A 3D modeling method to calculate the surface areas of coral branches

Jones, Alison; Cantin, Neal E.; Berkelmans, Ray; Sinclair, Billy; Negri, Andrew P.

doi:10.1007/s00338-008-0354-y

Cited by 26 publications

(35 citation statements)

References 23 publications

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“…We present three examples where this framework was used to quantify surface area, height profiles, volume and surface rugosity of coral reefs, across three different spatial extents and with high-resolution. Additionally, the validation analyses showed accuracies ranging from 79% (reefscape) to 90% (coral colony), in agreement with previous studies assessing accuracies for photogrammetric measures of coral colonies [28,31,43,[66][67][68]. These results show evidence of the utility of this framework to coral reef ecology and monitoring, in particular given the rapid degradation of coral reefs worldwide, for example they could enable the monitoring of coral reef flattening after a bleaching event [69].…”

Section: Discussionsupporting

confidence: 87%

Quantifying Multiscale Habitat Structural Complexity: A Cost-Effective Framework for Underwater 3D Modelling

Ferrari

McKinnon²,

et al. 2016

Remote Sensing

103

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Coral reef habitat structural complexity influences key ecological processes, ecosystem biodiversity, and resilience. Measuring structural complexity underwater is not trivial and researchers have been searching for accurate and cost-effective methods that can be applied across spatial extents for over 50 years. This study integrated a set of existing multi-view, image-processing algorithms, to accurately compute metrics of structural complexity (e.g., ratio of surface to planar area) underwater solely from images. This framework resulted in accurate, high-speed 3D habitat reconstructions at scales ranging from small corals to reef-scapes (10s km 2 ). Structural complexity was accurately quantified from both contemporary and historical image datasets across three spatial scales: (i) branching coral colony (Acropora spp.); (ii) reef area (400 m 2 ); and (iii) reef transect (2 km). At small scales, our method delivered models with <1 mm error over 90% of the surface area, while the accuracy at transect scale was 85.3%˘6% (CI). Advantages are: no need for an a priori requirement for image size or resolution, no invasive techniques, cost-effectiveness, and utilization of existing imagery taken from off-the-shelf cameras (both monocular or stereo). This remote sensing method can be integrated to reef monitoring and improve our knowledge of key aspects of coral reef dynamics, from reef accretion to habitat provisioning and productivity, by measuring and up-scaling estimates of structural complexity.

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Section: Discussionsupporting

confidence: 87%

Quantifying Multiscale Habitat Structural Complexity: A Cost-Effective Framework for Underwater 3D Modelling

Ferrari

McKinnon²,

et al. 2016

Remote Sensing

103

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“…This system is more generally accessible than X-ray computed tomography (CT) scans using hospital-based equipment (Veal et al 2010), although CT equipment importantly also allows the scanning of living colonies (Laforsch et al 2008). The 3D laser scanner provides an accurate alternative to methods involving wax dipping or the manual photogrammetric approach to building a 3D model (Jones et al 2008), and the less accurate foil-wrapping method (Veal et al 2010). …”

Section: Resultsmentioning

confidence: 99%

Responses to iron limitation in two colonies of Stylophora pistillata exposed to high temperature: Implications for coral bleaching

Iglic

Wells

Trick

et al. 2011

Limnology & Oceanography

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Exposing the coral Stylophora pistillata to seawater depleted in available iron by complexation with the strong chelator desferrioxamine B reduces the photosynthetic efficiency and alters the pigment composition in its symbiotic algae at high temperatures. Similar effects of iron limitation are known for free-living algae, but this is the first demonstration of low-iron stress in a dinoflagellate living endosymbiotically. Maintaining corals at elevated temperature (30uC and 31uC) under diminished iron availability leads to reduced maximum quantum yields (F v : F m ) of photosystem II (PSII), specifically on brightly illuminated surfaces of the coral. This reduction in maximum quantum yield is due in part to increased photoprotection, indicated by an increase in the photoprotective xanthophyll diatoxanthin, which promotes nonphotochemical quenching of excess light energy to restrict oxidative damage under conditions that impair photosynthetic electron transfer. However, photophysiological changes associated with the lowered maximum quantum yield did not prevent photodamage to PSII under the combined effects of elevated temperature and low iron availability, as shown by the decrease in maximum (F m ) that was not accompanied by significant change in the minimum (F o ) fluorescence yield. All of the foregoing is consistent with the potential of iron limitation to contribute to the underlying conditions by which thermal stress evokes the physiological response by corals that culminates in the symbiotic dysfunction of natural bleaching.

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“…Some 2D analysis methodologies (e.g., Jones et al 2008) that use the caliper methods on digital images by measuring branch diameter of 2D figures may experience similar inaccuracy. The methylene blue values were always lower than the 3D scanner measurements (13% to 46.4% lower).…”

Section: Assessmentmentioning

confidence: 99%

“…For this purpose, simple and accurate tools for measuring coral surface area are needed-tools that would allow comparative work on different species, localities, sizes, environmental conditions, and seasonality (Goreau 1959;Babcock 1991;Bak and Meesters 1998;Houlbreque et al 2003Houlbreque et al , 2004Jones et al 2008). These established techniques for measuring surface area of corals entail tightly wrapping coral fragments with aluminum foil (Marsh 1970); dipping in latex rubber sheet (Meyers and Schultz 1985;Klumpp et al 1988), paraffin wax (Stimson and Kinzie 1991), or dyes (such as methylene blue; Hoegh-Guldberg 1988); and analyzing the amount of covered/ adhering matter.…”

Section: Introductionmentioning

confidence: 99%

“…Although valid, each of the above approaches has its limitations and all are destructive, having inherent difficulties to achieve precise, reliable, and homogeneous outcomes. More recently, computer software methods have been developed for measuring coral surface area by 2D digital-image analysis (Bythell et al 2001;Cocito et al 2003;Negri et al 2005;Courtney et al 2007;Holmes 2008;Holmes et al 2008;Jones et al 2008) or by using fractals to quantify coral's structural parameters (Martin-Garin et al 2007). These methods, while nondestructive and amenable for fieldcollected data, are more suitable for massive coral structures or simple branch fragments and less suitable for reconstructing approximated surface areas for 3D assemblages, but they are inadequate for analyzing complex coral architectures (Courtney et al 2007) because of overlapping.…”

Section: Introductionmentioning

confidence: 99%

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Three‐dimensional laser scanning as an efficient tool for coral surface area measurements

Raz-Bahat

Faibish

Mass

et al. 2009

Limnology & Ocean Methods

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In scleractinian corals, as in many sessile colonial organisms, surface area serves as the prime descriptor for standardization and quantification of physiological and biochemical parameters. The complexity of colonial architecture, however, complicates measurement of surface area, yielding less than satisfactory results for the established methodologies. Here, we used a 3D desktop laser scanner for accurate measurements of skeletal surface area of various coral fragments. The original 127-µm accuracy of the scanner was tested on modules with increasing complexity. It showed a linear (R 2 = 0.912), but relatively small, increase of up to 9.67% accuracy error in complex modules. The scanner's maximum credibility error in repeated measurements was only 1.67%, representing an average error of 0.87 ± 0.66%. We compared the scanner's measured surface area results with those of four established methods: wax coating, foil paper wrapping, methylene blue dipping, and caliper measurements. In all methods, credibility and accuracy errors pointed to the superiority of the new method. Laser scanning is rapid (minimum 10 min per scan), efficient, easy to operate, and economically feasible as a common bench tool.

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A 3D modeling method to calculate the surface areas of coral branches

Cited by 26 publications

References 23 publications

Quantifying Multiscale Habitat Structural Complexity: A Cost-Effective Framework for Underwater 3D Modelling

Quantifying Multiscale Habitat Structural Complexity: A Cost-Effective Framework for Underwater 3D Modelling

Responses to iron limitation in two colonies of Stylophora pistillata exposed to high temperature: Implications for coral bleaching

Three‐dimensional laser scanning as an efficient tool for coral surface area measurements

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