Assessing the consistency and reliability of the line intercept transect method in coral cover estimation using structure from motion photogrammetry techniques

References

• Abadie A, Boissery P, Viala C. 2018. Georeferenced underwater photogrammetry to map marine habitats and submerged artificial structures. Photogramm Rec. 33(164):448–469. doi: 10.1111/phor.12263.
   Web of Science ®Google Scholar
• Adjeroud M, Kayal M, Iborra-Cantonnet C, Vercelloni J, Bosserelle P, Liao V, Chancerelle Y, Claudet J, Penin L. 2018. Recovery of coral assemblages despite acute and recurrent disturbances on a South Central Pacific reef. Sci Rep. 8(1):9680. doi: 10.1038/s41598-018-27891-3.
   PubMedGoogle Scholar
• Alvarez-Filip L, Dulvy NK, Gill JA, Côté IM, Watkinson AR. 2009. Flattening of Caribbean coral reefs: region-wide declines in architectural complexity. Proc Biol Sci. 276(1669):3019–3025. doi: 10.1098/rspb.2009.0339.
   PubMed Web of Science ®Google Scholar
• Anelli M, Julitta T, Fallati L, Galli P, Rossini M, Colombo R. 2019. Towards new applications of underwater photogrammetry for investigating coral reef morphology and habitat complexity in the Myeik Archipelago, Myanmar. Geocarto Int. 34(5):459–472. doi: 10.1080/10106049.2017.1408703.
   Web of Science ®Google Scholar
• Antervedi LGP, Chen Z, Anand H, Martin R, Arrowsmith R, Das J. 2021. Terrain-relative diver following with autonomous underwater vehicle for coral reef mapping. 2021 IEEE 17th International Conference on Automation Science and Engineering (CASE); Lyon, France. p. 2307–2312. doi: 10.1109/CASE49439.2021.9551624.
   Google Scholar
• Bayley D. 2019. Empirical and mechanistic approaches to understanding and projecting change in coastal marine communities [dissertation]. London: University College.
   Google Scholar
• Bayley DT, Mogg AO, Koldewey H, Purvis A. 2019. Capturing complexity: field-testing the use of ‘structure from motion’ derived virtual models to replicate standard measures of reef physical structure. PeerJ. 7:e6540. doi: 10.7717/peerj.6540.
   PubMed Web of Science ®Google Scholar
• Bejarano S, Mumby PJ, Sotheran I. 2011. Predicting structural complexity of reefs and fish abundance using acoustic remote sensing (RoxAnn). Mar Biol. 158(3):489–504. doi: 10.1007/s00227-010-1575-5.
   Web of Science ®Google Scholar
• Bellwood DR, Hughes TP, Folke C, Nyström M. 2004. Confronting the coral reef crisis. Nature. 429(6994):827–833. doi: 10.1038/nature02691.
   PubMed Web of Science ®Google Scholar
• Bennecke S, Kwasnitschka T, Metaxas A, Dullo WC. 2016. In situ growth rates of deep-water octocorals determined from 3D photogrammetric reconstructions. Coral Reefs. 35(4):1227–1239. doi: 10.1007/s00338-016-1471-7.
   Web of Science ®Google Scholar
• Birrell CL, McCook LJ, Willis BL, Diaz-Pulido GA. 2008. Effects of benthic algae on the replenishment of corals and the implications for the resilience of coral reefs. In: Oceanography and marine biology. CRC Press; p. 31–70.
   Google Scholar
• Brandl SJ, Goatley CH, Bellwood DR, Tornabene L. 2018. The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs. Biol Rev Camb Philos Soc. 93(4):1846–1873. doi: 10.1111/brv.12423.
   PubMed Web of Science ®Google Scholar
• Burns JHR, Delparte D, Gates RD, Takabayashi M. 2015. Utilizing underwater three-dimensional modeling to enhance ecological and biological studies of coral reefs. Int Arch Photogramm Remote Sens Spatial Inf Sci. XL-5/W5:61–66. doi: 10.5194/isprsarchives-XL-5-W5-61-2015.
   Google Scholar
• Bythell J, Pan P, Lee J. 2001. Three-dimensional morphometric measurements of reef corals using underwater photogrammetry techniques. Coral Reefs. 20(3):193–199. doi: 10.1007/s003380100157.
   Web of Science ®Google Scholar
• Carlot J, Rovère A, Casella E, Harris D, Grellet-Muñoz C, Chancerelle Y, Dormy E, Hedouin L, Parravicini V. 2020. Community composition predicts photogrammetry-based structural complexity on coral reefs. Coral Reefs. 39(4):967–975. doi: 10.1007/s00338-020-01916-8.
   Web of Science ®Google Scholar
• Casella E, Collin A, Harris D, Ferse S, Bejarano S, Parravicini V, Hench JL, Rovere A. 2017. Mapping coral reefs using consumer-grade drones and structure from motion photogrammetry techniques. Coral Reefs. 36(1):269–275. doi: 10.1007/s00338-016-1522-0.
   Web of Science ®Google Scholar
• CBD. 2022. Kunming-Montreal global biodiversity framework. Proceedings of the Conference of Parties to the Convention on Biological Diversity Fifteenth Meeting CBD/COP/15/L.25.
   Google Scholar
• Chave KE, Smith SV, Roy KJ. 1972. Carbonate production by coral reefs. Mar Geol. 12(2):123–140. doi: 10.1016/0025-3227(72)90024-2.
   Web of Science ®Google Scholar
• Czechowska K, Feldens P, Tuya F, Cosme de Esteban M, Espino F, Haroun R, Schönke M, Otero-Ferrer F. 2020. Testing side-scan sonar and multibeam echosounder to study black coral gardens: a case study from Macaronesia. Remote Sens. 12(19):3244. doi: 10.3390/rs12193244.
   Google Scholar
• D'Urban Jackson T, Williams GJ, Walker-Springett G, Davies AJ. 2020. Three-dimensional digital mapping of ecosystems: a new era in spatial ecology. Proc Biol Sci. 287(1920):20192383. doi: 10.1098/rspb.2019.2383.
   PubMed Web of Science ®Google Scholar
• Edmunds PJ. 2000. Patterns in the distribution of juvenile corals and coral reef community structure in St. John, US Virgin Islands. Mar Ecol Prog Ser. 202:113–124. doi: 10.3354/meps202113.
   Web of Science ®Google Scholar
• Elise S, Urbina-Barreto I, Pinel R, Mahamadaly V, Bureau S, Penin L, Adjeroud M, Kulbicki M, Bruggemann JH.,. 2019. Assessing key ecosystem functions through soundscapes: a new perspective from coral reefs. Ecol Indic. 107:105623. doi: 10.1016/j.ecolind.2019.105623.
   Web of Science ®Google Scholar
• English S, Wilkinson C, Baker V. 1997. Survey manual for tropical marine resources. 2nd ed. Townsville: Australian Institute of Marine Science.
   Google Scholar
• Fallati L, Saponari L, Savini A, Marchese F, Corselli C, Galli P. 2020. Multi-temporal UAV data and object-based image analysis (OBIA) for estimation of substrate changes in a post-bleaching scenario on a Maldivian reef. Remote Sens. 12(13):2093. doi: 10.3390/rs12132093.
   Google Scholar
• Ferrari R, Bryson M, Bridge T, Hustache J, Williams SB, Byrne M, Figueira W. 2016. Quantifying the response of structural complexity and community composition to environmental change in marine communities. Glob Chang Biol. 22(5):1965–1975. doi: 10.1111/gcb.13197.
   PubMed Web of Science ®Google Scholar
• Ferrari R, Figueira WF, Pratchett MS, Boube T, Adam A, Kobelkowsky-Vidrio T, Doo SS, Atwood TB, Byrne M. 2017. 3D photogrammetry quantifies growth and external erosion of individual coral colonies and skeletons. Sci Rep. 7(1):16737. doi: 10.1038/s41598-017-16408-z.
   PubMedGoogle Scholar
• Friedman A, Pizarro O, Williams SB, Johnson-Roberson M. 2012. Multi-Scale measures of rugosity, slope and aspect from benthic stereo image reconstructions. PLoS One. 7(12):e50440. doi: 10.1371/journal.pone.0050440.
   PubMed Web of Science ®Google Scholar
• Fukunaga A, Burns JH, Craig BK, Kosaki RK. 2019. Integrating three dimensional benthic habitat characterization techniques into ecological monitoring of coral reefs. JMSE. 7(2):27. doi: 10.3390/jmse7020027.
   Google Scholar
• Gardner TA, Côté IM, Gill JA, Grant A, Watkinson AR. 2003. Long-term region-wide declines in Caribbean corals. Science. 301(5635):958–960. doi: 10.1126/science.1086050.
   PubMed Web of Science ®Google Scholar
• Giles AB, Ren K, Davies JE, Abrego D, Kelaher B. 2023. Combining drones and deep learning to automate coral reef assessment with RGB imagery. Remote Sens. 15(9):2238. doi: 10.3390/rs15092238.
   Google Scholar
• Goodman JA, Lay M, Ramirez L, Ustin SL, Haverkamp PJ. 2020. Confidence levels, sensitivity, and the role of bathymetry in coral reef remote sensing. Remote Sens. 12(3):496. doi: 10.3390/rs12030496.
   Google Scholar
• Gove JM, Williams GJ, Lecky J, Brown E, Conklin E, Counsell C, Davis G, Donovan MK, Falinski K, Kramer L, et al. 2023. Coral reefs benefit from reduced land–sea impacts under ocean warming. Nature. 621(7979):536–542. doi: 10.1038/s41586-023-06394-w.
   PubMed Web of Science ®Google Scholar
• Hearn CJ. 2011. Perspectives in coral reef hydrodynamics. Coral Reefs. 30(S1):1–9. doi: 10.1007/s00338-011-0752-4.
   Google Scholar
• Hedley J, Roelfsema C, Chollett I, Harborne A, Heron S, Weeks S, Skirving W, Strong A, Eakin C, Christensen T, et al. 2016. Remote sensing of coral reefs for monitoring and management: a review. Remote Sens. 8(2):118. doi: 10.3390/rs8020118.
   Google Scholar
• Hedley JD, Roelfsema CM, Phinn SR, Mumby PJ. 2012. Environmental and sensor limitations in optical remote sensing of coral reefs: implications for monitoring and sensor design. Remote Sens. 4(1):271–302. doi: 10.3390/rs4010271.
   Google Scholar
• Heron SF, Maynard JA, Van Hooidonk R, Eakin CM. 2016. Warming trends and bleaching stress of the world’s coral reefs 1985–2012. Sci Rep. 6(1):38402. doi: 10.1038/srep38402.
   PubMedGoogle Scholar
• Hill J, Wilkinson CLIVE. 2004. Methods for ecological monitoring of coral reefs. Townsville: Australian Institute of Marine Science. doi: 10.1017/CBO9781107415324.004.
   Google Scholar
• Hochberg EJ, Atkinson MJ, Andréfouët S. 2003. Spectral reflectance of coral reef bottom-types worldwide and implications for coral reef remote sensing. Remote Sens Environ. 85(2):159–173. doi: 10.1016/S0034-4257(02)00201-8.
   Web of Science ®Google Scholar
• Hoegh-Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, Gomez E, Harvell CD, Sale PF, Edwards AJ, Caldeira K, et al. 2007. Coral reefs under rapid climate change and ocean acidification. Science. 318(5857):1737–1742. doi: 10.1126/science.115250.
   PubMed Web of Science ®Google Scholar
• Hughes TP, Kerry JT, Álvarez-Noriega M, Álvarez-Romero JG, Anderson KD, Baird AH, Babcock RC, Beger M, Bellwood DR, Berkelmans R, et al. 2017. Global warming and recurrent mass bleaching of corals. Nature. 543(7645):373–377. doi: 10.1038/nature21707.
   PubMed Web of Science ®Google Scholar
• Joyce KE, Phinn SR. 2013. Spectral index development for mapping live coral cover. J Appl Remote Sens. 7(1):073590. doi: 10.1117/1.JRS.7.073590.
   Google Scholar
• Joyce KE, Phinn SR, Roelfsema CM. 2013. Live coral cover index testing and application with hyperspectral airborne image data. Remote Sens. 5(11):6116–6137. doi: 10.3390/rs5116116.
   Google Scholar
• Knudby A, LeDrew E, Newman C. 2007. Progress in the use of remote sensing for coral reef biodiversity studies. Prog Phys Geogr. 31(4):421–434. doi: 10.1177/0309133307081292.
   Web of Science ®Google Scholar
• Lamb JB, Willis BL, Fiorenza EA, Couch CS, Howard R, Rader DN, True JD, Kelly LA, Ahmad A, Jompa J, et al. 2018. Plastic waste associated with disease on coral reefs. Science. 359(6374):460–462. doi: 10.1126/science.aar332.
   PubMed Web of Science ®Google Scholar
• Lange ID, Perry CT. 2020. A quick, easy and non-invasive method to quantify coral growth rates using photogrammetry and 3D model comparisons. Methods Ecol Evol. 11(6):714–726. doi: 10.1111/2041-210X.13388.
   Web of Science ®Google Scholar
• Lavy A, Eyal G, Neal B, Keren R, Loya Y, Ilan M. 2015. A quick, easy and non-intrusive method for underwater volume and surface area evaluation of benthic organisms by 3D computer modelling. Methods Ecol Evol. 6(5):521–531. doi: 10.1111/2041-210X.12331.
   Web of Science ®Google Scholar
• Le Quilleuc A, Collin A, Jasinski MF, Devillers R. 2021. Very high-resolution satellite-derived bathymetry and habitat mapping using Pleiades-1 and ICESat-2. Remote Sens. 14(1):133. doi: 10.3390/rs14010133.
   Google Scholar
• Lechene MAA, Haberstroh AJ, Byrne M, Figueira W, Ferrari R. 2019. Optimising sampling strategies in coral reefs using large-areas mosaics. Remote Sens. 11(24):2907. doi: 10.3390/rs11242907.
   Google Scholar
• Leon JX, Roelfsema CM, Saunders MI, Phinn SR. 2015. Measuring coral reef terrain roughness using ‘Structure-from-Motion’ close-range photogrammetry. Geomorphology. 242:21–28. doi: 10.1016/j.geomorph.2015.01.030.
   Web of Science ®Google Scholar
• Leujak W, Ormond RFG. 2007. Comparative accuracy and efficiency of six coral community survey methods. J Exp Mar Biol Ecol. 351(1–2):168–187. doi: 10.1016/j.jembe.2007.06.028.
   Web of Science ®Google Scholar
• Liao ZH. 2021. Spatial distribution of coral community and benthic algae and their ecological impacts across the south china sea [dissertation]. Guangxi University.
   Google Scholar
• McCarthy J, Benjamin J. 2014. Multi-image photogrammetry for underwater archaeological site recording: an accessible, diver-based approach. J Mari Arch. 9(1):95–114. doi: 10.1007/s11457-014-9127-7.
   Web of Science ®Google Scholar
• Modasshir M, Rekleitis I. 2020. Enhancing coral reef monitoring utilizing a deep semi-supervised learning approach. 2020 IEEE International Conference on Robotics and Automation (ICRA). p. 1874–1880. doi: 10.1109/ICRA40945.2020.9196528.
   Google Scholar
• Montalbetti E, Fallati L, Casartelli M, Maggioni D, Montano S, Galli P, Seveso D. 2022. Reef complexity influences distribution and habitat choice of the corallivorous seastar Culcita schmideliana in the Maldives. Coral Reefs. 41(2):253–264. doi: 10.1007/s00338-022-02230-1.
   Web of Science ®Google Scholar
• Muhamad MAH, Hasan RC, Said NM, Said MSM, Razali R. 2023. Marine habitat mapping using multibeam echosounder survey and underwater video observations: a case study from Tioman marine park. IOP Conf Ser: Earth Environ Sci. 1240(1):012006. doi: 10.1088/1755-1315/1240/1/012006.
   Google Scholar
• Neyer F, Nocerino E, Gruen A. 2018. Monitoring coral growth– the dichotomy between underwater photogrammetry and geodetic control network. Int Arch Photogramm Remote Sens Spatial Inf Sci. XLII-2:759–766. doi: 10.5194/isprs-archives-XLII-2-759-2018.
   Google Scholar
• Nocerino E, Menna F, Gruen A, Troyer M, Capra A, Castagnetti C, Rossi P, Brooks AJ, Schmitt RJ, Holbrook SJ. 2020. Coral reef monitoring by scuba divers using underwater photogrammetry and geodetic surveying. Remote Sens. 12(18):3036. doi: 10.3390/rs12183036.
   Google Scholar
• Obura DO, Aeby G, Amornthammarong N, Appeltans W, Bax N, Bishop J, Brainard RE, Chan S, Fletcher P, Gordon TAC, et al. 2019. Coral reef monitoring, reef assessment technologies, and ecosystem-based management. Front Mar Sci. 6:580. doi: 10.3389/fmars.2019.00580.
   Web of Science ®Google Scholar
• Palma M, Rivas Casado M, Pantaleo U, Cerrano C. 2017. High resolution orthomosaics of African coral reefs: a tool for wide-scale benthic monitoring. Remote Sens. 9(7):705. doi: 10.3390/rs9070705.
   Google Scholar
• Penin L, Michonneau F, Baird AH, Connolly SR, Pratchett MS, Kayal M, Adjeroud M. 2010. Early post-settlement mortality and the structure of coral assemblages. Mar Ecol Prog Ser. 408:55–64. doi: 10.3354/meps08554.
   Web of Science ®Google Scholar
• Perry CT, Alvarez-Filip L, Graham NAJ, Mumby PJ, Wilson SK, Kench PS, Manzello DP, Morgan KM, Slangen ABA, Thomson DP, et al. 2018. Loss of coral reef growth capacity to track future increases in sea level. Nature. 558(7710):396–400. doi: 10.1038/s41586-018-0194-z.
   PubMed Web of Science ®Google Scholar
• Pinheiro HT, MacDonald C, Santos RG, Ali R, Bobat A, Cresswell BJ, Francini-Filho R, Freitas R, Galbraith GF, Musembi P, et al. 2023. Plastic pollution on the world’s coral reefs. Nature. 619(7969):311–316. doi: 10.1038/s41586-023-06113-5.
   PubMed Web of Science ®Google Scholar
• Price DM, Robert K, Callaway A, Lo Lacono C, Hall RA, Huvenne VA. 2019. Using 3D photogrammetry from ROV video to quantify cold-water coral reef structural complexity and investigate its influence on biodiversity and community assemblage. Coral Reefs. 38(5):1007–1021. doi: 10.1007/s00338-019-01827-3.
   Web of Science ®Google Scholar
• Rossi P, Castagnetti C, Capra A, Brooks AJ, Mancini F. 2020. Detecting change in coral reef 3D structure using underwater photogrammetry: critical issues and performance metrics. Appl Geomat. 12(S1):3–17. doi: 10.1007/s12518-019-00263-w.
   Google Scholar
• Santos RG, Machovsky-Capuska GE, Andrades R. 2021. Plastic ingestion as an evolutionary trap: toward a holistic understanding. Science. 373(6550):56–60. doi: 10.1126/science.abh0945.
   PubMed Web of Science ®Google Scholar
• Simon N, Raubenheimer K, Urho N, Unger S, Azoulay D, Farrelly T, Sousa J, van Asselt H, Carlini G, Sekomo C, et al. 2021. A binding global agreement to address the life cycle of plastics. Science. 373(6550):43–47. doi: 10.1126/science.abi90.
   PubMed Web of Science ®Google Scholar
• Stella JS, Pratchett MS, Hutchings P, Jones GP. 2011. Coralasscociated invertebrates: diversity, ecological importance and vulnerability to disturbance. Oceanogr Mar Biol. 49:43–104.
   Web of Science ®Google Scholar
• Storlazzi CD, Dartnell P, Hatcher GA, Gibbs AE. 2016. End of the chain? Rugosity and fine-scale bathymetry from existing underwater digital imagery using structure-from-motion (SfM) technology. Coral Reefs. 35(3):889–894. 8-016-1462-8 doi: 10.1007/s0033.
   Web of Science ®Google Scholar
• Urbina-Barreto I, Chiroleu F, Pinel R, Fréchon L, Mahamadaly V, Elise S, Kulbicki M, Quod J-P, Dutrieux E, Garnier R, et al. 2021a. Quantifying the shelter capacity of coral reefs using photogrammetric 3D modelling, from colonies to reefscapes. Ecol Indicat. 121:107151. doi: 10.1016/j.ecolind.2020.107151.
   Web of Science ®Google Scholar
• Urbina-Barreto I, Garnier R, Elise S, Pinel R, Dumas P, Mahamadaly V, Facon M, Bureau S, Peignon C, Quod J-P, et al. 2021b. Which method for which purpose? A comparison of line intercept transect and underwater photogrammetry methods for coral reef surveys. Front Mar Sci. 8:636902. doi: 10.3389/fmars.2021.636902.
   Web of Science ®Google Scholar
• Westoby MJ, Brasington J, Glasser NF, Hambrey MJ, Reynolds JM. 2012. ‘Structure-from-Motion’ photogrammetry: a low-cost, effective tool for geoscience applications. Geomorphology. 179:300–314. doi: 10.1016/j.geomorph.2012.08.021.
   Web of Science ®Google Scholar
• Young GC, Dey S, Rogers AD, Exton D. 2017. Cost and time-effective method for multi-scale measures of rugosity, fractal dimension, and vector dispersion from coral reef 3D models. PLoS One. 12(4):e0175341. doi: 10.1371/journal.pone.0175341.
   PubMed Web of Science ®Google Scholar
• Zawada KJ, Madin JS, Baird AH, Bridge TC, Dornelas M. 2019. Morphological traits can track coral reef responses to the Anthropocene. Funct Ecol. 33(6):962–975. doi: 10.1111/1365-2435.
   Web of Science ®Google Scholar
• Zhou J, Zhou N, Che Y, Gao J, Zhao L, Huang H, Chen Y. 2022. Design and development of an autonomous underwater helicopter for ecological observation of coral reefs. Sensors (Basel). 22(5):1770. doi: 10.3390/s22051770.
   PubMed Web of Science ®Google Scholar