3%. The CDBCTC change detection analysis showed a decrease in CDBCTC of 32% at Palmyra Atoll, 25% at Kingman Reef, 40% at Baker Island Atoll, 25% at Howland Island, 35% at Tabuaeran Island, and 43% at Kiritimati Island. This research establishes a methodology for developing a robust classifier and the associated Controlled Parameter Cross-Validation (CPCV) process for evaluating how well the model will generalize to new data. It is an important step for improving the scientific understanding of temporal change within coral reefs around the globe

Exploring the relationships between biodiversity and benthic habitat in the Primeiras and Segundas Protected Area, Mozambique

A Reserva dos Arquipélagos Primeiras e Segundas, localizada no norte de Moçambique, é a maior zona marítima protegida de África, estendendo-se por mais de 200 km de costa. Apesar da sua importância para a economia local, informações sobre os seus ecossistemas marinhos, e particularmente habitats bênticos, são escassas. Doze atóis foram mapeados na região usando object-based image classification de imagens de satélite de muito alta resolução (IKONOS, Quickbird, and WorldView-2). Dados georreferenciados sobre a superficie bêntica e profundidade foram recolhidos em três campanhas de campo, abrangendo um total de quarto atóis e dois baixos. Os mapas produzidos permitem a estimativa de três tipos distintos de superfície coralina (campo, retalhos e falésias), a diferenciação de areia, cascalho e rocha e a detecção de ervas marinhas e macroalgas castanhas, identificando-se até 24 habitats bênticos, com precisão média superior a 50%. Novas informações recolhidas indicam a presença de superfícies bênticas profundas a prolongarem-se dos atóis, o que sugere a necessidade de pesquisa adicional, e está de acordo com o conhecimento actual da existência de um recife de coral quase contínuo desde o Quénia até Moçambique. A análise da biodiversidade das comunidades coralinas e ictiológicas apoia a percepção local de que os ecossistemas estão em declínio. Não foi, no entanto, possível confirmar a sua ligação a práticas de pesca, nem o pressuposto de que a biodiversidade de peixes é maior nas ilhas mais a sul, i.e. longe do principal porto de pesca. Este trabalho contribui para uma descrição detalhada dos habitats marinhos, adequada a usos de gestão e planeamento típicos, nomeadamente a definição de zonas de pesca e monitorização da superfície coralina, contribuindo simultaneamente para o desenvolvimento da aplicação de detecção remota aos campos da biodiversidade e conservação.The Primeiras and Segundas Archipelago Reserve, located in the waters of northern Mozambique, is the largest marine protected area in Africa, extending over 200 km of coastline. Despite the region’s importance for the local economic, information on the marine ecosystem, notably benthic habitat, is very scarce. Twelve atolls were mapped in the region using object-based image classification of very-high resolution satellite imagery (IKONOS, Quickbird, and WorldView-2). Geographically referenced data on benthic cover and depth were gathered in the course of three fieldwork expeditions covering a total of four atolls and two shallow reef structures. The resulting maps allow the estimation of three distinct types of coral cover (field, patches, spurs and grooves); the differentiation of sand, rubble and rock substrate; and the detection of seagrass and brown macroalgae, identifying up to 24 benthic habitats with overall accuracy above 50%. New information indicates the presence of deep benthic cover extending from the atolls, suggesting the need for further research, and supporting current knowledge of the existence of an almost continuous coral reef from Kenya to Mozambique. The results of the analysis of coralline and ichthyological data support the local perception that ecosystems are in decline. It was not possible to verify its connection with fishing practices and the assumption of greater fish biodiversity farther away from the main fishing harbour, i.e. in the southern islands. This work provides a detailed depiction of marine habitats adequate for standard management and planning purposes, namely in the definition of fishing zones and coral cover monitoring, while contributing to the advance of the application of remote sensing to the biodiversity and conservation fields.The Primeiras and Segundas Environmental Protected Area, located in the waters of northern Mozambique, is the largest marine protected area in Africa, extending over 200 km of coastline. Despite the region’s importance for the local economic, information on the marine ecosystem, notably benthic habitat is very scarce. Twelve islands surrounded by coral reefs were mapped in the region using very high resolution satellite images and descriptions of the sea bottom gathered in the field. The resulting maps allow the differentiation of sand, rubble and rock on the sea bottom; the detection of different types of maritime vegetation; and of three distinct types of coral cover. Three types of maps were produced, with different detail levels. The most detailed map has a maximum of 24 classes with an overall accuracy above 50%. The analysis of coral and fish biodiversity data indicate the local ecosystems decline – both quantity and diversity of coral and fish have registered a decrease when compared to 2006 values. It was not possible to verify that fish stocks are decreasing because of current fishing practices, nor that the southern islands, further away from the main fishing harbour, support larger and healthier fish communities. Unidentified structures extending from mapped coral were observed, suggesting the existence of a deeper benthic cover. Further research is recommended, as this additional extension of the coral reef systems could prove of great importance for local and regional ecosystems. With this work it was possible to provide a detailed description of local marine habitats and its coral and fish biodiversity, essential to the Protected Area management and planning, while contributing to the advance of the application of remote sensing to nature conservation

Remote sensing applications: an overview

Remote Sensing (RS) refers to the science of identification of earth surface features and estimation of their geo-biophysical properties using electromagnetic radiation as a medium of interaction. Spectral, spatial, temporal and polarization signatures are major characteristics of the sensor/target, which facilitate target discrimination. Earth surface data as seen by the sensors in different wavelengths (reflected, scattered and/or emitted) is radiometrically and geometrically corrected before extraction of spectral information. RS data, with its ability for a synoptic view, repetitive coverage with calibrated sensors to detect changes, observations at different resolutions, provides a better alternative for natural resources management as compared to traditional methods. Indian Earth Observation (EO) programme has been applications-driven and national development has been its prime motivation. From Bhaskara to Cartosat, India's EO capability has increased manifold. Improvements are not only in spatial, spectral, temporal and radiometric resolutions, but also in their coverage and value-added products. Some of the major operational application themes, in which India has extensively used remote sensing data are agriculture, forestry, water resources, land use, urban sprawl, geology, environment, coastal zone, marine resources, snow and glacier, disaster monitoring and mitigation, infrastructure development, etc. The paper reviews RS techniques and applications carried out using both optical and microwave sensors. It also analyses the gap areas and discusses the future perspectives

Workflow for the generation of expert-derived training and validation data: a view to global scale habitat mapping

Our ability to completely and repeatedly map natural environments at a global scale have increased significantly over the past decade. These advances are from delivery of a range of on-line global satellite image archives and global-scale processing capabilities, along with improved spatial and temporal resolution satellite imagery. The ability to accurately train and validate these global scale-mapping programs from what we will call “reference data sets” is challenging due to a lack of coordinated financial and personnel resourcing, and standardized methods to collate reference datasets at global spatial extents. Here, we present an expert-driven approach for generating training and validation data on a global scale, with the view to mapping the world’s coral reefs. Global reefs were first stratified into approximate biogeographic regions, then per region reference data sets were compiled that include existing point data or maps at various levels of accuracy. These reference data sets were compiled from new field surveys, literature review of published surveys, and from individually sourced contributions from the coral reef monitoring and management agencies. Reference data were overlaid on high spatial resolution satellite image mosaics (3.7 m × 3.7 m pixels; Planet Dove) for each region. Additionally, thirty to forty satellite image tiles; 20 km × 20 km) were selected for which reference data and/or expert knowledge was available and which covered a representative range of habitats. The satellite image tiles were segmented into interpretable groups of pixels which were manually labeled with a mapping category via expert interpretation. The labeled segments were used to generate points to train the mapping models, and to validate or assess accuracy. The workflow for desktop reference data creation that we present expands and up-scales traditional approaches of expert-driven interpretation for both manual habitat mapping and map training/validation. We apply the reference data creation methods in the context of global coral reef mapping, though our approach is broadly applicable to any environment. Transparent processes for training and validation are critical for usability as big data provide more opportunities for managers and scientists to use global mapping products for science and conservation of vulnerable and rapidly changing ecosystems

A review of marine geomorphometry, the quantitative study of the seafloor

Geomorphometry, the science of quantitative terrain characterization, has traditionally focused on the investigation of terrestrial landscapes. However, the dramatic increase in the availability of digital bathymetric data and the increasing ease by which geomorphometry can be investigated using geographic information systems (GISs) and spatial analysis software has prompted interest in employing geomorphometric techniques to investigate the marine environment. Over the last decade or so, a multitude of geomorphometric techniques (e.g. terrain attributes, feature extraction, automated classification) have been applied to characterize seabed terrain from the coastal zone to the deep sea. Geomorphometric techniques are, however, not as varied, nor as extensively applied, in marine as they are in terrestrial environments. This is at least partly due to difficulties associated with capturing, classifying, and validating terrain characteristics underwater. There is, nevertheless, much common ground between terrestrial and marine geomorphometry applications and it is important that, in developing marine geomorphometry, we learn from experiences in terrestrial studies. However, not all terrestrial solutions can be adopted by marine geomorphometric studies since the dynamic, four-dimensional (4-D) nature of the marine environment causes its own issues throughout the geomorphometry workflow. For instance, issues with underwater positioning, variations in sound velocity in the water column affecting acousticbased mapping, and our inability to directly observe and measure depth and morphological features on the seafloor are all issues specific to the application of geomorphometry in the marine environment. Such issues fuel the need for a dedicated scientific effort in marine geomorphometry. This review aims to highlight the relatively recent growth of marine geomorphometry as a distinct discipline, and offers the first comprehensive overview of marine geomorphometry to date. We address all the five main steps of geomorphometry, from data collection to the application of terrain attributes and features. We focus on how these steps are relevant to marine geomorphometry and also highlight differences and similarities from terrestrial geomorphometry. We conclude with recommendations and reflections on the future of marine geomorphometry. To ensure that geomorphometry is used and developed to its full potential, there is a need to increase awareness of (1) marine geomorphometry amongst scientists already engaged in terrestrial geomorphometry, and of (2) geomorphometry as a science amongst marine scientists with a wide range of backgrounds and experiences.peer-reviewe

SeeCucumbers: using deep learning and drone iagery to detect sea cucumbers on coral reef flats

Sea cucumbers (Holothuroidea or holothurians) are a valuable fishery and are also crucial nutrient recyclers, bioturbation agents, and hosts for many biotic associates. Their ecological impacts could be substantial given their high abundance in some reef locations and thus monitoring their populations and spatial distribution is of research interest. Traditional in situ surveys are laborious and only cover small areas but drones offer an opportunity to scale observations more broadly, especially if the holothurians can be automatically detected in drone imagery using deep learning algorithms. We adapted the object detection algorithm YOLOv3 to detect holothurians from drone imagery at Hideaway Bay, Queensland, Australia. We successfully detected 11,462 of 12,956 individuals over 2.7ha with an average density of 0.5 individual/m2. We tested a range of hyperparameters to determine the optimal detector performance and achieved 0.855 mAP, 0.82 precision, 0.83 recall, and 0.82 F1 score. We found as few as ten labelled drone images was sufficient to train an acceptable detection model (0.799 mAP). Our results illustrate the potential of using small, affordable drones with direct implementation of open-source object detection models to survey holothurians and other shallow water sessile species

Multiple stable states and catastrophic shifts in coastal wetlands: Progress, challenges, and opportunities in validating theory using remote sensing and other methods

open5siThe analysis by K.B. Moffett was partially supported by National Science Foundation grant EAR-1013843 to Stanford University. Any opinions, findings, and onclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. The analysis by W. Nardin was partially supported by Office of Naval Research Award N00014-14-1-0114 to Boston University. The analysis by C. Wang was partially supported by National Natural Science Funds of China (41376120 and 41401413). The analysis by C. Wang and S. Temmerman was also partially supported by the European Union Programme Erasmus Mundus External Cooperation Window (EMECW)-Lot 14-China. K.B. Moffett thanks B.C. Smith for the analysis for the Wax Lake Delta example of Section 4.2 and S.M. Gorelick for the funding leading to the San Francisco Bay example of Section 4.3. W. Nardin thanks S. Fagherazzi and C. Woodcock for the funding leading to the Mekong River Delta example of Section 4.1. S. Silvestri thanks M. Marani for inspiring ideas and research on coastal wetland processes.Multiple stable states are established in coastal tidal wetlands (marshes, mangroves, deltas, seagrasses) by ecological, hydrological, and geomorphological feedbacks. Catastrophic shifts between states can be induced by gradual environmental change or by disturbance events. These feedbacks and outcomes are key to the sustainability and resilience of vegetated coastlines, especially as modulated by human activity, sea level rise, and climate change. Whereas multiple stable state theory has been invoked to model salt marsh responses to sediment supply and sea level change, there has been comparatively little empirical verification of the theory for salt marshes or other coastal wetlands. Especially lacking is long-term evidence documenting if or how stable states are established and maintained at ecosystem scales. Laboratory and field-plot studies are informative, but of necessarily limited spatial and temporal scope. For the purposes of long-term, coastal-scale monitoring, remote sensing is the best viable option. This review summarizes the above topics and highlights the emerging promise and challenges of using remote sensing-based analyses to validate coastal wetland dynamic state theories. This significant opportunity is further framed by a proposed list of scientific advances needed to more thoroughly develop the field.openMoffett K.B.; Nardin W.; Silvestri S.; Wang C.; Temmerman S.Moffett K.B.; Nardin W.; Silvestri S.; Wang C.; Temmerman S

Bias Reduction in Machine Learning Classifiers for Spatiotemporal Analysis of Coral Reefs using Remote Sensing Images

This dissertation is an evaluation of the generalization characteristics of machine learning classifiers as applied to the detection of coral reefs using remote sensing images. Three scientific studies have been conducted as part of this research: 1) Evaluation of Spatial Generalization Characteristics of a Robust Classifier as Applied to Coral Reef Habitats in Remote Islands of the Pacific Ocean 2) Coral Reef Change Detection in Remote Pacific Islands using Support Vector Machine Classifiers 3) A Generalized Machine Learning Classifier for Spatiotemporal Analysis of Coral Reefs in the Red Sea. The aim of this dissertation is to propose and evaluate a methodology for developing a robust machine learning classifier that can effectively be deployed to accurately detect coral reefs at scale. The hypothesis is that Landsat data can be used to train a classifier to detect coral reefs in remote sensing imagery and that this classifier can be trained to generalize across multiple sites. Another objective is to identify how well different classifiers perform under the generalized conditions and how unique the spectral signature of coral is as environmental conditions vary across observation sites. A methodology for validating the generalization performance of a classifier to unseen locations is proposed and implemented (Controlled Parameter Cross-Validation,). Analysis is performed using satellite imagery from nine different locations with known coral reefs (six Pacific Ocean sites and three Red Sea sites). Ground truth observations for four of the Pacific Ocean sites and two of the Red Sea sites were used to validate the proposed methodology. Within the Pacific Ocean sites, the consolidated classifier (trained on data from all sites) yielded an accuracy of 75.5% (0.778 AUC). Within the Red Sea sites, the consolidated classifier yielded an accuracy of 71.0% (0.7754 AUC). Finally, long-term change detection analysis is conducted for each of the sites evaluated. In total, over 16,700 km2 was analyzed for benthic cover type and cover change detection analysis. Within the Pacific Ocean sites, decreases in coral cover ranged from 25.3% reduction (Kingman Reef) to 42.7% reduction (Kiritimati Island). Within the Red Sea sites, decrease in coral cover ranged from 3.4% (Umluj) to 13.6% (Al Wajh)

Coastal and Inland Aquatic Data Products for the Hyperspectral Infrared Imager (HyspIRI)

The HyspIRI Aquatic Studies Group (HASG) has developed a conceptual list of data products for the HyspIRI mission to support aquatic remote sensing of coastal and inland waters. These data products were based on mission capabilities, characteristics, and expected performance. The topic of coastal and inland water remote sensing is very broad. Thus, this report focuses on aquatic data products to keep the scope of this document manageable. The HyspIRI mission requirements already include the global production of surface reflectance and temperature. Atmospheric correction and surface temperature algorithms, which are critical to aquatic remote sensing, are covered in other mission documents. Hence, these algorithms and their products were not evaluated in this report. In addition, terrestrial products (e.g., land use land cover, dune vegetation, and beach replenishment) were not considered. It is recognized that coastal studies are inherently interdisciplinary across aquatic and terrestrial disciplines. However, products supporting the latter are expected to already be evaluated by other components of the mission. The coastal and inland water data products that were identified by the HASG, covered six major environmental and ecological areas for scientific research and applications: wetlands, shoreline processes, the water surface, the water column, bathymetry and benthic cover types. Accordingly, each candidate product was evaluated for feasibility based on the HyspIRI mission characteristics and whether it was unique and relevant to the HyspIRI science objectives