2021
Journal article  Open Access

Needs and gaps in optical underwater technologies and methods for the investigation of marine animal forest 3D-structural complexity

Rossi P., Ponti M., Righi S., Castagnetti C., Simonini R., Mancini F., Agrafiotis P., Bassani L., Bruno F., Cerrano C., Cignoni P., Corsini M., Drap P., Dubbini M., Garrabou J., Gori A., Gracias N., Ledoux J. B., Linares C., Mantas T. P., Menna F., Nocerino E., Palma M., Pavoni G., Ridolfi A., Rossi S., Skarlatos D., Treibitz T., Turicchia E., Yuval M., Capra A.

Aquatic Science  AUV  biodiversity  Ocean Engineering  Semantic segmentation  Research data  Biodiversitat  Underwater photogrammetry  Civil Engineering  robotics  Fauna marina  semantic segmentation  Oceanography  Biodiversity  3D monitoring  Engineering and Technology  biogenic reefs conservation  Dades de recerca  Marine fauna  Water Science and Technology  Global and Planetary Change  Biogenic reefs conservation  underwater photogrammetry 

Marine animal forests are benthic communities dominated by sessile suspension feeders (such as sponges, corals, and bivalves) able to generate three-dimensional (3D) frameworks with high structural complexity. The biodiversity and functioning of marine animal forests are strictly related to their 3D complexity. The present paper aims at providing new perspectives in underwater optical surveys. Starting from the current gaps in data collection and analysis that critically limit the study and conservation of marine animal forests, we discuss the main technological and methodological needs for the investigation of their 3D structural complexity at different spatial and temporal scales. Despite recent technological advances, it seems that several issues in data acquisition and processing need to be solved, to properly map the different benthic habitats in which marine animal forests are present, their health status and to measure structural complexity. Proper precision and accuracy should be chosen and assured in relation to the biological and ecological processes investigated. Besides, standardized methods and protocols are strictly necessary to meet the FAIR (findability, accessibility, interoperability, and reusability) data principles for the stewardship of habitat mapping and biodiversity, biomass, and growth data.

Source: Frontiers in Marine Science 8 (2021). doi:10.3389/fmars.2021.591292

Publisher: , Svizzera


Agrafiotis, P., Karantzalos, K., Georgopoulos, A., and Skarlatos, D. (2020). Correcting image refraction: towards accurate aerial image-based bathymetry mapping in shallow waters. Remote Sens. 12:322. doi: 10.3390/rs12020322
Agrafiotis, P., Skarlatos, D., Forbes, T., Poullis, C., Skamantzari, M., and Georgopoulos, A. (2018). Underwater photogrammetry in very shallow waters: main challenges and caustics effect removal. Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci. XLII-2, 15-22. doi: 10.5194/isprs-archives-XLII-2-15- 2018
Beijbom, O., Edmunds, P. J., Roelfsema, C., Smith, J., Kline, D. I., Neal, B. P., et al. (2015). Towards automated annotation of benthic survey images: variability of human experts and operational modes of automation. PLoS One 10:e0130312. doi: 10.1371/journal.pone.0130312
Berman, D., Levy, D., Avidan, S., and Treibitz, T. (2020). Underwater single image color restoration using haze-lines and a new quantitative dataset. IEEE Trans. Pattern Anal. Mach. Intell. doi: 10.1109/tpami.2020.2977624
Bosch, J., Isteniè, K., Gracias, N., Garcia, R., and Ridao, P. (2019). Omnidirectional multi-camera video stitching using depth maps. IEEE J. Oceanic Eng. 99, 1-16. doi: 10.1109/JOE.2019.2924276
Bruno, F., Barbieri, L., Muzzupappa, M., Tusa, S., Fresina, A., Oliveri, F., et al. (2019). Enhancing learning and access to underwater cultural heritage through digital technologies: the case study of the “Cala Minnola” shipwreck site. Digit. Appl. Archaeol. Cult. Herit 13:e00103. doi: 10.1016/j.daach.2019. e00103
Burns, J. H. R., Delparte, D., Gates, R. D., and Takabayashi, M. (2015). Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs. PeerJ 3:e1077. doi: 10.7717/peerj.1077
Caldwell, J. M., Ushijima, B., Couch, C. S., and Gates, R. D. (2017). Intra-colony disease progression induces fragmentation of coral fluorescent pigments. Sci. Rep. 7:14596. doi: 10.1038/s41598-017-15084-3
Casella, E., Collin, A., Harris, D., Ferse, S., Bejarano, S., Parravicini, V., et al. (2017). Mapping coral reefs using consumer-grade drones and structure from motion photogrammetry techniques. Coral Reefs 36, 269-275. doi: 10.1007/s00338- 016-1522-0
Cerrano, C., Bastari, A., Calcinai, B., Di Camillo, C., Pica, D., Puce, S., et al. (2019). Temperate mesophotic ecosystems: gaps and perspectives of an emerging conservation challenge for the Mediterranean Sea. Eur. Zool. J. 86, 370-388. doi: 10.1080/24750263.2019.1677790
Cerrano, C., Bavestrello, G., Bianchi, C. N., Cattaneo-Vietti, R., Bava, S., Morganti, C., et al. (2000). A catastrophic mass-mortality episode of gorgonians and other organisms in the Ligurian Sea (North-western Mediterranean), summer 1999. Ecol. Lett. 3, 284-293. doi: 10.1046/j.1461-0248.2000. 00152.x
Çiçek, Ö, Abdulkadir, A., Lienkamp, S. S., Brox, T., and Ronneberger, O. (2016). “3D U-Net: learning dense volumetric segmentation from sparse annotation,” in MICCAI Medical. Image Computing and Computer-Assisted Intervention, Vol. 424-432, eds S. Ourselin, W. S. Wells, M. R. Sabuncu, G. Unal, and L. Joskowicz (New York, NY: Springer). doi: 10.1007/978-3-319-46 723-8_49
Coma, R., Ribes, M., Zabala, M., and Gili, J. M. (1998). Growth in a modular colonial marine invertebrate. Estuar. Coast. Shelf Sci. 47, 459-470. doi: 10.1006/ ecss.1998.0375
Czechowska, K., Feldens, P., Tuya, F., de Esteban, M. C., Espino, F., Haroun, R., et al. (2020). Testing side-scan sonar and multibeam echosounder to study black coral gardens: a case study from Macaronesia. Remote Sens. 12:3244. doi: 10.3390/rs12193244
Dai, A., and Nießner, M. (2018). “3dmv: joint 3d-multi-view prediction for 3d semantic scene segmentation,” in Proceedings of the 15th European Conference, Munich, Germany, September 8-14, 2018, Munich, 452-468.
Davidson, T. M., Altieri, A. H., Ruiz, G. M., and Torchin, M. E. (2018). Bioerosion in a changing world: a conceptual framework. Ecol. Lett. 21, 422-438. doi: 10.1111/ele.12899
Edwards, C., Eynaud, Y., Williams, G. J., Pedersen, N. E., Zgliczyn-ski, B. J., Gleason, A. C. R., et al. (2017). Large-area imaging reveals biologically driven non-random spatial patterns of corals at a remote reef. Coral Reefs 36, 1291- 1305. doi: 10.1007/s00338-017-1624-3
Farber, C., Titschack, J., Schonberg, C., Ehrig, K., Boos, K., Illerhaus, B., et al. (2016). Long-term macrobioerosion in the Mediterranean Sea assessed by micro-computed tomography. Biogeoscience 13, 3461-3474. doi: 10.5194/bg13-3461-2016
Franchi, M., Ridolfi, A., and Zacchini, L. (2018). “A forward-looking sonar-based system for underwater mosaicing and acoustic odometry,” in Proceedings of the IEEE/OES Autonomous Underwater Vehicle Workshop (AUV), Porto. doi: 10.1109/auv.2018.8729795
Garrabou, J., Gómez-Gras, D., Ledoux, J. B., Linares, C., Bensoussan, N., LópezSendino, P., et al. (2019). Collaborative database to track mass mortality events in the Mediterranean Sea. Front. Mar. Sci. 6:707. doi: 10.3389/fmars.2019. 00707
Gerovasileiou, V., Smith, C. J., Sevastou, K., Papadopoulou, N., Dailianis, T., Bekkby, T., et al. (2019). Habitat mapping in the European Seas-is it fit for purpose in the marine restoration agenda? Mar. Policy 106:103521. doi: 10. 1016/j.marpol.2019.103521
Gori, A., Rossi, S., Berganzo, E., Pretus, J. L., Dale, M. R. T., and Gili, J. M. (2011). Spatial distribution patterns of the gorgonians Eunicella singularis, Paramuricea clavata, and Leptogorgia sarmentosa (Cap de Creus, northwestern Mediterranean Sea). Mar. Biol. 158, 143-158. doi: 10.1007/s00227-01 0-1548-8
Guarino, N., Oberle, D., and Staab, S. (2009). What is an Ontology? Handbook on Ontologies. Heidelberg: Springer, 1-17.
Han, X. F., Laga, H., and Bennamoun, M. (2019). Image-based 3d object reconstruction: state-of-the-art and trends in the deep learning era. IEEE Trans. Pattern. Anal. Mach. Intell, 1. doi: 10.1109/tpami.2019.2954885
House, J. E., Brambilla, V., Bidaut, L. M., Christie, A. P., Pizarro, O., Madin, J. S., et al. (2018). Moving to 3D: relationships between coral planar area, surface area and volume. PeerJ 6:e4280. doi: 10.7717/peerj.4280
Istenicˇ, K., Gracias, N., Arnaubec, A., Escartín, J., and Garcia, R. (2020). Automatic scale estimation of structure from motion based 3D models using laser scalers in underwater scenarios. ISPRS J. Photogramm. Remote Sens. 159, 13-25. doi: 10.1016/j.isprsjprs.2019.10.007
Jones, C. G., Lawton, J. H., and Shachak, M. (1994). Organisms as ecosystem engineers. Oikos 69, 373-386. doi: 10.2307/3545850
Kersting, D. K., and Linares, C. (2019). Living evidence of a fossil survival strategy raises hope for warming-affected corals. Sci. Adv. 5:eaax2950. doi: 10.1126/ sciadv.aax2950
Kružic´, P. S., and Benkovic´, L. (2012). The impact of seawater temperature on coral growth parameters of the colonial coral Cladocora caespitosa (Anthozoa, Scleractinia) in the eastern Adriatic Sea. Facies 58, 477-491. doi: 10.1007/ s10347-012-0306-4
Lagudi, A., Bianco, G., Muzzupappa, M., and Bruno, F. (2016). An alignment method for the integration of underwater 3D data captured by a stereovision system and an acoustic camera. Sensors 16:536. doi: 10.3390/s16040536
Ledoux, J. B., Frias-Vidal, S., Montero-Serra, I., Antunes, A., Casado, B. C., Civit, S., et al. (2020). Assessing the impact of population decline on mating system in the overexploited mediterranean red coral. Aquatic Conserv. Mar. Freshw. Ecosyst. 30, 1149-1159. doi: 10.1002/aqc.3327
Ledoux, J. B., Garrabou, J., Bianchimani, O., Drap, P., Féral, J. P., and Aurelle, D. (2010). Fine-scale genetic structure and inferences on population biology in the threatened mediterranean red coral, Corallium rubrum. Mol. Ecol. 19, 4204-4216. doi: 10.1111/j.1365-294X.2010.04814.x
Liu, B., Liu, Z., Men, S., Li, Y., Ding, Z., He, J., et al. (2020). Underwater hyperspectral imaging technology and its applications for detecting and mapping the seafloor: a review. Sensors 20:4962. doi: 10.3390/s20174962
Maldonado, M., López-Acosta, M., Sánchez-Tocino, L., and Sitjà, C. (2013). The rare, giant gorgonian Ellisella paraplexauroides: demographics and conservation concerns. Mar. Ecol. Prog. Ser. 479, 127-141. doi: 10.3354/ meps10172
Marschal, C., Garrabou, J., Harmelin, J. G., and Pichon, M. (2004). A new method for measuring growth and age in the precious mediterranean red coral Corallium rubrum (L.). Coral Reefs 23, 423-432. doi: 10.1007/s00338-00 4-0398-6
Menna, F., Nocerino, E., Nawaf, M. M., Seinturier, J., Torresani, A., Drap, P., et al. (2019). “Towards real-time underwater photogrammetry for subsea metrology applications,” in Proceedings of the OCEANS 2019, Marseille, 1-10. doi: 10.1109/ OCEANSE.2019.8867285
Montero-Serra, I. (2018). Resilience of Long-Lived Mediterranean Gorgonians in a Changing World: Insights From Life History Theory and Quantitative Ecology. Ph.D. thesis, University of Barcelona, Barcelona.
Montero-Serra, I., Garrabou, J., Doak, D. F., Ledoux, J. B., and Linares, C. (2019). Marine protected areas enhance structural complexity but do not buffer the consequences of ocean warming for an overexploited precious coral. J. Appl. Ecol 56, 1063-1074. doi: 10.1111/1365-2664.13321
Montseny, M., Linares, C., Viladrich, N., Olariaga, A., Carreras, M., Palomeras, N., et al. (2019). First attempts towards the restoration of gorgonian populations on the Mediterranean continental shelf. Aquat. Conserv. Mar. Freshwater Ecosyst. 29, 1278-1284. doi: 10.1002/aqc.3118
Nocerino, E., Dubbini, M., Menna, F., Remondino, F., Gattelli, M., and Covi, D. (2017). Geometric calibration and radiometric correction of the MAIA multispectral camera. Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci. 42, 149-156. doi: 10.5194/isprs-archives-xlii-3-w3-149-2017
Nocerino, E., Neyer, F., Grün, A., Troyer, M., Menna, F., Brooks, A. J., et al. (2019). Comparison of diver-operated underwater photogrammetric systems for coral reef monitoring. Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci. 42, 143-150. doi: 10.5194/isprs-archives-xlii-2-w10-143-2019
Olinger, L. K., Scott, A. R., McMurray, S. E., and Pawlik, J. R. (2019). Growth estimates of Caribbean reef sponges on a shipwreck using 3D photogrammetry. Sci. Rep. 9:18398. doi: 10.1038/s41598-019-54681-2
Ordoñez, A., Wangpraseurt, D., Lyndby, N. H., Kühl, M., and Diaz-Pulido, G. (2019). Elevated CO2 leads to enhanced photosynthesis but decreased growth in early life stages of reef building coralline algae. Front. Mar.Sci. 5:495. doi: 10.3389/fmars.2018.00495
Palma, M., Casado, M., Pantaleo, U., Pavoni, G., Pica, D., and Cerrano, C. (2018). SfM-based method to assess gorgonian forests (Paramuricea clavata (Cnidaria. Octocorallia). Remote Sens. 10:1154. doi: 10.3390/rs100 71154
Palomer, A., Ridao, P., Forest, J., and Ribas, D. (2019). Underwater laser scanner: Ray-based model and calibration. IEEE/ASME Trans. Mechatron. 24, 1986- 1997. doi: 10.1109/tmech.2019.2929652
Pavoni, G., Corsini, M., Fiameni, G., Callieri, M., Edwards, C., and Cignoni, P. (2020). On improving the training of models for the semantic segmentation of benthic communities from orthographic imagery. Remote Sens. 12:3106. doi: 10.3390/rs12183106
Pedersen, N. E., Edwards, C. B., Eynaud, Y., Gleason, A. C. R., Smith, J. E., and Sandin, S. A. (2019). The influence of habitat and adults on the spatial distribution of juvenile corals. Ecography 42, 1703-1713. doi: 10.1111/ecog. 04520
Peirano, A., Morri, C., Bianchi, C. N., and Rodolfo-Metalpa, R. (2001). Biomass, carbonate standing stock and production of the mediterranean coral Cladocora caespitosa (L.). Facies 44, 75-80. doi: 10.1007/bf02668168
Piazza, P., Cummings, V. J., Lohrer, D. M., Marini, S., Marriott, P., Menna, F., et al. (2018). Divers-operated underwater photogrammetry: applications in the study of antarctic benthos. Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci. 42, 885-892. doi: 10.5194/isprs-archives-XLII-2-885-2018
Ponti, M., Turicchia, E., Ferro, F., Cerrano, C., and Abbiati, M. (2018). The understorey of gorgonian forests in mesophotic temperate reefs. Aquat. Conserv. 28, 1153-1166. doi: 10.1002/aqc.2928
Qi, C. R., Yi, L., Su, H., and Guibas, L. J. (2017). “Pointnet++: deep hierarchical feature learning on point sets in a metric space,” in Proceedings of the 31st International Conference on Neural Information Processing Systems, 5099-5108.
Righi, S., Prevedelli, D., and Simonini, R. (2020). Ecology, distribution and expansion of a mediterranean native invader, the fireworm Hermodice carunculata (Annelida). Mediterr. Mar. Sci. 21, 575-591. doi: 10.12681/mms. 23117
Robinson, K. L., Luo, J. Y., Sponaugle, S., Guigand, C., and Cowen, R. K. (2017). A tale of two crowds: public engagement in plankton classification. Front. Mar. Sci. 4:7. doi: 10.3389/fmars.2017.00082
Rossi, P., Castagnetti, C., Capra, A., Brooks, A. J., and Mancini, F. (2020). Detecting change in coral reef 3D structure using underwater photogrammetry: critical issues and performance metrics. Appl. Geomatics 12, 1-15. doi: 10.1007/s12518- 019-00263-w
Rossi, S., Bramanti, L., Gori, A., and Orejas, C. (2017). Marine Animal Forests. The Ecology of Benthic Biodiversity Hotspots. Cham: Springer International Publishing.
Rossi, S., and Orejas, C. (2019). “Approaching cold-water corals to the society: novel ways to transfer knowledge,” in Proceding of the Mediterranean ColdWater Corals: Past, Present and Future, (Cham: Springer), 473-480. doi: 10. 1007/978-3-319-91608-8_39
Sandin, S. A., Edwards, C. B., Pedersen, N. E., Vid, P., Gaia, P., Esmeralda, A., et al. (2020). Considering the rates of growth in two taxa of coral across Pacific islands. Adv. Mar. Biol. 87, 167-191. doi: 10.1016/bs.amb.2020.08.006
Scaradozzi, D., Zingaretti, S., Ciuccoli, N., Costa, D., Palmieri, G., Bruno, F., et al. (2018). Lab4Dive mobile smart lab for augmented archaeological dives. IOP Conf. Ser. Mater. Sci. Eng. 364:012054. doi: 10.1088/1757-899x/364/1/012054
Shihavuddin, A. S. M., Gracias, N., Garcia, R., Gleason, A., and Ginter, B. (2013). Image-based coral reef classification and thematic mapping. Remote Sens. 5, 1809-1841. doi: 10.3390/rs5041809
Stanghellini, G., Del Bianco, F., and Gasperini, L. (2020). OpenSWAP, an open architecture, low cost class of autonomous surface vehicles for geophysical surveys in the shallow water environment. Remote Sens. 12:2575. doi: 10.3390/ rs12162575
Trabes, E., and Jordan, M. A. (2017). A node-based method for SLAM navigation in self-similar underwater environments: a case study. Robotics 6:29. doi: 10. 3390/robotics6040029
Turicchia, E., Abbiati, M., Sweet, M., and Ponti, M. (2018). Mass mortality hits gorgonian forests at montecristo island. Dis. Aquat. Org. 131, 79-85. doi: 10. 3354/dao03284
Verdura, J., Linares, C., Ballesteros, E., Coma, R., Uriz, M. J., Bensoussan, N., et al. (2019). Biodiversity loss in a mediterranean ecosystem due to an extreme warming event unveil the role of an engineering gorgonian species. Sci. Rep. 9:5911. doi: 10.1038/s41598-019-41929-0
Vidal, E., Palomeras, N., Istenicˇ, K., Gracias, N., and Carreras, M. (2020). Multisensor online 3D view planning for autonomous underwater exploration. J. Field Rob. 37, 1-25. doi: 10.1002/rob.21951
Westoby, M. J., Brasington, J., Glasser, N. F., Hambrey, M. J., and Reynolds, J. M. (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
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., et al. (2016). The FAIR guiding principles for scientific data management and stewardship. Sci. Data 3:160018. doi: 10.1038/sdata. 2016.18
Zweifler, A., Akkaynak, D., Mass, T., and Treibitz, T. (2017). In situ analysis of coral recruits using fluorescence imaging. Front. Mar. Sci. 4:273. doi: 10.3389/fmars. 2017.00273

Metrics



Back to previous page
BibTeX entry
@article{oai:it.cnr:prodotti:458843,
	title = {Needs and gaps in optical underwater technologies and methods for the investigation of marine animal forest 3D-structural complexity},
	author = {Rossi P. and Ponti M. and Righi S. and Castagnetti C. and Simonini R. and Mancini F. and Agrafiotis P. and Bassani L. and Bruno F. and Cerrano C. and Cignoni P. and Corsini M. and Drap P. and Dubbini M. and Garrabou J. and Gori A. and Gracias N. and Ledoux J. B. and Linares C. and Mantas T. P. and Menna F. and Nocerino E. and Palma M. and Pavoni G. and Ridolfi A. and Rossi S. and Skarlatos D. and Treibitz T. and Turicchia E. and Yuval M. and Capra A.},
	publisher = {, Svizzera},
	doi = {10.3389/fmars.2021.591292},
	journal = {Frontiers in Marine Science},
	volume = {8},
	year = {2021}
}