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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 

This protocol outlines a method of quantitatively measuring the degree of bleaching of a coral colony nondestructively in the field using image analysis. Previous studies have shown that mean intensity grey (MIG), also known as percent whiteness, is highly correlated with chlorophyll a and Symbiodiniaceae density (Chow et al. 2016, Amid et al. 2018), and therefore can be used to quantify the bleaching intensity of a coral colony. Color analysis can be done using digital photographs of live coral colonies either in situ (e.g., Maguire et al. 2003) or exsitu in the lab (Amid et al. 2018; this protocol). Photographs must be taken prior to any preservation or processing of tissue, such as freezing, use of preservatives or fixatives, airbrushing etc., to ensure no alteration of the original coral color occurs. In this protocol, corals are photographed in front of a white reference standard and the resulting color images are subsequently converted to 8-bit greyscale and analyzed. There are two steps to this protocol: 1) Photographing live coral fragments 2) Image analysis of mean grey value 

Coral morphology is influenced by genetics, the environment, or the interaction of both, and thus is highly variable. This protocol outlines a non-destructive and relatively simple method for measuring Scleractinian coral subcorallite skeletal structures (such as the septa length, theca thickness, and corallite diameter, etc.) using digital images produced as a result of digital microscopy or from scanning electron microscopy. This method uses X and Y coordinates of points placed onto photomicrographs to automatically calculate the length and/or diameter of a variety of sub-corallite skeletal structures in the Scleractinian coral Porites lobata. However, this protocol can be easily adapted for other coral species - the only difference may be the specific skeletal structures that are measured (for example, not all coral species have a pronounced columella or pali, or even circular corallites). This protocol is adapted from the methods described in Forsman et al. (2015) & Tisthammer et al. (2018). There are 4 steps to this protocol: 1) Removal of Organic Tissue from Coral Skeletons 2) Imaging of Coral Skeletons 3) Photomicrograph Image Analysis 4) Calculation of Corallite Microstructure Size dx.doi.org/10.17504/protocols.io.bx5bpq2n