Photogrammetric surveys and geometric processes to analyse and monitor red coral colonies
Pierre Drap, Joaquim Garrabou
Jean-Philip Royer, Mohamad Motasem Nawaf, Djamal Merad, Mauro Saccone,
Jean-Baptiste Ledoux, Angel Lopez-Sanz
As the result of more than 10 years collaboration between the computer science community and biologists specialized in underwater organisms, this work has now reached a mature state. Through three kinds of the surveys, we developed different tools that can be applied to coral study (and more especially, in our case, to the Mediterranean red coral study), thus helping to preserve it and protecting its fragile ecosystem.
Photogrammetry is the core of framework developed. Now widely used by many different communities, the challenge is to extract relevant information from the reconstructed models.
First, we presented a graphical software enabling manual 3D measurements on couples of oriented photos, showing coral colonies by a quadrat, which is used as scale tool and surface standard. The software provides reliable measurements (residuals generally lesser than 1 mm), for different estimations of the characteristics of colonies.
Next, we described a set of tools especially designed to study temporal changes. Monitoring the evolution of coral colonies along time and determining the correlations between genetic and spatial distances is the main goal of this survey. The orthophotos of the studied sites are used to visualize the coral colonies and then to compute true geodesic distances. Other tools, such as those used for orthophoto blending at different times, help advanced end users interpret the data.
Finally, the last survey presented was focused on archiving large colonies and extracting relevant data from them. New approaches, including NPR representations and skeletonization of the 3D models, were developed in order to automatically compute morphological information, like volume and branch lengths, as well as getting simplified representations of these dense colonies. This density can prevent or make difficult observations by knowledgeable people.
Much work remains in order to increase the accuracy of estimated measurements of large coral colonies. Even if this study is focused on red coral, the different tools in this frame to better understand and characterize the functioning of benthic communities could be easily extended to other species with similar arborescent growth forms.
Beyond the geometrical and morphological survey and analysis we have done, we have started managing the huge quantity of data collected since the beginning of this collaboration. This data is mainly heterogeneous, incomplete, produced and used by different teams working with different scientific backgrounds. We decided to use an ontology to manage all these data, indeed LSIS have already a long experience in managing photogrammetric data with ontologies in an archaeological context  and both the photogrammetric and the dimensional data of the coral colonies are already stored using Ontology Web Language (OWL) formalism. We are currently working on an extension of this approach in a 3D Information System dedicated to red coral survey based on photogrammetry survey and knowledge representation for spatial reasoning.
Here is a list of related published papers:
• Montero-Serra, I., Linares, C., García, M., Pancaldi, F., Frleta-Valić, M., Ledoux, J.-B., Zuberer, F., Merad, D., Drap, P., Garrabou, J., 2015. Harvesting Effects, Recovery Mechanisms, and Management Strategies for a Long-Lived and Structural Precious Coral. Plos One 10, e0117250.
• Ignasi Montero-Serra, Cristina Linares, Daniel F Doak, Jean-Baptiste Ledoux, Pierre Drap, and Joaquim Garrabou. (2017). Different effects of warming and marine protected areas shape the resilience and structural complexity of the Mediterranean red coral. European Coral Reef Symposium, Wednesday, December 13, 2017 - Friday, December 15, 2017, at Oxford, UK.
• Drap, P., Royer, J.-P., Nawaf, M., Saccone, M., Merad, D., Garrabou, J., 2017. Underwater photogrammetry, coded target and plenoptic technology: a set of tools for monitoring red coral in mediterranean sea, 3D Arch, 3D Virtual Reconstruction and Visualization of Complex Architectures and Scenarios, NAFPLIO, GREECE.
• Pierre Drap, Djamel Merad, Amine Mahiddine, Julien Seinturier, Pierrick Gerenton, Daniela Peloso, Jean-Marc Boï, Olivier Bianchimani, & Joaquim Garrabou. (2014). In situ underwater measurements of red coral: Non-intrusive approach based on coded targets and photogrammetry. International Journal of Heritage in the Digital Era.