{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T20:40:11Z","timestamp":1775076011146,"version":"3.50.1"},"reference-count":48,"publisher":"MDPI AG","issue":"20","license":[{"start":{"date-parts":[[2019,10,16]],"date-time":"2019-10-16T00:00:00Z","timestamp":1571184000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100005623","name":"North Carolina Sea Grant, North Carolina State University","doi-asserted-by":"publisher","award":["2017-R\/MG-1710"],"award-info":[{"award-number":["2017-R\/MG-1710"]}],"id":[{"id":"10.13039\/100005623","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005618","name":"North Carolina Space Grant","doi-asserted-by":"publisher","award":["2017-R\/MG-1710"],"award-info":[{"award-number":["2017-R\/MG-1710"]}],"id":[{"id":"10.13039\/100005618","id-type":"DOI","asserted-by":"publisher"}]},{"name":"North Carolina Coastal Recreational Fishing License Grants Program","award":["2017-H-068"],"award-info":[{"award-number":["2017-H-068"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Remote Sensing"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/rs11202394","type":"journal-article","created":{"date-parts":[[2019,10,17]],"date-time":"2019-10-17T04:46:06Z","timestamp":1571287566000},"page":"2394","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Rapid and Accurate Monitoring of Intertidal Oyster Reef Habitat Using Unoccupied Aircraft Systems and Structure from Motion"],"prefix":"10.3390","volume":"11","author":[{"given":"Anna","family":"Windle","sequence":"first","affiliation":[{"name":"Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University Marine Laboratory, 135 Duke Marine Lab Rd, Beaufort, NC 28516, USA"}]},{"given":"Sarah","family":"Poulin","sequence":"additional","affiliation":[{"name":"Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University Marine Laboratory, 135 Duke Marine Lab Rd, Beaufort, NC 28516, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2424-036X","authenticated-orcid":false,"given":"David","family":"Johnston","sequence":"additional","affiliation":[{"name":"Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University Marine Laboratory, 135 Duke Marine Lab Rd, Beaufort, NC 28516, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9744-4588","authenticated-orcid":false,"given":"Justin","family":"Ridge","sequence":"additional","affiliation":[{"name":"Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University Marine Laboratory, 135 Duke Marine Lab Rd, Beaufort, NC 28516, USA"}]}],"member":"1968","published-online":{"date-parts":[[2019,10,16]]},"reference":[{"key":"ref_1","unstructured":"Murphy, S., and Allison, S. (2017). Oyster-generated marine habitats: Their services, enhancement, restoration, and monitoring. Routledge Handbook of Ecological and Environmental Restoration, Taylor & Francis Group\/Routledge."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1525\/bio.2012.62.10.10","article-title":"Economic valuation of ecosystem services provided by oyster reefs","volume":"62","author":"Grabowski","year":"2012","journal-title":"BioScience"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.ecss.2014.09.025","article-title":"Use of oysters to mitigate eutrophication in coastal waters","volume":"151","author":"Kellogg","year":"2014","journal-title":"Estuar. Coast. Shelf Sci."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"McLeod, I.M., zu Ermgassen, P.S., Gillies, C.L., Hancock, B., and Humphries, A. (2019). Can Bivalve Habitat Restoration Improve Degraded Estuaries?. Coasts and Estuaries, Elsevier.","DOI":"10.1016\/B978-0-12-814003-1.00025-3"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Smaal, A.C., Ferreira, J.G., Grant, J., Petersen, J.K., and Strand, \u00d8. (2018). Goods and Services of Marine Bivalves, Springer.","DOI":"10.1007\/978-3-319-96776-9"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Ysebaert, T., Walles, B., Haner, J., and Hancock, B. (2019). Habitat modification and coastal protection by ecosystem-engineering reef-building bivalves. Goods and Services of Marine Bivalves, Springer.","DOI":"10.1007\/978-3-319-96776-9_13"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"13096","DOI":"10.1073\/pnas.0405150101","article-title":"Fishing down the coast: historical expansion and collapse of oyster fisheries along continental margins","volume":"101","author":"Kirby","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1007\/s12237-012-9559-y","article-title":"Quantifying the loss of a marine ecosystem service: Filtration by the eastern oyster in US estuaries","volume":"36","author":"Spalding","year":"2013","journal-title":"Estuaries Coasts"},{"key":"ref_9","unstructured":"Airoldi, L., and Beck, M.W. (2007). Loss, status and trends for coastal marine habitats of Europe. Oceanography and Marine Biology, CRC Press."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1146\/annurev-marine-010814-015646","article-title":"Infectious diseases affect marine fisheries and aquaculture economics","volume":"7","author":"Lafferty","year":"2015","journal-title":"Annu. Rev. Mar. Sci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"131","DOI":"10.3354\/meps09161","article-title":"Overfishing, disease, habitat loss, and potential extirpation of oysters in upper Chesapeake Bay","volume":"436","author":"Wilberg","year":"2011","journal-title":"Mar. Ecol. Prog. Ser."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3393","DOI":"10.1098\/rspb.2012.0313","article-title":"Historical ecology with real numbers: past and present extent and biomass of an imperiled estuarine habitat","volume":"279","author":"Spalding","year":"2012","journal-title":"Proc. R. Soc. B Biol. Sci."},{"key":"ref_13","unstructured":"Baggett, P.L., Powers, S.P., Brumbaugh, R., Coen, L.D., DeAngelis, B., Greene, J., Hancock, B., and Morlock, S. (2014). Oyster Habitat Restoration Monitoring and Assessment Handbook, The Nature Conservancy."},{"key":"ref_14","unstructured":"Brumbaugh, R.D., Beck, M.W., Coen, L.D., Craig, L., and Hicks, P. (2006). A Practitioner\u2019s Guide to the Design & Monitoring of Shellfish Restoration Projects: An Ecosystem Services Approach, The Nature Conservancy."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/S0925-8574(00)00084-7","article-title":"Developing success criteria and goals for evaluating oyster reef restoration: ecological function or resource exploitation?","volume":"15","author":"Coen","year":"2000","journal-title":"Ecol. Eng."},{"key":"ref_16","unstructured":"Oyster Metrics Workgroup (OMW) (2011). Restoration Goals, Quantitative Metrics and Assessment Protocols for Evaluating Success on Restored Oyster Reef Sanctuaries, Sustainable Fisheries Goal Implementation Team of the NOAA Chesapeake Bay Program. Available online: http:\/\/www.chesapeakebay.net\/channel_files\/ 17932\/oyster_restoration_success_metrics_final.pdf."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"303","DOI":"10.3354\/meps341303","article-title":"Ecosystem services related to oyster restoration","volume":"341","author":"Coen","year":"2007","journal-title":"Mar. Ecol. Prog. Ser."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S1875-306X(07)80017-7","article-title":"Restoring oyster reefs to recover ecosystem services","volume":"4","author":"Grabowski","year":"2007","journal-title":"Ecosyst. Eng. Plants Protists"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1111\/rec.12262","article-title":"Guidelines for evaluating performance of oyster habitat restoration","volume":"23","author":"Baggett","year":"2015","journal-title":"Restor. Ecol."},{"key":"ref_20","unstructured":"Thayer, G.W., McTigue, T.A., Salz, R.J., Merkey, D.H., Burrows, F.M., and Gayaldo, P.F. (2005). Chapter 4: Restoration monitoring of oyster reefs, Science-Based Restoration Monitoring of Coastal Habitats, Volume Two: Tools for Monitoring Coastal Habitats."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"11409","DOI":"10.1002\/ece3.3473","article-title":"Evidence of exceptional oyster-reef resilience to fluctuations in sea level","volume":"7","author":"Ridge","year":"2017","journal-title":"Ecol. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"14785","DOI":"10.1038\/srep14785","article-title":"Maximizing oyster-reef growth supports green infrastructure with accelerating sea-level rise","volume":"5","author":"Ridge","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/nclimate2216","article-title":"Oyster reefs can outpace sea-level rise","volume":"4","author":"Rodriguez","year":"2014","journal-title":"Nat. Clim. Chang."},{"key":"ref_24","first-page":"749","article-title":"Historical changes in intertidal oyster (Crassostrea virginica) reefs in a Florida lagoon potentially related to boating activities","volume":"21","author":"Grizzle","year":"2002","journal-title":"J. Shellfish Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.2983\/035.037.0514","article-title":"Distribution and Condition of Intertidal Eastern Oyster (Crassostrea virginica) Reefs in Apalachicola Bay Florida Based on High-Resolution Satellite Imagery","volume":"37","author":"Grizzle","year":"2018","journal-title":"J. Shellfish Res."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Twichell, D.C., Andrews, B.D., Edmiston, H.L., and Stevenson, W.R. (2019, May 01). Geophysical Mapping of Oyster Habitats in a Shallow Estuary, Apalachicola Bay, Florida: U.S. Geological Survey Open-File Report 2006-1381, Available online: http:\/\/pubs.usgs.gov\/of\/2006\/1381\/.","DOI":"10.3133\/ofr20061381"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.seares.2015.11.007","article-title":"From artificial structures to self-sustaining oyster reefs","volume":"108","author":"Walles","year":"2016","journal-title":"J. Sea Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"927","DOI":"10.2983\/035.029.0425","article-title":"A caution against interpreting and quantifying oyster habitat loss from historical surveys","volume":"29","author":"Power","year":"2010","journal-title":"J. Shellfish Res."},{"key":"ref_29","unstructured":"Schill, S.R., Porter, D.E., Coen, L.D., Bushek, D., and Vincent, J. (2006). Development of an automated mapping technique for monitoring and managing shellfish distributions. NOAA\/UNH Cooperative Institute for Coastal and Estuarine Environmental Technology (CICEET), University of New Hampshire."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3710","DOI":"10.3390\/rs70403710","article-title":"Remote sensing of epibenthic shellfish using synthetic aperture radar satellite imagery","volume":"7","author":"Nieuwhof","year":"2015","journal-title":"Remote Sens."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"251","DOI":"10.2983\/035.034.0206","article-title":"Formation, movement, and restoration of dead intertidal oyster reefs in Canaveral National Seashore and Mosquito Lagoon, Florida","volume":"34","author":"Garvis","year":"2015","journal-title":"J. Shellfish Res."},{"key":"ref_32","unstructured":"ASMFC (2007). The Importance of Habitat Created by Molluscan Shellfish to Managed Species along the Atlantic Coast of the United States, Atlantic States Marine Fisheries Commission."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1890\/ES11-00205.1","article-title":"Decadal changes in oyster reefs in the Big Bend of Florida\u2019s Gulf Coast","volume":"2","author":"Seavey","year":"2011","journal-title":"Ecosphere"},{"key":"ref_34","unstructured":"NOAA Coastal Services Center (2018, September 16). Pilot Investigation of Remote Sensing for Intertidal Oyster Mapping in Coastal South Carolina: A Methods Comparison, Available online: https:\/\/coast.noaa.gov\/data\/digitalcoast\/pdf\/oyster-mapping.pdf."},{"key":"ref_35","unstructured":"South Carolina Department of Natural Resources (SCDNR), Marine Resources Division (2018, September 16). Final Report for South Carolina\u2019s 2004-05 Intertidal Oyster Survey and Related Reef Restoration\/Enhancement Program, Available online: http:\/\/www.oyster-restoration.org\/wp-content\/uploads\/2012\/06\/Final-Report-for-Oyster-Survey-and-Recovery-Phase-II-with-appendices.pdf."},{"key":"ref_36","unstructured":"Guillen, G., and Mokrech, M. (2019, May 01). Mapping Shallow Reefs Using Low-Cost Scanning Sonar and Drone Photography Systems, Available online: https:\/\/www.sciencebase.gov\/catalog\/item\/5bf82b0fe4b045bfcae2eaae."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1146\/annurev-marine-010318-095323","article-title":"Unoccupied Aircraft Systems in Marine Science and Conservation","volume":"11","author":"Johnston","year":"2019","journal-title":"Ann. Rev. Mar. Sci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1071\/MF17380","article-title":"Principles and practice of acquiring drone-based image data in marine environments","volume":"70","author":"Joyce","year":"2018","journal-title":"Mar. Freshw. Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.2112\/JCOASTRES-D-15-00005.1","article-title":"Coastal and environmental remote sensing from unmanned aerial vehicles: An overview","volume":"31","author":"Klemas","year":"2015","journal-title":"J. Coast. Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"6880","DOI":"10.3390\/rs5126880","article-title":"Using unmanned aerial vehicles (UAV) for high-resolution reconstruction of topography: The structure from motion approach on coastal environments","volume":"5","author":"Mancini","year":"2013","journal-title":"Remote Sens."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"704","DOI":"10.2112\/JCOASTRES-D-17-00088.1","article-title":"Deploying fixed wing Unoccupied Aerial Systems (UAS) for coastal morphology assessment and management","volume":"34","author":"Seymour","year":"2017","journal-title":"J. Coast. Res."},{"key":"ref_42","unstructured":"R Core Team (2013). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ecss.2016.01.039","article-title":"Hyperspectral remote sensing of wild oyster reefs","volume":"172","author":"Rosa","year":"2016","journal-title":"Estuar. Coast. Shelf Sci."},{"key":"ref_44","unstructured":"O\u2019Keife, K., Arnold, W., and Reed, D. (2006). Tampa Bay oyster bar mapping and assessment. Final Report to Tampa Bay Estuary Program, Technical Publication."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/s00338-016-1522-0","article-title":"Mapping coral reefs using consumer-grade drones and structure from motion photogrammetry techniques","volume":"36","author":"Casella","year":"2017","journal-title":"Coral Reefs"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Sturdivant, E., Lentz, E., Thieler, E.R., Farris, A., Weber, K., Remsen, D., Miner, S., and Henderson, R. (2017). UAS-SfM for coastal research: Geomorphic feature extraction and land cover classification from high-resolution elevation and optical imagery. Remote Sens., 9.","DOI":"10.3390\/rs9101020"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Yaney-Keller, A., Tomillo, P.S., Marshall, J.M., and Paladino, F.V. (2019). Using Unmanned Aerial Systems (UAS) to assay mangrove estuaries on the Pacific coast of Costa Rica. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0217310"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"e1077","DOI":"10.7717\/peerj.1077","article-title":"Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs","volume":"3","author":"Burns","year":"2015","journal-title":"Peer J."}],"container-title":["Remote Sensing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-4292\/11\/20\/2394\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T13:26:46Z","timestamp":1760189206000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-4292\/11\/20\/2394"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,16]]},"references-count":48,"journal-issue":{"issue":"20","published-online":{"date-parts":[[2019,10]]}},"alternative-id":["rs11202394"],"URL":"https:\/\/doi.org\/10.3390\/rs11202394","relation":{},"ISSN":["2072-4292"],"issn-type":[{"value":"2072-4292","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,10,16]]}}}