Rapid and Accurate Monitoring of Intertidal Oyster Reef Habitat Using Unoccupied Aircraft Systems and Structure from Motion

Abstract

Oysters support an economically important fishery in many locations in the United States and provide benefits to the surrounding environment by filtering water, providing habitat for fish, and stabilizing shorelines. Changes in oyster reef health reflect variations in factors such as recreational and commercial harvests, predation, disease, storms, and broader anthropogenic influences, such as climate change. Consistent measurements of reef area and morphology can help effectively monitor oyster habitat across locations. However, traditional approaches to acquiring these data are time-consuming and can be costly. Unoccupied aircraft systems (UAS) present a rapid and reliable method for assessing oyster habitat that may overcome these limitations, although little information on the accuracy of platforms and processing techniques is available. In the present study, oyster reefs ranging in size from 30 m2 to 300 m2 were surveyed using both fixed-wing and multirotor UAS and compared with ground-based surveys of each reef conducted with a real-time kinematic global positioning system (RTK-GPS). Survey images from UAS were processed using structure from motion (SfM) stereo photogrammetry techniques, with and without the use of ground control point (GCP) correction, to create reef-scale measures of area and morphology for comparison to ground-based measures. UAS-based estimates of both reef area and morphology were consistently lower than ground-based estimates, and the results of matched pairs analyses revealed that differences in reef area did not vary significantly by aircraft or the use of GCPs. However, the use of GCPs increased the accuracy of UAS-based reef morphology measurements, particularly in areas with the presence of water and/or homogeneous spectral characteristics. Our results indicate that both fixed-wing and multirotor UAS can be used to accurately monitor intertidal oyster reefs over time and that proper ground control techniques will improve measurements of reef morphology. These non-destructive methods help modernize oyster habitat monitoring by providing useful and accurate knowledge about the structure and health of oyster reefs ecosystems.

Trends in Oyster Populations in the Northeastern Gulf of Mexico: An Assessment of River Discharge and Fishing Effects over Time and Space

“…Our oyster density results over time and space also show declines in oyster counts, with the largest declines occurring in inshore areas, which may be becoming more like offshore and nearshore regions based on counts ( Figure 6). What is not known is whether these inshore losses are offset by the formation of new reefs elsewhere, although this could possibly be assessed through satellite, drone-based, or other surveys (Grizzle et al 2018;Windle et al 2019). Seavey et al (2011) reported the inland colonization of a salt marsh by oysters in inshore areas of Suwannee Sound, but those increases did not offset net losses experienced in nearshore and offshore reefs.…”

Quantifying Intertidal Habitat Relative Coverage in a Florida Estuary Using UAS Imagery and GEOBIA

“…26 [32]. In pre-processing, the ground control targets were located in the imagery and associated with their respective coordinates to enhance the spatial accuracy of outputs [19]. Pix4D Mapper was used to estimate the position, angular orientation, and camera calibration parameters of the images, and to subsequently generate an orthomosaic and DSM.…”

“…The NOAA Oyster Restoration Workgroup suggests monitoring metrics such as population structure, recruitment, disease, and vertical relief of oyster reefs to provide a more complete outlook on the health of reefs and populations [7,12]. UASs can provide informative data on these metrics, the most direct application being vertical relief and morphology, which has been conducted successfully for eastern oyster reefs in other areas such as off the coast of North Carolina, USA [19].…”

“…However, current sampling techniques for mapping and monitoring coastal habitats are often time-and cost-intensive. For instance, standard methods for studying intertidal reefs include quadrat sampling to quantify oyster densities (e.g., [18]), the use of GPS receivers to measure reef morphology in situ (e.g., [19]), and satellite imagery to quantify declines at a broader spatial scale (e.g., [20]). Satellite imagery is used as a cost-effective alternative to in situ sampling of intertidal reefs [20,21]; however, the coarse spatial resolution of data does not allow for analyses that are detailed enough for practical, fine-scale monitoring, management, and restoration efforts.…”

“…While the collection of in situ data may still be necessary, depending on the purpose of the surveys, UAS imagery provides a spatial context for the ecological processes that may contribute to reef decline or marsh expansion and can be analyzed alongside biological data. UAS imagery has been used successfully to manually delineate habitats, and has proven to be reliable and cost-efficient when compared to traditional methods (e.g., [19]); however, further decreases in processing time and cost may be possible with the automation of image processing and habitat classification.…”