Mapping and classification of ecologically sensitive marine habitats using unmanned aerial vehicle (UAV) imagery and object-based image analysis (OBIA)

Nowadays, emerging technologies, such as long-range transmitters, increasingly miniaturized components for positioning, and enhanced imaging sensors, have led to an upsurge in the availability of new ecological applications for remote sensing based on unmanned aerial vehicles (UAVs), sometimes referred to as “drones”. In fact, structure-from-motion (SfM) photogrammetry coupled with imagery acquired by UAVs offers a rapid and inexpensive tool to produce high-resolution orthomosaics, giving ecologists a new way for responsive, timely, and cost-effective monitoring of ecological processes. Here, we adopted a lightweight quadcopter as an aerial survey tool and object-based image analysis (OBIA) workflow to demonstrate the strength of such methods in producing very high spatial resolution maps of sensitive marine habitats. Therefore, three different coastal environments were mapped using the autonomous flight capability of a lightweight UAV equipped with a fully stabilized consumer-grade RGB digital camera. In particular we investigated a Posidonia oceanica seagrass meadow, a rocky coast with nurseries for juvenile fish, and two sandy areas showing biogenic reefs of Sabelleria alveolata. We adopted, for the first time, UAV-based raster thematic maps of these key coastal habitats, produced after OBIA classification, as a new method for fine-scale, low-cost, and time saving characterization of sensitive marine environments which may lead to a more effective and efficient monitoring and management of natural resource

Guidance for benthic habitat mapping: an aerial photographic approach

This document, Guidance for Benthic Habitat Mapping: An Aerial Photographic Approach, describes proven technology that can be applied in an operational manner by state-level scientists and resource managers. This information is based on the experience gained by NOAA Coastal Services Center staff and state-level cooperators in the production of a series of benthic habitat data sets in Delaware, Florida, Maine, Massachusetts, New York, Rhode Island, the Virgin Islands, and Washington, as well as during Center-sponsored workshops on coral remote sensing and seagrass and aquatic habitat assessment. (PDF contains 39 pages) The original benthic habitat document, NOAA Coastal Change Analysis Program (C-CAP): Guidance for Regional Implementation (Dobson et al.), was published by the Department of Commerce in 1995. That document summarized procedures that were to be used by scientists throughout the United States to develop consistent and reliable coastal land cover and benthic habitat information. Advances in technology and new methodologies for generating these data created the need for this updated report, which builds upon the foundation of its predecessor

Improving Approaches to Mapping Seagrass within the Great Barrier Reef: From Field to Spaceborne Earth Observation

Seagrass meadows are a key ecosystem of the Great Barrier Reef World Heritage Area, providing one of the natural heritage attributes underpinning the reef’s outstanding universal value. We reviewed approaches employed to date to create maps of seagrass meadows in the optically complex waters of the Great Barrier Reef and explored enhanced mapping approaches with a focus on emerging technologies, and key considerations for future mapping. Our review showed that field-based mapping of seagrass has traditionally been the most common approach in the GBR-WHA, with few attempts to adopt remote sensing approaches and emerging technologies. Using a series of case studies to harness the power of machine-and deep-learning, we mapped seagrass cover with PlanetScope and UAV-captured imagery in a variety of settings. Using a machine-learn-ing pixel-based classification coupled with a bootstrapping process, we were able to significantly improve maps of seagrass, particularly in low cover, fragmented and complex habitats. We also used deep-learning models to derive enhanced maps from UAV imagery. Combined, these lessons and emerging technologies show that more accurate and efficient seagrass mapping approaches are possible, producing maps of higher confidence for users and enabling the upscaling of seagrass mapping into the future

Shallow-water benthic habitats of St. John, U.S. Virgin Islands

Coral reef ecosystems of the Virgin Islands Coral Reef National Monument, Virgin Islands National Park and the surrounding waters of St. John, U.S. Virgin Islands are a precious natural resource worthy of special protection and conservation. The mosaic of habitats including coral reefs, seagrasses and mangroves, are home to a diversity of marine organisms. These benthic habitats and their associated inhabitants provide many important ecosystem services to the community of St. John, such as fishing, tourism and shoreline protection. However, coral reef ecosystems throughout the U.S. Caribbean are under increasing pressure from environmental and anthropogenic stressors that threaten to destroy the natural heritage of these marine habitats. Mapping of benthic habitats is an integral component of any effective ecosystem-based management approach. Through the implementation of a multi-year interagency agreement, NOAA’s Center for Coastal Monitoring and Assessment - Biogeography Branch and the U.S. National Park Service (NPS) have completed benthic habitat mapping, field validation and accuracy assessment of maps for the nearshore marine environment of St. John. This work is an expansion of ongoing mapping and monitoring efforts conducted by NOAA and NPS in the U.S. Caribbean and replaces previous NOAA maps generated by Kendall et al. (2001) for the waters around St. John. The use of standardized protocols enables the condition of the coral reef ecosystems around St. John to be evaluated in context to the rest of the Virgin Island Territories and other U.S. coral ecosystems. The products from this effort provide an accurate assessment of the abundance and distribution of marine habitats surrounding St. John to support more effective management and conservation of ocean resources within the National Park system. This report documents the entire process of benthic habitat mapping in St. John. Chapter 1 provides a description of the benthic habitat classification scheme used to categorize the different habitats existing in the nearshore environment. Chapter 2 describes the steps required to create a benthic habitat map from visual interpretation of remotely sensed imagery. Chapter 3 details the process of accuracy assessment and reports on the thematic accuracy of the final maps. Finally, Chapter 4 is a summary of the basic map content and compares the new maps to a previous NOAA effort. Benthic habitat maps of the nearshore marine environment of St. John, U.S. Virgin Islands were created by visual interpretation of remotely sensed imagery. Overhead imagery, including color orthophotography and IKONOS satellite imagery, proved to be an excellent source from which to visually interpret the location, extent and attributes of marine habitats. NOAA scientists were able to accurately and reliably delineate the boundaries of features on digital imagery using a Geographic Information System (GIS) and fi eld investigations. The St. John habitat classification scheme defined benthic communities on the basis of four primary coral reef ecosystem attributes: 1) broad geographic zone, 2) geomorphological structure type, 3) dominant biological cover, and 4) degree of live coral cover. Every feature in the benthic habitat map was assigned a designation at each level of the scheme. The ability to apply any component of this scheme was dependent on being able to identify and delineate a given feature in remotely sensed imagery

Coral reef and associated habitat mapping using ALOS satellite imagery

Coral reefs are rich in biodiversity and ecosystem services. However increase in degradation are still occurring at an alarming rate. In management of this ecosystem, determination of its spatial distribution is of importance. Satellite imageries can be used to map distribution extent using spectral characteristics which is a fundamental parameter in mapping. The aims of this study were to determine the spectral characteristics of corals and associated habitats and to map its spatial distribution using 2009 ALOS advanced visible and near infrared radiometer type 2 (AVNIR-2) satellite imagery. Results indicated that coral and habitats surrounding the area display variation in the spectral characteristics magnitude but displays similar spectral curve. Spectral characteristics from the corals and surrounding habitats were determined by presence of benthic microalgae and calcium carbonate. Maximum likelihood classification on the image produced five main classes. Spatial distribution of coral and associated habitats indicated five main zones which are sandy shore zone, sandy intertidal zone, seagrass zone, coral/submerged sandy zone and rocky zone. Distribution of live corals indicated coverage of 0.54 km2, sea grass (0.94 km2), sandy bottom (1.31 km2) and rocky shores (0.19 km2). The results of this study indicated that ALOS satellite data was able to determine variation in spectral characteristics of coral reefs and other habitats thus is capable of mapping the ecosystems spatial distribution

Biogeographic analysis of the Tortugas Ecological Reserve: Examining the refuge effect following reserve establishment

Almost 120 days at sea aboard three NOAA research vessels and one fishing vessel over the past three years have supported biogeographic characterization of Tortugas Ecological Reserve (TER). This work initiated measurement of post-implementation effects of TER as a refuge for exploited species. In Tortugas South, seafloor transect surveys were conducted using divers, towed operated vehicles (TOV), remotely operated vehicles (ROV), various sonar platforms, and the Deepworker manned submersible. ARGOS drifter releases, satellite imagery, ichthyoplankton surveys, sea surface temperature, and diver census were combined to elucidate potential dispersal of fish spawning in this environment. Surveys are being compiled into a GIS to allow resource managers to gauge benthic resource status and distribution. Drifter studies have determined that within the ~ 30 days of larval life stage for fishes spawning at Tortugas South, larvae could reach as far downstream as Tampa Bay on the west Florida coast and Cape Canaveral on the east coast. Together with actual fish surveys and water mass delineation, this work demonstrates that the refuge status of this area endows it with tremendous downstream spillover and larval export potential for Florida reef habitats and promotes the maintenance of their fish communities. In Tortugas North, 30 randomly selected, permanent stations were established. Five stations were assigned to each of the following six areas: within Dry Tortugas National Park, falling north of the prevailing currents (Park North); within Dry Tortugas National Park, falling south of the prevailing currents (Park South); within the Ecological Reserve falling north of the prevailing currents (Reserve North); within the Ecological Reserve falling south of the prevailing currents (Reserve South); within areas immediately adjacent to these two strata, falling north of the prevailing currents (Out North); and within areas immediately adjacent to these two strata, falling south of the prevailing currents (Out South). Intensive characterization of these sites was conducted using multiple sonar techniques, TOV, ROV, diver-based digital video collection, diver-based fish census, towed fish capture, sediment particle-size, benthic chlorophyll analyses, and stable isotope analyses of primary producers, fish, and, shellfish. In order to complement and extend information from studies focused on the coral reef, we have targeted the ecotone between the reef and adjacent, non-reef habitats as these areas are well-known in ecology for indicating changes in trophic relationships at the ecosystem scale. Such trophic changes are hypothesized to occur as top-down control of the system grows with protection of piscivorous fishes. Preliminary isotope data, in conjunction with our prior results from the west Florida shelf, suggest that the shallow water benthic habitats surrounding the coral reefs of TER will prove to be the source of a significant amount of the primary production ultimately fueling fish production throughout TER and downstream throughout the range of larval fish dispersal. Therefore, the status and influence of the previously neglected, non-reef habitat within the refuge (comprising ~70% of TER) appears to be intimately tied to the health of the coral reef community proper. These data, collected in a biogeographic context, employing an integrated Before-After Control Impact design at multiple spatial scales, leave us poised to document and quantify the postimplementation effects of TER. Combined with the work at Tortugas South, this project represents a multi-disciplinary effort of sometimes disparate disciplines (fishery oceanography, benthic ecology, food web analysis, remote sensing/geography/landscape ecology, and resource management) and approaches (physical, biological, ecological). We expect the continuation of this effort to yield critical information for the management of TER and the evaluation of protected areas as a refuge for exploited species. (PDF contains 32 pages.

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.Peer ReviewedPostprint (published version