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1. Image capture and pre-filtering for 3D photogrammetry of coral colonies

   https://doi.org/10.17504/protocols.io.bgdcjs2w  

   Million, W; Kenkel, C (July 2020, Protocolsio)

   null (Ed.)

   This is a protocol for generating images to be used in 3D model building via Agisoft Metashape for coral photogrametry. This will cover underwater, field-based methods and tips to collect photographs and preprocessing of photos to improve model building. Image capture is the most important part of 3D photogrammetry because the photos taken at this point will be all that you'll have to build models and collect data. As such, you want to ensure you have enough photos to work with in the future so, in general, more is better. That being said, too many blurry or out of focus pictures will hamper model building. You can optimize your time in the field by taking enough photos from the appropriate angles, however efficiency will come with practice. This is the protocol developed and used by the Kenkel lab to phenotype Acropora cervicornis colonies as part of field operations in the Florida Keys. We incorporate Agisoft Metashape markers in this workflow to scale models and improved model building. The scaling objects used by the Kenkel lab are custom-made, adjustable PVC arrays that include unique markers and bleaching color cards, affectionately called the "Tomahawk". Specs for building a Tomahawk are included in this protocol. Filtering and pre-processing of photos is not always necessary but can be used to salvage 3D models that would be otherwise blurry or incomplete. Here, we describe photo editing in Adobe Lightroom to adjust several characteristics of hundreds of images simultaneously. For a walkthrough and scripts to run Agisoft Metashape on the command line, see https://github.com/wyattmillion/Coral3DPhotogram. For directions to phenotype coral from 3D models see our Phenotyping in MeshLab protocol. These protocols, while created for branching coral, can be applied to 3D models of any coral morphology or any object really. Our goal is to make easy-to-use protocols using accessible softwares in the hopes of creating a standardized method for 3D photogrammetry in coral biology. DOI dx.doi.org/10.17504/protocols.io.bgdcjs2w 

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2. Rapid imaging in the field followed by photogrammetry digitally captures the otherwise lost dimensions of plant specimens

   https://doi.org/10.1002/aps3.11547  

   James, Nicole; Adkinson, Alex; Mast, Austin (September 2023, Applications in Plant Sciences)

   Abstract PremiseWe recognized the need for a customized imaging protocol for plant specimens at the time of collection for the purpose of three‐dimensional (3D) modeling, as well as the lack of a broadly applicable photogrammetry protocol that encompasses the heterogeneity of plant specimen geometries and the challenges introduced by processes such as wilting. Methods and ResultsWe developed an equipment list and set of detailed protocols describing how to capture images of plant specimens in the field prior to their deformation (e.g., with pressing) and how to produce a 3D model from the image sets in Agisoft Metashape Professional. ConclusionsThe equipment list and protocols represent a foundation on which additional improvements can be made for specimen geometries outside of the range of the six types considered, and an easy entry into photogrammetry for those who have not previously used it. 

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3. Three competitors in three dimensions: photogrammetry reveals rapid overgrowth of coral during multispecies competition with sponges and algae

   https://doi.org/10.3354/meps13579  

   Olinger, LK; Chaves-Fonnegra, A; Enochs, IC; Brandt, ME (January 2021, Marine Ecology Progress Series)

   null (Ed.)

   Competition for limited space is an important driver of benthic community structure on coral reefs. Studies of coral-algae and coral-sponge interactions often show competitive dominance of algae and sponges over corals, but little is known about the outcomes when these groups compete in a multispecies context. Multispecies competition is increasingly common on Caribbean coral reefs as environmental degradation drives loss of reef-building corals and proliferation of alternative organisms such as algae and sponges. New methods are needed to understand multispecies competition, whose outcomes can differ widely from pairwise competition and range from coexistence to exclusion. In this study, we used 3D photogrammetry and image analyses to compare pairwise and multispecies competition on reefs in the US Virgin Islands. Sponges ( Desmapsamma anchorata, Aplysina cauliformis ) and macroalgae ( Lobophora variegata ) were attached to coral ( Porites astreoides ) and arranged to simulate multispecies (coral-sponge-algae) and pairwise (coral-sponge, coral-algae) competition. Photogrammetric 3D models were produced to measure surface area change of coral and sponges, and photographs were analyzed to measure sponge-coral, algae-coral, and algae-sponge overgrowth. Coral lost more surface area and was overgrown more rapidly by the sponge D. anchorata in multispecies treatments, when the sponge was also in contact with algae. Algae contact may confer a competitive advantage to the sponge D. anchorata, but not to A. cauliformis , underscoring the species-specificity of these interactions. This first application of photogrammetry to study competition showed meaningful losses of living coral that, combined with significant overgrowths by competitors detected from image analyses, exposed a novel outcome of multispecies competition. 

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4. 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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5. Geometric Method for Estimating Coral Surface Area Using Image Analysis

   https://doi.org/10.17504/protocols.io.bpxcmpiw  

   McLachlan, RH; Grottoli, AG (January 2021, Protocolsio)

   This protocol outlines a non-destructive geometric method for estimating the surface area of Scleractinian coral samples with relatively simple morphologies (e.g., not densely branching). The geometric method was one of the earliest used for estimating the surface area of marine organisms (Odum et al. 1958). The basic principle of this method involves selecting geometric shapes or forms which closely resemble the morphology of a coral fragment (e.g., cylinders, cones, pyramids, hemispheres etc.), measuring the dimensional parameters of the coral, and applying the area equation for a given geometric shape to obtain the surface area estimate for the coral. This method has been commonly used in coral research previously (Szmant-Froelich 1985; Roberts and Ormond 1987; Babcock 1991; Bak and Meesters 1998; Naumann et al. 2009). URL: dx.doi.org/10.17504/protocols.io.bpxcmpiw 

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