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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
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This content will become publicly available on February 1, 2026
CoralCT : A platform for transparent and collaborative analyses of growth parameters in coral skeletal cores
Abstract We present CoralCT, a software application for analysis of annual extension, density, and calcification in coral skeletal cores. CoralCT can be used to analyze computed tomography (CT) scans or X‐ray images of skeletal cores through a process in which observers interact with images of a core to define the locations of annual density bands. The application streamlines this process by organizing the observer‐defined banding patterns and automatically measuring growth parameters. Analyses can be conducted in two or three dimensions, and observers have the option to utilize an automatic band‐detection feature. CoralCT is linked to a server that stores the raw CT and X‐ray image data, as well as output growth rate data for hundreds of cores. Overall, this server‐based system enables broad collaborations on coral core analysis with standardized methods and—crucially—creates a pathway for implementing multiobserver analysis. We assess the method by comparing multiple techniques for measuring annual extension and density, including a corallite‐tracing approach, medical imaging software, two‐dimensional vs. three‐dimensional analyses, and between multiple observers. We recommend that CoralCT be used not only as a measurement tool but also as a platform for data archiving and conducting open, collaborative science.
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- Award ID(s):
- 2444864
- PAR ID:
- 10581070
- Publisher / Repository:
- Limnology and Oceanography Methods
- Date Published:
- Journal Name:
- Limnology and Oceanography: Methods
- Volume:
- 23
- Issue:
- 2
- ISSN:
- 1541-5856
- Page Range / eLocation ID:
- 97 to 116
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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