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1. Coral Reef Monitoring by Scuba Divers Using Underwater Photogrammetry and Geodetic Surveying

   https://doi.org/10.3390/rs12183036  

   Nocerino, Erica; Menna, Fabio; Gruen, Armin; Troyer, Matthias; Capra, Alessandro; Castagnetti, Cristina; Rossi, Paolo; Brooks, Andrew J.; Schmitt, Russell J.; Holbrook, Sally J. (September 2020, Remote Sensing)

   null (Ed.)

   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. 

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2. High Accuracy Underwater Photogrammetric Surveying.

   Capra, A.; Castagnetti, C.; Dubbini, M.; Gruen, A.; Guo, T.; Mancini, F. T.; Neyer, F.; Rossi, P.; Troyer, M. (October 2017, 3rd IMEKO International Conference on Metrology for Archeology and Cultural Heritage)

   The evolution of underwater photogrammetry allows to realize 3D models of submerged object and structures throughout the use of rapid and efficient procedures either in terms of data acquisition and data processing. These procedures are based on solutions that are applied using natural control points, signalized markers and tie points; the most common algorithms are based on Structure from Motion (SfM) approach. The limit of these applications is sometimes due to the final accuracy, especially when the goal is a centimeter level of accuracy. This accuracy should be necessary when dealing with a survey devoted to deformation control purposes. An example is the underwater photogrammetry for the determination of coral growth; it is effectively a movement or a deformation detection issue where the geometric change is almost at centimeter or few centimeters accuracy level. When dealing with deformation control applications, a geodetic network is essential to realize a stable and unambiguous reference frame through the accurate and permanent installation of Ground Control Points (GCPs). Such a network, indeed, permits a robust reference frame for the georeferencing of images blocks in the different époques of data acquisition. Therefore, the comparison among subsequent photogrammetric restitutions is based on homogeneous 3D models that have been oriented in the same absolute reference system. The photogrammetric survey is based on a methodological approach especially adapted to underwater biometry (like coral growth determination) and to underwater archaeology. The approach is suitable both for modeling objects of relatively reduced dimensions and for structures with a length of ten meters or more, such as coral barriers, wrecks and long walls. The paper describes underwater photogrammetric surveys on sites at different extensions, the geodetic GCPs reference network installation and measurements (distance and elevation difference observations) as well as preliminary results of the network adjustment. A brief description of image acquisition at a different scales and the resulting 3D model of first campaign are also shown. 

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3. Quantifying the Loss of Coral from a Bleaching Event Using Underwater Photogrammetry and AI-Assisted Image Segmentation

   https://doi.org/10.3390/rs15164077  

   Kopecky, Kai L; Pavoni, Gaia; Nocerino, Erica; Brooks, Andrew J; Corsini, Massimiliano; Menna, Fabio; Gallagher, Jordan P; Capra, Alessandro; Castagnetti, Cristina; Rossi, Paolo; et al (August 2023, Remote Sensing)

   Detecting the impacts of natural and anthropogenic disturbances that cause declines in organisms or changes in community composition has long been a focus of ecology. However, a tradeoff often exists between the spatial extent over which relevant data can be collected, and the resolution of those data. Recent advances in underwater photogrammetry, as well as computer vision and machine learning tools that employ artificial intelligence (AI), offer potential solutions with which to resolve this tradeoff. Here, we coupled a rigorous photogrammetric survey method with novel AI-assisted image segmentation software in order to quantify the impact of a coral bleaching event on a tropical reef, both at an ecologically meaningful spatial scale and with high spatial resolution. In addition to outlining our workflow, we highlight three key results: (1) dramatic changes in the three-dimensional surface areas of live and dead coral, as well as the ratio of live to dead colonies before and after bleaching; (2) a size-dependent pattern of mortality in bleached corals, where the largest corals were disproportionately affected, and (3) a significantly greater decline in the surface area of live coral, as revealed by our approximation of the 3D shape compared to the more standard planar area (2D) approach. The technique of photogrammetry allows us to turn 2D images into approximate 3D models in a flexible and efficient way. Increasing the resolution, accuracy, spatial extent, and efficiency with which we can quantify effects of disturbances will improve our ability to understand the ecological consequences that cascade from small to large scales, as well as allow more informed decisions to be made regarding the mitigation of undesired impacts. 

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4. Coral Identification and Counting with an Autonomous Underwater Vehicle

   https://doi.org/10.1109/ROBIO.2018.8664785  

   Modasshir, Md; Rahman, Sharmin; Youngquist, Oscar; Rekleitis, Ioannis (December 2018, 2018 IEEE International Conference on Robotics and Biomimetics (ROBIO))

   Monitoring coral reef populations as part of environmental assessment is essential. Recently, many marine science researchers are employing low-cost and power efficient Autonomous Underwater Vehicles (AUV) to survey coral reefs. While the counting problem, in general, has rich literature, little work has focused on estimating the density of coral population using AUVs. This paper proposes a novel approach to identify, count, and estimate coral populations. A Convolutional Neural Network (CNN) is utilized to detect and identify the different corals, and a tracking mechanism provides a total count for each coral species per transect. Experimental results from an Aqua2 underwater robot and a stereo hand-held camera validated the proposed approach for different image qualities. 

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5. Incident light on mesophotic corals is constrained by reef topography and colony morphology

   https://doi.org/10.3354/meps13756  

   Lesser, MP; Mobley, CD; Hedley, JD; Slattery, M (July 2021, Marine Ecology Progress Series)

   Mesophotic coral reefs, generally defined as deep reefs between 30 and 150 m, are found worldwide and are largely structured by changes in the underwater light field. Additionally, it is increasingly understood that reef-to-reef variability in topography, combined with quantitative and qualitative changes in the underwater light field with increasing depth, significantly influence the observed changes in coral distribution and abundance. Here, we take a modeling approach to examine the effects of the inherent optical properties of the water column on the irradiance that corals are exposed to along a shallow to mesophotic depth gradient. In particular, the roles of reef topography including horizontal, sloping and vertical substrates are quantified, as well as the differences between mounding, plating and branching colony morphologies. Downwelling irradiance and reef topography interact such that for a water mass of similar optical properties, the irradiance reaching the benthos varies significantly with topography (i.e. substrate angle). Coral morphology, however, is also a factor; model results show that isolated hemispherical colonies consistently ‘see’ greater incident irradiances across depths, and throughout the day, compared to plating and branching morphologies. These modeled geometric-based differences in the incident irradiances on different coral morphologies are not, however, consistent with actual depth-dependent distributions of these coral morphotypes, where plating morphologies dominate as you go deeper. Other factors, such as the cost of calcification, arguably contribute to these differences, but irradiance-driven patterns are a strong proximate cause for the observed differences in mesophotic communities on sloping versus vertical reef substrates. 

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