{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T23:58:56Z","timestamp":1775001536872,"version":"3.50.1"},"reference-count":50,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2020,9,17]],"date-time":"2020-09-17T00:00:00Z","timestamp":1600300800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["OCE 16-37396"],"award-info":[{"award-number":["OCE 16-37396"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Prof. Matthias Troyer through the Institute of Theoretical Physics, ETH Zurich","award":["XXX"],"award-info":[{"award-number":["XXX"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Remote Sensing"],"abstract":"<jats:p>Underwater photogrammetry is increasingly being used by marine ecologists because of its ability to produce accurate, spatially detailed, non-destructive measurements of benthic communities, coupled with affordability and ease of use. However, independent quality control, rigorous imaging system set-up, optimal geometry design and a strict modeling of the imaging process are essential to achieving a high degree of measurable accuracy and resolution. If a proper photogrammetric approach that enables the formal description of the propagation of measurement error and modeling uncertainties is not undertaken, statements regarding the statistical significance of the results are limited. In this paper, we tackle these critical topics, based on the experience gained in the Moorea Island Digital Ecosystem Avatar (IDEA) project, where we have developed a rigorous underwater photogrammetric pipeline for coral reef monitoring and change detection. Here, we discuss the need for a permanent, underwater geodetic network, which serves to define a temporally stable reference datum and a check for the time series of photogrammetrically derived three-dimensional (3D) models of the reef structure. We present a methodology to evaluate the suitability of several underwater camera systems for photogrammetric and multi-temporal monitoring purposes and stress the importance of camera network geometry to minimize the deformations of photogrammetrically derived 3D reef models. Finally, we incorporate the measurement and modeling uncertainties of the full photogrammetric process into a simple and flexible framework for detecting statistically significant changes among a time series of models.<\/jats:p>","DOI":"10.3390\/rs12183036","type":"journal-article","created":{"date-parts":[[2020,9,17]],"date-time":"2020-09-17T08:29:43Z","timestamp":1600331383000},"page":"3036","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":53,"title":["Coral Reef Monitoring by Scuba Divers Using Underwater Photogrammetry and Geodetic Surveying"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3511-4967","authenticated-orcid":false,"given":"Erica","family":"Nocerino","sequence":"first","affiliation":[{"name":"LIS UMR 7020, Aix-Marseille Universit\u00e9, CNRS, ENSAM, Universit\u00e9 De Toulon, Domaine Universitaire de Saint-J\u00e9r\u00f4me, B\u00e2timent Polytech, Avenue Escadrille Normandie-Niemen, 13397 Marseille, France"}]},{"given":"Fabio","family":"Menna","sequence":"additional","affiliation":[{"name":"3DOM\u20143D Optical Metrology Unit, FBK\u2014Bruno Kessler foundation, 38123 Trento, Italy"}]},{"given":"Armin","family":"Gruen","sequence":"additional","affiliation":[{"name":"Institute of Theoretical Physics, ETH Zurich, 8093 Zurich, Switzerland"}]},{"given":"Matthias","family":"Troyer","sequence":"additional","affiliation":[{"name":"Microsoft Corporation, Redmond, WA 98052, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6660-3291","authenticated-orcid":false,"given":"Alessandro","family":"Capra","sequence":"additional","affiliation":[{"name":"DIEF Department, University of Modena and Reggio Emilia, 41125 Modena, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6591-4802","authenticated-orcid":false,"given":"Cristina","family":"Castagnetti","sequence":"additional","affiliation":[{"name":"DIEF Department, University of Modena and Reggio Emilia, 41125 Modena, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5001-8266","authenticated-orcid":false,"given":"Paolo","family":"Rossi","sequence":"additional","affiliation":[{"name":"DIEF Department, University of Modena and Reggio Emilia, 41125 Modena, Italy"}]},{"given":"Andrew J.","family":"Brooks","sequence":"additional","affiliation":[{"name":"Coastal Research Center, Marine Science Institute, University of California, Santa Barbara, CA 93106, USA"}]},{"given":"Russell J.","family":"Schmitt","sequence":"additional","affiliation":[{"name":"Coastal Research Center, Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA"}]},{"given":"Sally J.","family":"Holbrook","sequence":"additional","affiliation":[{"name":"Coastal Research Center, Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA"}]}],"member":"1968","published-online":{"date-parts":[[2020,9,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/2757283","article-title":"The ROV 3D Project: Deep-sea underwater survey using photogrammetry: Applications for underwater archaeology","volume":"8","author":"Drap","year":"2015","journal-title":"J. Comput. Cult. Herit. (JOCCH)"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/j.culher.2018.02.017","article-title":"State of the art and applications in archaeological underwater 3D recording and mapping","volume":"33","author":"Menna","year":"2018","journal-title":"J. Cult. Herit."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"16883","DOI":"10.3390\/rs71215859","article-title":"Accuracy and precision of habitat structural complexity metrics derived from underwater photogrammetry","volume":"7","author":"Figueira","year":"2015","journal-title":"Remote Sens."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.geomorph.2015.01.030","article-title":"Measuring coral reef terrain roughness using \u2018Structure-from-Motion\u2019 close-range photogrammetry","volume":"242","author":"Leon","year":"2015","journal-title":"Geomorphology"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1007\/s00338-016-1462-8","article-title":"End of the chain? Rugosity and fine-scale bathymetry from existing underwater digital imagery using structure-from-motion (SfM) technology","volume":"35","author":"Storlazzi","year":"2016","journal-title":"Coral Reefs"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Menna, F., Nocerino, E., Nawaf, M.M., Seinturier, J., Torresani, A., Drap, P., Remondino, F., and Chemisky, B. (2019, January 17\u201319). Towards real-time underwater photogrammetry for subsea metrology applications. Proceedings of the IEEE OCEANS 2019-Marseille, Marseille, France.","DOI":"10.1109\/OCEANSE.2019.8867285"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"885","DOI":"10.5194\/isprs-archives-XLII-2-885-2018","article-title":"Divers-operated underwater photogrammetry: Applications in the study of antarctic benthos","volume":"42","author":"Piazza","year":"2018","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"67","DOI":"10.5194\/isprsarchives-XL-5-W5-67-2015","article-title":"3D reconstruction of an underwater archaelogical site: Comparison between low cost cameras","volume":"40","author":"Capra","year":"2015","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"821","DOI":"10.5194\/isprs-archives-XLI-B5-821-2016","article-title":"Accuracy assessment of underwater photogrammetric three dimensional modelling for coral reefs","volume":"41","author":"Guo","year":"2016","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_10","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":"PeerJ"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Mangeruga, M., Bruno, F., Cozza, M., Agrafiotis, P., and Skarlatos, D. (2018). Guidelines for underwater image enhancement based on benchmarking of different methods. Remote Sens., 10.","DOI":"10.3390\/rs10101652"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Menna, F., Nocerino, E., Fassi, F., and Remondino, F. (2016). Geometric and optic characterization of a hemispherical dome port for underwater photogrammetry. Sensors, 16.","DOI":"10.3390\/s16010048"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"18140","DOI":"10.3390\/s150818140","article-title":"On the accuracy potential in underwater\/multimedia photogrammetry","volume":"15","author":"Maas","year":"2015","journal-title":"Sensors"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"759","DOI":"10.5194\/isprs-archives-XLII-2-759-2018","article-title":"Monitoring coral growth\u2013the dichotomy between underwater photogrammetry and geodetic control network","volume":"XLII-2","author":"Neyer","year":"2018","journal-title":"ISPRS-Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_15","unstructured":"Capra, A., Castagnetti, C., Dubbini, M., Gruen, A., Guo, T., Mancini, F.T., Neyer, F., Rossi, P., and Troyer, M. (2017, January 23\u201325). High Accuracy Underwater Photogrammetric Surveying. Proceedings of the 3rd IMEKO International Conference on Metrology for Archeology and Cultural Heritage, Castello Carlo, Italy."},{"key":"ref_16","unstructured":"Skarlatos, D., Agrafiotis, P., Menna, F., Nocerino, E., and Remondino, F. (2017, January 23\u201325). Ground control networks for underwater photogrammetry in archaeological excavations. Proceedings of the 3rd IMEKO International Conference on Metrology for Archaeology and Cultural Heritage, Lecce, Italy."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"175","DOI":"10.5194\/isprs-archives-XLII-2-W10-175-2019","article-title":"Precision potential of underwater networks for archaeological excavation through trilateration and photogrammetry","volume":"42","author":"Skarlatos","year":"2019","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"5669","DOI":"10.1002\/ece3.3127","article-title":"Characterization of measurement errors using structure-from-motion and photogrammetry to measure marine habitat structural complexity","volume":"7","author":"Bryson","year":"2017","journal-title":"Ecol. Evol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Raoult, V., Reid-Anderson, S., Ferri, A., and Williamson, J.E. (2017). How reliable is Structure from Motion (SfM) over time and between observers? A case study using coral reef bommies. Remote Sens., 9.","DOI":"10.3390\/rs9070740"},{"key":"ref_20","unstructured":"(2020, July 27). Moorea Island Digital Ecosystem Avatar Project. Available online: https:\/\/mooreaidea.ethz.ch\/."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"143","DOI":"10.5194\/isprs-archives-XLII-2-W10-143-2019","article-title":"Comparison of diver-operated underwater photogrammetric systems for coral reef monitoring","volume":"42","author":"Nocerino","year":"2019","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1769","DOI":"10.1002\/esp.4125","article-title":"3-D uncertainty-based topographic change detection with structure-from-motion photogrammetry: Precision maps for ground control and directly georeferenced surveys","volume":"42","author":"James","year":"2017","journal-title":"Earth Surf. Process. Landf."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"6240","DOI":"10.1109\/TGRS.2019.2905045","article-title":"Rigorous Error Modeling for sUAS Acquired Image-Derived Point Clouds","volume":"57","author":"Rodarmel","year":"2019","journal-title":"IEEE Trans. Geosci. Remote Sens."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/s12518-019-00263-w","article-title":"Detecting change in coral reef 3D structure using underwater photogrammetry: Critical issues and performance metrics","volume":"12","author":"Rossi","year":"2019","journal-title":"Appl. Geomat."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/517255a","article-title":"Tropical paradise inspires virtual ecology lab","volume":"517","author":"Cressey","year":"2015","journal-title":"Nature"},{"key":"ref_26","unstructured":"Gruen, A., Troyer, M., and Guo, T. (2017, January 12\u201318). Spatiotemporal physical modeling of tropical islands within the Digital Ecosystem Avatar (IDEA) Project. Proceedings of the 19 Internationale Geod\u00e4tische Woche Obergurgl 2017, Obergurgl, Austria."},{"key":"ref_27","unstructured":"Guillaume, S., Muller, C., and Cattin, P.-H. (2008). Trinet+, Logiciel de Compensation 3D Version 6.1, Mode d\u2019Emploi, HEIG-VD."},{"key":"ref_28","unstructured":"(2020, July 27). GAMA. Available online: http:\/\/www.gnu.org\/software\/gama\/."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Menna, F., Nocerino, E., and Remondino, F. (2017, January 26\u201327). Optical aberrations in underwater photogrammetry with flat and hemispherical dome ports. Proceedings of the Videometrics, Range Imaging, and Applications XIV, Munich, Germany.","DOI":"10.1117\/12.2270765"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"329","DOI":"10.5194\/isprs-archives-XLII-1-329-2018","article-title":"Multi-camera system calibration of a low-cost remotely operated vehicle for underwater cave exploration","volume":"42","author":"Nocerino","year":"2018","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Akkaynak, D., and Treibitz, T. (2019, January 16\u201320). Sea-thru: A method for removing water from underwater images. Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Long Beach, CA, USA.","DOI":"10.1109\/CVPR.2019.00178"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"135","DOI":"10.5194\/isprs-archives-XLII-2-W10-135-2019","article-title":"Image Quality Improvements in Low-Cost Underwater Photogrammetry","volume":"42","author":"Neyer","year":"2019","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_33","unstructured":"(2020, July 27). Agisoft Metashape, Version 1.6 Professional Edition. Available online: http:\/\/www.agisoft.com\/."},{"key":"ref_34","unstructured":"(2020, July 27). DBAT. Available online: https:\/\/github.com\/niclasborlin\/dbat\/."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1111\/phor.12037","article-title":"Bundle adjustment with and without damping","volume":"28","author":"Grussenmeyer","year":"2013","journal-title":"Photogramm. Rec."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"481","DOI":"10.5194\/isprs-archives-XLII-2-W3-481-2017","article-title":"Flat versus hemispherical dome ports in underwater photogrammetry","volume":"42","author":"Menna","year":"2017","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1002\/esp.3609","article-title":"Mitigating systematic error in topographic models derived from UAV and ground-based image networks","volume":"39","author":"James","year":"2014","journal-title":"Earth Surf. Process. Landf."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"465","DOI":"10.5194\/isprsarchives-XL-5-465-2014","article-title":"Accuracy of typical photogrammetric networks in cultural heritage 3D modeling projects","volume":"XL-5","author":"Nocerino","year":"2014","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"977","DOI":"10.5194\/isprs-archives-XLIII-B2-2020-977-2020","article-title":"Mitigating image residuals systematic patterns in underwater photogrammetry","volume":"43","author":"Menna","year":"2020","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.isprsjprs.2013.04.009","article-title":"Accurate 3D comparison of complex topography with terrestrial laser scanner: Application to the Rangitikei canyon (NZ)","volume":"82","author":"Lague","year":"2013","journal-title":"ISPRS J. Photogramm. Remote Sens."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1561\/0600000052","article-title":"Multi-view stereo: A tutorial","volume":"9","author":"Furukawa","year":"2015","journal-title":"Found. Trends Comput. Graph. Vis."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1109\/TPAMI.2011.172","article-title":"High accuracy and visibility-consistent dense multiview stereo","volume":"34","author":"Vu","year":"2011","journal-title":"IEEE Trans. Pattern Anal. Mach. Intell."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Kuhn, A., Mayer, H., Hirschm\u00fcller, H., and Scharstein, D. (2014, January 8\u201311). A TV prior for high-quality local multi-view stereo reconstruction. Proceedings of the IEEE 2014 2nd International Conference on 3D Vision, Tokyo, Japan.","DOI":"10.1109\/3DV.2014.76"},{"key":"ref_44","first-page":"72","article-title":"Adaptive least squares correlation with geometrical constraints","volume":"Volume 595","author":"Gruen","year":"1986","journal-title":"Computer Vision for Robots"},{"key":"ref_45","unstructured":"Borradaile, G.J. (2003). Statistics of Earth Science Data: Their Distribution in Time, Space and Orientation, Springer Science & Business Media."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Zach, C., Pock, T., and Bischof, H. (2007, January 14\u201321). A globally optimal algorithm for robust tv-l 1 range image integration. Proceedings of the 2007 IEEE 11th International Conference on Computer Vision, Rio de Janeiro, Brazil.","DOI":"10.1109\/ICCV.2007.4408983"},{"key":"ref_47","unstructured":"(2020, July 27). Cloud-to-Mesh Distance, CloudCompare. Available online: https:\/\/www.cloudcompare.org\/doc\/wiki\/index.php?title=Cloud-to-Mesh_Distance."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"699","DOI":"10.5194\/isprs-archives-XLII-2-699-2018","article-title":"Improving underwater accuracy by empirical weighting of image observations","volume":"42","author":"Menna","year":"2018","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."},{"key":"ref_49","unstructured":"d\u2019Autume, M.G. (August, January 24). Le traitement des erreurs systematique dans l\u2019aerotriangulation. Proceedings of the XIIth Congress of the ISP, Commission 3, Ottawa, ON, Canada."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"151","DOI":"10.5194\/isprs-archives-XLII-2-W10-151-2019","article-title":"Semantic segmentation of benthic communities rom ortho-mosaic maps","volume":"XLII-2","author":"Pavoni","year":"2019","journal-title":"Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci."}],"container-title":["Remote Sensing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-4292\/12\/18\/3036\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:10:56Z","timestamp":1760177456000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-4292\/12\/18\/3036"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,9,17]]},"references-count":50,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2020,9]]}},"alternative-id":["rs12183036"],"URL":"https:\/\/doi.org\/10.3390\/rs12183036","relation":{},"ISSN":["2072-4292"],"issn-type":[{"value":"2072-4292","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,9,17]]}}}