Quantifying the shelter capacity of coral reefs using photogrammetric 3D modeling: From colonies to reefscapes

Urbina-Barreto, Isabel; Chiroleu, Frédéric; Pinel, Romain; Louis, Fréchon; Mahamadaly, Vincent; Simon, Elise; Kulbicki, Michel; Quod, Jean-Pascal; Dutrieux, Éric; Garnier, Rémi; Bruggemann, J. Henrich; Penin, Lucie; Adjeroud, Mehdi

doi:10.1016/j.ecolind.2020.107151

Cited by 43 publications

(55 citation statements)

References 56 publications

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“…We uncover an exponential relationship between TLE and V inter where marginal increases in TLE result in larger increases in V inter as corals grow, indicating positive allometry. Similar positive allometry was observed in multiple coral morphotypes for shelter volume-colony diameter and planar area relationships (Urbina-Barreto et al, 2020), and between colony surface complexity and colony volume (Zawada et al, 2019). The allometric relationship observed here between TLE and V inter means that small colonies create interstitial space at a slower rate than larger colonies.…”

Section: Relationships Between Tle and Higher Order Traitssupporting

confidence: 81%

“…Coral restoration can benefit from reliable predictors of key performance traits that can be used to guide propagation and outplanting of corals with desired traits (van Oppen et al, 2015). We tested the predictive power of initial growth by relating it to growth in subsequent time intervals.…”

Section: Predictive Power Of Initial Growthmentioning

confidence: 99%

“…Traits such as "compactness, " "topheaviness" (Zawada et al, 2019), and "proportion occupied" (Doszpot et al, 2019) quantify complex, ecologically relevant aspects of colony morphology that can easily be accessed using digital 3D models. For example, V inter quantifies the absolute amount of space created between the branches of a coral, similar to shelter volume (Urbina-Barreto et al, 2020). Interstitial space provides important habitat for reef fishes (Wilson et al, 2008;Noonan et al, 2012;Urbina-Barreto et al, 2020) helping to maintain populations (Wilson et al, 2008;Graham, 2014).…”

Section: Broader Applicationsmentioning

confidence: 99%

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Colony-Level 3D Photogrammetry Reveals That Total Linear Extension and Initial Growth Do Not Scale With Complex Morphological Growth in the Branching Coral, Acropora cervicornis

2021

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The ability to quantify changes in the structural complexity of reefs and individual coral colonies that build them is vital to understanding, managing, and restoring the function of these ecosystems. However, traditional methods for quantifying coral growth in situ fail to accurately quantify the diversity of morphologies observed both among and within species that contribute to topographical complexity. Three-dimensional (3D) photogrammetry has emerged as a powerful tool for the quantification of reefscape complexity but has yet to be broadly adopted for quantifying the growth and morphology of individual coral colonies. Here we debut a high-throughput method for colony-level 3D photogrammetry and apply this technique to explore the relationship between linear extension and other growth metrics in Acropora cervicornis. We fate-tracked 156 individual coral transplants to test whether initial growth can be used to predict subsequent patterns of growth. We generated photographic series of fragments in a restoration nursery immediately before transplanting to natural reef sites and re-photographed coral at 6 months and 1 year post-transplantation. Photosets were used to build 3D models with Agisoft Metashape, which was automated to run on a high-performance computing system using a custom script to serially process models without the need for additional user input. Coral models were phenotyped in MeshLab to obtain measures of total linear extension (TLE), surface area, volume, and volume of interstitial space (i.e., the space between branches). 3D-model based measures of TLE were highly similar to by-hand measurements made in the field (r = 0.98), demonstrating that this method is compatible with established techniques without additional in water effort. However, we identified an allometric relationship between the change in TLE and the volume of interstitial space, indicating that growth in higher order traits is not necessarily a linear function of growth in branch length. Additionally, relationships among growth measures weakened when comparisons were made across time points, implying that the use of early growth to predict future performance is limited. Taken together, results show that 3D photogrammetry is an information rich method for quantifying colony-level growth and its application can help address contemporary questions in coral biology.

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Section: Relationships Between Tle and Higher Order Traitssupporting

confidence: 81%

Section: Predictive Power Of Initial Growthmentioning

confidence: 99%

Section: Broader Applicationsmentioning

confidence: 99%

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Colony-Level 3D Photogrammetry Reveals That Total Linear Extension and Initial Growth Do Not Scale With Complex Morphological Growth in the Branching Coral, Acropora cervicornis

2021

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“…Quantifying shelter is an important step towards assessing the restored reef's capacity to support biodiversity [30]. We infered the shelter volume (ie.…”

Section: Total Volumementioning

confidence: 99%

“…Diameter of coral colonies was shown to be a good indicator of their shelter volume [30]. We need to check our machine learning estimates against the volume that we measured manually from the pictures.…”

Section: Volumementioning

confidence: 99%

Assessment of coral restoration’s contribution to reef recovery using machine learning

Morand¹,

Dixon²,

Berre³

2020

Preprint

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Coral restoration emerged globally as a form of life support for coral reefs, awaiting urgent mitigation of anthropogenic pressure. Yet its efficiency is difficult to assess, as ambitious transplantation programs handle hundreds of thousands of fragments, with survival rates inherently time-intensive to monitor. Due to limited available data, the influence of most environmental and methodological factors is still unknown.We therefore propose a new method which leverages machine learning to track each colony’s individual health and growth on a large sample size. This is the first time artificial intelligence techniques were used to monitor coral at a colony scale, providing an unprecedented amount of data on coral health and growth. Here we show the influence of genus, depth and initial fragment size, alongside providing an outlook on coral restoration’s efficiency.We show that among 77,574 fragments, individual survival rate was 31% after 2 years (21% after 4 years), which is much lower than most reported results. In the absence of significant anthropogenic pressure, we showed that there was a depth limit below which Pocillopora fragments outperformed Acropora fragments, while the opposite was true past this threshold. During the mid-2019 heatwave, our research indicates that Pocillopora fragments were 37% more likely to survive than Acropora fragments.Overall, the total amount of live coral steadily increased over time, by more than 3,700 liters a year, as growth compensated for mortality. This supports the use of targeted coral restoration to accelerate reef recovery after mass bleaching events.

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Identifying key factors for coral survival in reef restoration projects using deep learning

Morand

Dixon

Berre

2022

Aquatic Conservation

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1. Coral restoration has emerged globally as a form of life support for coral reefs, awaiting urgent mitigation of anthropogenic pressures. Yet its efficiency is difficult to assess, as sizeable transplantation programmes handle hundreds of thousands of fragments, with survival rates inherently time intensive to monitor.Owing to limited available data, the influence of most environmental and methodological factors is still unknown. 2. To address this issue, machine learning and computer vision were used to track individual colonies' survival, in a world first. Fragments from several species of Acropora and Pocillopora were transplanted over 12 sites across two Maldivian atolls. These colonies grew on coral frames, placed between 1 and 30 m deep.Analysis of monitoring pictures provided health and growth data on 77,574 individual coral colonies to inform the influence of genus, depth, initial fragment size, and substrate on their survival.3. Among 77,574 fragments, individual survival rate was 31% after 2 years (21% after 4 years), which is much lower than most reported results. Deeper placement was an important success factor for Acropora transplants, but not for Pocillopora.In both genera, smaller initial fragment size was key to increased survival rates.Pocillopora fragments survived better than Acropora fragments at shallow depths (≤7 m), regardless of initial fragment size. Deeper, both genera had similar survival rates, which were influenced by initial fragment size and depth with comparable importance. During the mid-2019 heat wave, previously transplanted Acropora fragments were 38% more likely to die than Pocillopora fragments. 4. Overall, the total volume of live coral steadily increased over time, by more than 3.7 Â 10 6 cm 3 per year, as the volume increase in surviving fragments more than compensated for the volume loss due to mortality. This finding supports the use of targeted coral restoration to accelerate reef recovery after mass bleaching events.

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Quantifying the shelter capacity of coral reefs using photogrammetric 3D modeling: From colonies to reefscapes

Cited by 43 publications

References 56 publications

Colony-Level 3D Photogrammetry Reveals That Total Linear Extension and Initial Growth Do Not Scale With Complex Morphological Growth in the Branching Coral, Acropora cervicornis

Colony-Level 3D Photogrammetry Reveals That Total Linear Extension and Initial Growth Do Not Scale With Complex Morphological Growth in the Branching Coral, Acropora cervicornis

Assessment of coral restoration’s contribution to reef recovery using machine learning

Identifying key factors for coral survival in reef restoration projects using deep learning

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