Benthic Habitat Mapping Using Multispectral High-Resolution Imagery: Evaluation of Shallow Water Atmospheric Correction Techniques

Impact of Atmospheric Correction on Classification and Quantification of Seagrass Density from WorldView-2 Imagery

Mapping the seagrass distribution and density in the underwater landscape can improve global Blue Carbon estimates. However, atmospheric absorption and scattering introduce errors in space-based sensors' retrieval of sea surface reflectance, affecting seagrass presence, density, and above-ground carbon (AGC seagrass ) estimates. This study assessed atmospheric correction's impact on mapping seagrass using WorldView-2 satellite imagery from Saint Joseph Bay, Saint George Sound, and Keaton Beach in Florida, USA. Coincident in situ measurements of water-leaving radiance (L W ), optical properties, and seagrass leaf area index (LAI) were collected. Seagrass classification and the retrieval of LAI were compared after empirical line height (ELH) and dark-object subtraction (DOS) methods were used for atmospheric correction. DOS left residual brightness in the blue and green bands but had minimal impact on the seagrass classification accuracy. However, the brighter reflectance values reduced LAI retrievals by up to 50% compared to ELH-corrected images and ground-based observations. This study offers a potential correction for LAI underestimation due to incomplete atmospheric correction, enhancing the retrieval of seagrass density and above-ground Blue Carbon from WorldView-2 imagery without in situ observations for accurate atmospheric interference correction.

Preliminary Classification of Selected Farmland Habitats in Ireland Using Deep Neural Networks

Ireland has a wide variety of farmlands that includes arable fields, grassland, hedgerows, streams, lakes, rivers, and native woodlands. Traditional methods of habitat identification rely on field surveys, which are resource intensive, therefore there is a strong need for digital methods to improve the speed and efficiency of identification and differentiation of farmland habitats. This is challenging because of the large number of subcategories having nearly indistinguishable features within the habitat classes. Heterogeneity among sites within the same habitat class is another problem. Therefore, this research work presents a preliminary technique for accurate farmland classification using stacked ensemble deep convolutional neural networks (DNNs). The proposed approach has been validated on a high-resolution dataset collected using drones. The image samples were manually labelled by the experts in the area before providing them to the DNNs for training purposes. Three pre-trained DNNs customized using the transfer learning approach are used as the base learners. The predicted features derived from the base learners were then used to train a DNN based meta-learner to achieve high classification rates. We analyse the obtained results in terms of convergence rate, confusion matrices, and ROC curves. This is a preliminary work and further research is needed to establish a standard technique.

Comparing Sentinel-2 and WorldView-3 Imagery for Coastal Bottom Habitat Mapping in Atlantic Canada

Satellite remote sensing is a valuable tool to map and monitor the distribution of marine macrophytes such as seagrass and seaweeds that perform many ecological functions and services in coastal habitats. Various satellites have been used to map the distribution of these coastal bottom habitat-forming species, with each sensor providing unique benefits. In this study, we first explored optimal methods to create bottom habitat maps using WorldView-3 satellite imagery. We secondly compared the WorldView-3 bottom habitat maps to previously produced Sentinel-2 maps in a temperate, optically complex environment in Nova Scotia, Canada to identify the top performing classification and the advantages and disadvantages of each sensor. Sentinel-2 provides a global, freely accessible dataset where four bands are available at a 10-m spatial resolution in the visible and near infrared spectrum. Conversely, WorldView-3 is a commercial satellite where eight bands are available at a 2-m spatial resolution in the visible and near infrared spectrum, but data catalogs are costly and limited in scope. Our optimal WorldView-3 workflow processed images from digital numbers to habitat classification maps, and included a semiautomatic stripe correction. Our comparison of bottom habitat maps explored the impact of improved WorldView-3 spatial resolution in isolation, and the combined advantage of both WorldView’s increased spatial and spectral resolution relative to Sentinel-2. We further explored the effect of tidal height on classification success, and relative changes in water clarity between images collected at different dates. As expected, both sensors are suitable for bottom habitat mapping. The value of WorldView-3 came from both its increased spatial and spectral resolution, particularly for fragmented vegetation, and the value of Sentinel-2 imagery comes from its global dataset that readily allows for large scale habitat mapping. Given the variation in scale, cost and resolution of the two sensors, we provide recommendations on their use for mapping and monitoring marine macrophyte habitat in Atlantic Canada, with potential applications to other coastal areas of the world.

Fusion of Drone-Based RGB and Multi-Spectral Imagery for Shallow Water Bathymetry Inversion

Shallow bathymetry inversion algorithms have long been applied in various types of remote sensing imagery with relative success. However, this approach requires that imagery with increased radiometric resolution in the visible spectrum be available. The recent developments in drones and camera sensors allow for testing current inversion techniques on new types of datasets with centimeter resolution. This study explores the bathymetric mapping capabilities of fused RGB and multispectral imagery as an alternative to costly hyperspectral sensors for drones. Combining drone-based RGB and multispectral imagery into a single cube dataset provides the necessary radiometric detail for shallow bathymetry inversion applications. This technique is based on commercial and open-source software and does not require the input of reference depth measurements in contrast to other approaches. The robustness of this method was tested on three different coastal sites with contrasting seafloor types with a maximum depth of six meters. The use of suitable end-member spectra, which are representative of the seafloor types of the study area, are important parameters in model tuning. The results of this study are promising, showing good correlation (R2 > 0.75 and Lin’s coefficient > 0.80) and less than half a meter average error when they are compared with sonar depth measurements. Consequently, the integration of imagery from various drone-based sensors (visible range) assists in producing detailed bathymetry maps for small-scale shallow areas based on optical modelling.

Inland Reservoir Water Quality Inversion and Eutrophication Evaluation Using BP Neural Network and Remote Sensing Imagery: A Case Study of Dashahe Reservoir

In this study, an inland reservoir water quality parameters’ inversion model was developed using a back propagation (BP) neural network to conduct reservoir eutrophication evaluation, according to multi-temporal remote sensing images and field observations. The inversion model based on the BP neural network (the BP inversion model) was applied to a large inland reservoir in Jiangmen city, South China, according to the field observations of five water quality parameters, namely, Chlorophyl-a (Chl-a), Secchi Depth (SD), total phosphorus (TP), total nitrogen (TN), and Permanganate of Chemical Oxygen Demand (CODMn), and twelve periods of Landsat8 satellite remote sensing images. The reservoir eutrophication was evaluated. The accuracy of the BP inversion model for each water parameter was compared with that of the linear inversion model, and the BP inversion models of two parameters (i.e., Chl-a and CODMn) with larger fluctuation range were superior to the two multiple linear inversion models due to the ability of improving the generalization of the BP neural network. The Dashahe Reservoir was basically in the state of mesotrophication and light eutrophication. The area of light eutrophication accounted for larger proportions in spring and autumn, and the reservoir inflow was the main source of nutrient salts.

Emerging Sensor Platforms Allow for Seagrass Extent Mapping in a Turbid Estuary and from the Meadow to Ecosystem Scale

Seagrass meadows are globally important habitats, protecting shorelines, providing nursery areas for fish, and sequestering carbon. However, both anthropogenic and natural environmental stressors have led to a worldwide reduction seagrass habitats. For purposes of management and restoration, it is essential to produce accurate maps of seagrass meadows over a variety of spatial scales, resolutions, and at temporal frequencies ranging from months to years. Satellite remote sensing has been successfully employed to produce maps of seagrass in the past, but turbid waters and difficulty in obtaining low-tide scenes pose persistent challenges. This study builds on an increased availability of affordable high temporal frequency imaging platforms, using seasonal unmanned aerial vehicle (UAV) surveys of seagrass extent at the meadow scale, to inform machine learning classifications of satellite imagery of a 40 km2 bay. We find that object-based image analysis is suitable to detect seasonal trends in seagrass extent from UAV imagery and find that trends vary between individual meadows at our study site Bahía de San Quintín, Baja California, México, during our study period in 2019. We further suggest that compositing multiple satellite imagery classifications into a seagrass probability map allows for an estimation of seagrass extent in turbid waters and report that in 2019, seagrass covered 2324 ha of Bahía de San Quintín, indicating a recovery from losses reported for previous decades.

Coral Reef Mapping with Remote Sensing and Machine Learning: A Nurture and Nature Analysis in Marine Protected Areas

Mapping habitats is essential to assist strategic decisions regarding the use and protection of coral reefs. Coupled with machine learning (ML) algorithms, remote sensing has allowed detailed mapping of reefs at meaningful scales. Here we integrated WorldView-3 and Landsat-8 imagery and ML techniques to produce a map of suitable habitats for the occurrence of a model species, the hydrocoral Millepora alcicornis, in coral reefs located inside marine protected areas in Northeast Brazil. Conservation and management efforts in the region were also analyzed, integrating human use layers to the ecological seascape. Three ML techniques were applied: two to derive base layers, namely geographically weighted regressions for bathymetry and support vector machine classifier (SVM) for habitat mapping, and one to build the species distribution model (MaxEnt) for Millepora alcicornis, a conspicuous and important reef-building species in the area. Additionally, human use was mapped based on the presence of tourists and fishers. SVM yielded 15 benthic classes (e.g., seagrass, sand, coral), with an overall accuracy of 79%. Bathymetry and its derivative layers depicted the topographical complexity of the area. The Millepora alcicornis distribution model identified distance from the shore and depth as topographical factors limiting the settling and growth of coral colonies. The most important variables were ecological, showing the importance of maintaining high biodiversity in the ecosystem. The comparison of the habitat suitability model with species absence and human use maps indicated the impact of direct human activities as potential inhibitors of coral development. Results reinforce the importance of the establishment of no-take zones and other protective measures for maintaining local biodiversity.

Analysis of Very High Spatial Resolution Images for Automatic Shoreline Extraction and Satellite-Derived Bathymetry Mapping

The amount of Earth observation images available to the public has been the main source of information, helping governments and decision-makers tackling the current world’s most pressing global challenge. However, a number of highly skilled and qualified personnel are still needed to fill the gap and help turn these data into intelligence. In addition, the accuracy of this intelligence relies on the quality of these images in times of temporal, spatial, and spectral resolution. For the purpose of contributing to the global effort aiming at monitoring natural and anthropic processes affecting coastal areas, we proposed a framework for image processing to extract the shoreline and the shallow water depth on GeoEye-1 satellite image and orthomosaic image acquired by an unmanned aerial vehicle (UAV) on the coast of San Vito Lo Capo, with image preprocessing steps involving orthorectification, atmospheric correction, pan sharpening, and binary imaging for water and non-water pixels analysis. Binary imaging analysis step was followed by automatic instantaneous shoreline extraction on a digital image and satellite-derived bathymetry (SDB) mapping on GeoEye-1 water pixels. The extraction of instantaneous shoreline was conducted automatically in ENVI software using a raster to vector (R2V) algorithm, whereas the SDB was computed in ArcGIS software using a log-band ratio method applied on the satellite image and available field data for calibration and vertical referencing. The results obtained from these very high spatial resolution images demonstrated the ability of remote sensing techniques in providing information where techniques using traditional methods present some limitations, especially due to their inability to map hard-to-reach areas and very dynamic near shoreline waters. We noticed that for the period of 5 years, the shoreline of San Vito Lo Capo sand beach migrated about 15 m inland, indicating the high dynamism of this coastal area. The bathymetric information obtained on the GeoEye-1 satellite image provided water depth until 10 m deep with R2 = 0.753. In this paper, we presented cost-effective and practical methods for automatic shoreline extraction and bathymetric mapping of shallow water, which can be adopted for the management and the monitoring of coastal areas.

Multiplatform Earth Observation Systems for Monitoring Water Quality in Vulnerable Inland Ecosystems: Maspalomas Water Lagoon

The accurate monitoring of water quality indicators, bathymetry and distribution of benthic habitats in vulnerable ecosystems is key to assessing the effects of climate change, the quality of natural areas and to guide appropriate biodiversity, tourism or fisheries policies. Coastal and inland water ecosystems are very complex but crucial due to their richness and primary production. In this context, remote sensing can be a reliable way to monitor these areas, mainly thanks to satellite sensors’ improved spatial and spectral capabilities and airborne or drone instruments. In general, mapping bodies of water is challenging due to low signal-to-noise (SNR) at sensor level, due to the very low reflectance of water surfaces as well as atmospheric effects. Therefore, the main objective of this work is to provide a robust processing framework to estimate water quality parameters in inland shallow waters using multiplatform data. More specifically, we measured chlorophyll concentrations (Chl-a) from multispectral and hyperspectral sensors on board satellites, aircrafts and drones. The Natural Reserve of Maspalomas, Canary Island (Spain), was chosen for the study because of its complexity as well as being an inner lagoon with considerable organic and inorganic matter and chlorophyll concentration. This area can also be considered a well-known coastal-dune ecosystem attracting a large amount of tourists. The water quality parameter estimated by the remote sensing platforms has been validated using co-temporal in situ measurements collected during field campaigns, and quite satisfactory results have been achieved for this complex ecosystem. In particular, for the drone hyperspectral instrument, the root mean square error, computed to quantify the differences between the estimated and in situ chlorophyll-a concentrations, was 3.45 with a bias of 2.96.

Satellite-Based Bathymetric Modeling Using a Wavelet Network Model

Accurate bathymetric modeling is required for safe maritime navigation in shallow waters as well as for other marine operations. Traditionally, bathymetric modeling is commonly carried out using linear models, such as the Stumpf method. Linear methods are developed to derive bathymetry using the strong linear correlation between the grey values of satellite imagery visible bands and the water depth where the energy of these visible bands, received at the satellite sensor, is inversely proportional to the depth of water. However, without satisfying homogeneity of the seafloor topography, this linear method fails. The current state-of-the-art is represented by artificial neural network (ANN) models, which were developed using a non-linear, static modeling function. However, more accurate modeling can be achieved using a highly non-linear, dynamic modeling function. This paper investigates a highly non-linear wavelet network model for accurate satellite-based bathymetric modeling with dynamic non-linear wavelet activation function that has been proven to be a valuable modeling method for many applications. Freely available Level-1C satellite imagery from the Sentinel-2A satellite was employed to develop and justify the proposed wavelet network model. The top-of-atmosphere spectral reflectance values for the multispectral bands were employed to establish the wavelet network model. It is shown that the root-mean-squared (RMS) error of the developed wavelet network model was about 1.82 m, and the correlation between the wavelet network model depth estimate and “truth” nautical chart depths was about 95%, on average. To further justify the proposed model, a comparison was made among the developed, highly non-linear wavelet network method, the Stumpf log-ratio method, and the ANN method. It is concluded that the developed, highly non-linear wavelet network model is superior to the Stumpf log-ratio method by about 37% and outperforms the ANN model by about 21%, on average, on the basis of the RMS errors. Also, the accuracy of the bathymetry-derived wavelet network model was evaluated on the basis of the International Hydrographic Organization (IHO)’s standards for all survey orders. It is shown that the accuracy of the bathymetry derived from the wavelet network model does not meet the IHO’s standards for all survey orders; however, the wavelet network model can still be employed as an accurate and powerful tool for survey planning when conducting hydrographic surveys for new, shallow water areas.

Use of Drones for the Topo-Bathymetric Monitoring of the Reservoirs of the Segura River Basin

The Segura River Basin (SRB), located in the South East of Spain, has the lowest percentage of renewable water resources of all the Spanish basins. Therefore, knowledge of the annual rate of water reservoir sedimentation is an important issue to be resolved in one of the most water-stressed regions in the western Mediterranean basin. This paper describes the sensors developed in collaboration with technology-based enterprises (aerial drone, floating drone, and underwater drone), and the methodology for integration of the different types of data acquired to monitor the reservoirs of the SRB. The proposed solution was applied to 21 reservoirs of the SRB. The proposed methodology is based on the use of unmanned aerial vehicles (UAV) for photogrammetry of the reservoir surface area. For each reservoir, two flights were completed, with 20 cm and 5 cm resolution, respectively. Then, a triangular irregular network mesh was generated by GIS techniques. Surface water vehicles (USV) and underwater remote-operated vehicles (ROV) were used to undertake bathymetric surveys. In addition, water quality measurements were made with an ROV device. The main results consist of topographic and bathymetric measurements for each reservoir, obtained by using equipment based on OpenSource technology. According to the results, the annual rate of storage capacity loss of water resources in the SRB´s reservoirs is 0.33%.

Seabed Mapping in Coastal Shallow Waters Using High Resolution Multispectral and Hyperspectral Imagery

Coastal ecosystems experience multiple anthropogenic and climate change pressures. To monitor the variability of the benthic habitats in shallow waters, the implementation of effective strategies is required to support coastal planning. In this context, high-resolution remote sensing data can be of fundamental importance to generate precise seabed maps in coastal shallow water areas. In this work, satellite and airborne multispectral and hyperspectral imagery were used to map benthic habitats in a complex ecosystem. In it, submerged green aquatic vegetation meadows have low density, are located at depths up to 20 m, and the sea surface is regularly affected by persistent local winds. A robust mapping methodology has been identified after a comprehensive analysis of different corrections, feature extraction, and classification approaches. In particular, atmospheric, sunglint, and water column corrections were tested. In addition, to increase the mapping accuracy, we assessed the use of derived information from rotation transforms, texture parameters, and abundance maps produced by linear unmixing algorithms. Finally, maximum likelihood (ML), spectral angle mapper (SAM), and support vector machine (SVM) classification algorithms were considered at the pixel and object levels. In summary, a complete processing methodology was implemented, and results demonstrate the better performance of SVM but the higher robustness of ML to the nature of information and the number of bands considered. Hyperspectral data increases the overall accuracy with respect to the multispectral bands (4.7% for ML and 9.5% for SVM) but the inclusion of additional features, in general, did not significantly improve the seabed map quality.