{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T13:37:45Z","timestamp":1790689065580,"version":"4.1.0"},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T00:00:00Z","timestamp":1596153600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T00:00:00Z","timestamp":1596153600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["17H04974"],"award-info":[{"award-number":["17H04974"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Over the last 3 decades, a large portion of coral cover has been lost around the globe. This significant decline necessitates a rapid assessment of coral reef health to enable more effective management. In this paper, we propose an efficient method for coral cover estimation and demonstrate its viability. A large-scale 3-D structure model, with resolutions in the x, y and z planes of 0.01\u00a0m, was successfully generated by means of a towed optical camera array system (Speedy Sea Scanner). The survey efficiency attained was 12,146 m<jats:sup>2<\/jats:sup>\/h. In addition, we propose a segmentation method utilizing U-Net architecture and estimate coral coverage using a large-scale 2-D image. The U-Net-based segmentation method has shown higher accuracy than pixelwise CNN modeling. Moreover, the computational cost of a U-Net-based method is much lower than that of a pixelwise CNN-based one. We believe that an array of these survey tools can contribute to the rapid assessment of coral reefs.<\/jats:p>","DOI":"10.1038\/s41598-020-69400-5","type":"journal-article","created":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T10:05:51Z","timestamp":1596189951000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["An efficient coral survey method based on a large-scale 3-D structure model obtained by Speedy Sea Scanner and U-Net segmentation"],"prefix":"10.1038","volume":"10","author":[{"given":"Katsunori","family":"Mizuno","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kei","family":"Terayama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seiichiro","family":"Hagino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shigeru","family":"Tabeta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shingo","family":"Sakamoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toshihiro","family":"Ogawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenichi","family":"Sugimoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hironobu","family":"Fukami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,7,31]]},"reference":[{"key":"69400_CR1","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1126\/science.1086050","volume":"301","author":"TA Gardner","year":"2003","unstructured":"Gardner, T. A., Cote, I. M., Gill, J. A., Grant, A. & Watkinson, A. R. Long-term region-wide declines in caribbean corals. Science 301, 958\u2013960 (2003).","journal-title":"Science"},{"key":"69400_CR2","unstructured":"ESI, Endangered species international, https:\/\/www.endangeredspeciesinternational.org\/ (2017)."},{"key":"69400_CR3","doi-asserted-by":"publisher","first-page":"e711","DOI":"10.1371\/journal.pone.0000711","volume":"2","author":"JF Bruno","year":"2007","unstructured":"Bruno, J. F. & Selig, E. R. Regional decline of coral cover in the indo-pacific: timing, extent, and subregional comparisons. PLoS ONE 2, e711 (2007).","journal-title":"PLoS ONE"},{"key":"69400_CR4","doi-asserted-by":"publisher","first-page":"1725","DOI":"10.1126\/science.1104258","volume":"307","author":"JM Pandolfi","year":"2005","unstructured":"Pandolfi, J. M. et al. Are US coral reefs on the slippery slope to slime?. Science 307, 1725\u20131726 (2005).","journal-title":"Science"},{"key":"69400_CR5","doi-asserted-by":"publisher","first-page":"18866","DOI":"10.1073\/pnas.0702737104","volume":"104","author":"JG Canadell","year":"2007","unstructured":"Canadell, J. G. et al. Contributions to accelerating atmospheric Co2 growth from economic activity, carbon intensity, and efficiency of natural sinks. Proc. Natl. Acad. Sci. 104, 18866\u201318870 (2007).","journal-title":"Proc. Natl. Acad. Sci."},{"key":"69400_CR6","doi-asserted-by":"publisher","first-page":"10288","DOI":"10.1073\/pnas.0700609104","volume":"104","author":"MR Raupach","year":"2007","unstructured":"Raupach, M. R. et al. Global and regional drivers of accelerating Co2 emissions. Proc. Natl. Acad. Sci. 104, 10288\u201310293 (2007).","journal-title":"Proc. Natl. Acad. Sci."},{"key":"69400_CR7","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1126\/science.1097403","volume":"305","author":"CL Sabine","year":"2004","unstructured":"Sabine, C. L. et al. The oceanic sink for anthropogenic Co2. Science 305, 367\u2013371 (2004).","journal-title":"Science"},{"key":"69400_CR8","first-page":"215","volume":"53","author":"MS Pratchett","year":"2015","unstructured":"Pratchett, M. S. et al. Spatial, temporal and taxonomic variation in coral growth\u2014implications for the structure and function of coral reef ecosystems. Oceanogr. Mar. Biol. 53, 215\u2013295 (2015).","journal-title":"Oceanogr. Mar. Biol."},{"key":"69400_CR9","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1111\/2041-210X.12380","volume":"6","author":"PJ Mumby","year":"2015","unstructured":"Mumby, P. J. & Anthony, K. Resilience metrics to inform ecosystem management under global change with application to coral reefs. Method Ecol. Evol. 6, 1088\u20131096 (2015).","journal-title":"Method Ecol. Evol."},{"key":"69400_CR10","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/j.jembe.2008.10.002","volume":"368","author":"P Dumas","year":"2009","unstructured":"Dumas, P., Bertaud, A., Peignon, C., Leopold, M. & Pelletier, D. A quick and clean photographic method for the description of coral reef habitats. J. Exp. Mar. Biol. Ecol. 368, 161\u2013168 (2009).","journal-title":"J. Exp. Mar. Biol. Ecol."},{"key":"69400_CR11","doi-asserted-by":"publisher","first-page":"379","DOI":"10.4236\/ojms.2015.54031","volume":"5","author":"M Safuan","year":"2015","unstructured":"Safuan, M., Boo, W. H., Siang, H. Y., Chark, L. H. & Bachok, Z. Optimization of coral video transect technique for coral reef survey: comparison with intercept transect technique. Open J. Mar. Sci. 5, 379 (2015).","journal-title":"Open J. Mar. Sci."},{"key":"69400_CR12","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1002\/rob.21658","volume":"34","author":"M Johnson-Roberson","year":"2017","unstructured":"Johnson-Roberson, M. et al. High resolution underwater robotic vision based mapping and three dimensional reconstruction for archaeology. J. Field Robot. 34, 625\u2013643 (2017).","journal-title":"J. Field Robot."},{"key":"69400_CR13","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/j.ecoinf.2017.02.003","volume":"38","author":"K Mizuno","year":"2017","unstructured":"Mizuno, K. et al. A simple and efficient method for making a high-resolution seagrass map and quantification of dugong feeding trail distribution: a field test at Mayo Bay Philippines. Ecol. Inform. 38, 89\u201394 (2017).","journal-title":"Ecol. Inform."},{"key":"69400_CR14","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1023\/B:SSTA.0000018445.25977.f3","volume":"5","author":"H Singh","year":"2004","unstructured":"Singh, H. et al. Imaging coral I: imaging coral habitats with the SeaBED AUV. J. Subsurf. Sens. Technol. Appl. 5, 25\u201342 (2004).","journal-title":"J. Subsurf. Sens. Technol. Appl."},{"key":"69400_CR15","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1109\/JOE.2012.2204152","volume":"37","author":"R Prados","year":"2012","unstructured":"Prados, R., Garcia, R., Gracias, N., Escartin, J. & Neumann, L. A novel blending technique for underwater gigamosaicing. IEEE J. Ocean. Eng. 37, 626\u2013644 (2012).","journal-title":"IEEE J. Ocean. Eng."},{"key":"69400_CR16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1109\/JSEN.2016.2616227","volume":"16","author":"J Hern\u00e1ndez","year":"2016","unstructured":"Hern\u00e1ndez, J. et al. Autonomous underwater navigation and optical mapping in unknown natural environments. Sensors 16, 1\u201327 (2016).","journal-title":"Sensors"},{"key":"69400_CR17","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1002\/rob.21713","volume":"35","author":"DL Bongiorno","year":"2018","unstructured":"Bongiorno, D. L., Bryson, M., Bridge, T. C., Dansereau, D. G. & Williams, S. B. Coregistered hyperspectral and stereo image seafloor mapping from an autonomous underwater vehicle. J. Field Robot. 35, 312\u2013329 (2018).","journal-title":"J. Field Robot."},{"key":"69400_CR18","doi-asserted-by":"crossref","unstructured":"Mahmood, A. et al. Coral classification with hybrid feature representations. In 2016 IEEE International Conference on Image Processing (ICIP), pp. 519\u2013523 (2016).","DOI":"10.1109\/ICIP.2016.7532411"},{"key":"69400_CR19","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1007\/s10661-006-9239-0","volume":"125","author":"D Lirman","year":"2007","unstructured":"Lirman, D. et al. Development and application of a video-mosaic survey technology to document the status of coral reef communities. Environ. Monit. Assess. 125, 59\u201373 (2007).","journal-title":"Environ. Monit. Assess."},{"key":"69400_CR20","doi-asserted-by":"publisher","first-page":"1809","DOI":"10.3390\/rs5041809","volume":"5","author":"ASM Shihavuddin","year":"2013","unstructured":"Shihavuddin, A. S. M., Gracias, N., Garcia, R., Gleason, A. & Gintert, B. Image-based coral reef classification and thematic mapping. Remote Sens. 5, 1809\u20131841 (2013).","journal-title":"Remote Sens."},{"key":"69400_CR21","first-page":"1097","volume":"25","author":"A Krizhevsky","year":"2012","unstructured":"Krizhevsky, A. & Hinton, G. E. Imagenet classification with deep convolutional neural networks. Proc. Adv. Neural Inf. Process. Syst. 25, 1097\u20131105 (2012).","journal-title":"Proc. Adv. Neural Inf. Process. Syst."},{"key":"69400_CR22","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1007\/s11263-015-0816-y","volume":"115","author":"O Russakovsky","year":"2015","unstructured":"Russakovsky, O. et al. Imagenet large scale visual recognition challenge. Int. J. Comput. Vis. 115, 211\u2013252 (2015).","journal-title":"Int. J. Comput. Vis."},{"key":"69400_CR23","doi-asserted-by":"publisher","first-page":"23166","DOI":"10.1038\/srep23166","volume":"6","author":"O Beijbom","year":"2016","unstructured":"Beijbom, O. et al. Improving automated annotation of benthic survey images using wide-band fluorescence. Sci. Rep. 6, 23166 (2016).","journal-title":"Sci. Rep."},{"key":"69400_CR24","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/j.eswa.2018.10.010","volume":"118","author":"A G\u00f3mez-R\u00edos","year":"2019","unstructured":"G\u00f3mez-R\u00edos, A. et al. Towards highly accurate coral texture images classification using deep convolutional neural networks and data augmentation. Expert Syst. Appl. 118, 315\u2013328 (2019).","journal-title":"Expert Syst. Appl."},{"key":"69400_CR25","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1109\/JOE.2017.2786878","volume":"44","author":"A Mahmood","year":"2019","unstructured":"Mahmood, A. et al. Deep image representations for coral image classification. IEEE J. Ocean. Eng. 44, 121\u2013131 (2019).","journal-title":"IEEE J. Ocean. Eng."},{"key":"69400_CR26","doi-asserted-by":"publisher","DOI":"10.1109\/JOE.2020.2983865","author":"K Mizuno","year":"2019","unstructured":"Mizuno, K. et al. Development of an efficient coral-coverage estimation method using a towed optical camera array system [Speedy Sea Scanner (SSS)] and deep-learning-based segmentation: a sea trial at the Kujuku-Shima islands. IEEE J. Ocean. Eng. https:\/\/doi.org\/10.1109\/JOE.2020.2983865 (2019).","journal-title":"IEEE J. Ocean. Eng."},{"key":"69400_CR27","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1002\/rob.21682","volume":"34","author":"A Bodenmann","year":"2017","unstructured":"Bodenmann, A., Thornton, B. & Ura, T. Generation of high-resolution three-dimensional reconstructions of the seafloor in color using a single camera and structured light. J. Field Robot. 34, 833\u2013851 (2017).","journal-title":"J. Field Robot."},{"key":"69400_CR28","doi-asserted-by":"crossref","unstructured":"Ronneberger, O., Philipp, F. & Thomas, B. U-net: convolutional networks for biomedical image segmentation. In International Conference on Medical image computing and computer-assisted intervention. Springer, Cham, pp. 234\u2013231 (2015).","DOI":"10.1007\/978-3-319-24574-4_28"},{"key":"69400_CR29","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/s41592-018-0261-2","volume":"16","author":"T Falk","year":"2019","unstructured":"Falk, T. et al. U-Net: deep learning for cell counting, detection, and morphometry. Nat. Methods 16, 67\u201370 (2019).","journal-title":"Nat. Methods"},{"key":"69400_CR30","doi-asserted-by":"publisher","first-page":"6880","DOI":"10.3390\/rs5126880","volume":"5","author":"F Mancini","year":"2013","unstructured":"Mancini, F. et al. Using unmanned aerial vehicles (UAV) for high-resolution reconstruction of topography: the structure from motion approach on coastal environments. Remote Sens. 5, 6880\u20136898 (2013).","journal-title":"Remote Sens."},{"key":"69400_CR31","doi-asserted-by":"publisher","first-page":"2218","DOI":"10.1080\/01431161.2017.1285082","volume":"38","author":"CHW De Souza","year":"2017","unstructured":"De Souza, C. H. W., Lamparelli, R. A. C., Rocha, J. V. & Magalh\u00e3es, P. S. G. Height estimation of sugarcane using an unmanned aerial system (UAS) based on structure from motion (SfM) point clouds. Int. J. Remote Sens. 38, 2218\u20132230 (2017).","journal-title":"Int. J. Remote Sens."},{"key":"69400_CR32","unstructured":"Chollet, F. Keras. https:\/\/keras.io (2015)."},{"key":"69400_CR33","unstructured":"Abadi, M. et al. TensorFlow: a system for large-scale machine learning, pp. 265\u2013283 (2016)."},{"key":"69400_CR34","doi-asserted-by":"crossref","unstructured":"He, K., Zhang, X., Ren, S. & Sun, J. Deep residual learning for image recognition. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 770\u2013778 (2016).","DOI":"10.1109\/CVPR.2016.90"},{"key":"69400_CR35","unstructured":"Kingma, D. P. & Ba, J. L. ADAM: a method for stochastic optimization. In Proceedings of International Conference on Learning Representations. arXiv preprint arXiv:1412.6980 (2015)."},{"key":"69400_CR36","first-page":"165","volume":"13","author":"O Dekel","year":"2012","unstructured":"Dekel, O. & Xiao, L. Optimal distributed online prediction using mini-batches. J. Mach. Learn. Res. 13, 165\u2013202 (2012).","journal-title":"J. Mach. Learn. Res."},{"key":"69400_CR37","volume-title":"Deep Learning","author":"I Goodfellow","year":"2016","unstructured":"Goodfellow, I., Bengio, Y. & Courville, A. Deep Learning (MIT Press, Cambridge, 2016)."},{"key":"69400_CR38","doi-asserted-by":"publisher","first-page":"276","DOI":"10.3389\/fmars.2019.00276","volume":"6","author":"G Marre","year":"2019","unstructured":"Marre, G. et al. Monitoring marine habitats with photogrammetry: a cost-effective accurate precise and high-resolution reconstruction method. Front. Mar. Sci. 6, 276 (2019).","journal-title":"Front. Mar. Sci."},{"key":"69400_CR39","doi-asserted-by":"publisher","first-page":"299","DOI":"10.3354\/meps235299","volume":"235","author":"S Spagnol","year":"2002","unstructured":"Spagnol, S. et al. An error frequently made in the evaluation of advective transport in two-dimensional Lagrangian models of advection-diffusion in coral reef waters. Mar. Ecol. Prog. Ser. 235, 299\u2013302 (2002).","journal-title":"Mar. Ecol. Prog. Ser."},{"key":"69400_CR40","doi-asserted-by":"publisher","first-page":"1395","DOI":"10.1016\/j.csr.2005.11.014","volume":"26","author":"A Jouon","year":"2006","unstructured":"Jouon, A., Douillet, P., Ouillon, S. & Frauni\u00e9, P. Calculations of hydrodynamic time parameters in a semi-opened coastal zone using a 3D hydrodynamic model. Cont. Shelf Res. 26, 1395\u20131415 (2006).","journal-title":"Cont. Shelf Res."},{"key":"69400_CR41","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.ecss.2016.01.036","volume":"171","author":"K Critchell","year":"2016","unstructured":"Critchell, K. & Lambrechts, J. Modelling accumulation of marine plastics in the coastal zone; what are the dominant physical processes?. Estuar. Coast. Shelf. Sci. 171, 111\u2013122 (2016).","journal-title":"Estuar. Coast. Shelf. Sci."},{"key":"69400_CR42","unstructured":"Okinawa Prefecture, H23 Coral Reef Resource Information Development Project Report (2011)."},{"key":"69400_CR43","doi-asserted-by":"publisher","first-page":"17","DOI":"10.3755\/galaxea.19.1_17","volume":"19","author":"H Kayanne","year":"2017","unstructured":"Kayanne, H., Ssuzuki, R. & Liu, G. Bleaching in the Ryukyu Islands in 2016 and associated degree heating week threshold. Galaxea J. Coral Reef Stud. 19, 17\u201318 (2017).","journal-title":"Galaxea J. Coral Reef Stud."},{"key":"69400_CR44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41524-019-0262-4","volume":"5","author":"Y Saito","year":"2019","unstructured":"Saito, Y. et al. Deep-learning-based quality filtering of mechanically exfoliated 2D crystals. npj Comput. Mater. 5, 1\u20136 (2019).","journal-title":"npj Comput. Mater."},{"key":"69400_CR45","unstructured":"Kohl, S., et al. A probabilistic u-net for segmentation of ambiguous images. In Advances in Neural Information Processing Systems, pp. 6965\u20136975 (2018)."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-69400-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-69400-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-69400-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,6]],"date-time":"2022-12-06T14:49:18Z","timestamp":1670338158000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-020-69400-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,31]]},"references-count":45,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["69400"],"URL":"https:\/\/doi.org\/10.1038\/s41598-020-69400-5","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,31]]},"assertion":[{"value":"14 April 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 July 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 July 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interest.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"12416"}}