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Area and Timing data and R script for: 3D scanning as a tool to measure growth rates of live coral microfragments used for coral reef restoration


Koch, Hanna et al. (2021), Area and Timing data and R script for: 3D scanning as a tool to measure growth rates of live coral microfragments used for coral reef restoration, Dryad, Dataset,


Rapid and widespread declines in coral health and abundance have driven increased investments in coral reef restoration interventions to jumpstart population recovery. Microfragmentation, an asexual propagation technique, is used to produce large numbers of corals for research and restoration. As part of resilience-based restoration, coral microfragments of different genotypes and species are exposed to various stressors to identify candidates for propagation. Growth rate is one of several important fitness-related traits commonly used in candidate selection, and being able to rapidly and accurately quantify growth rates of different genotypes is ideal for high-throughput stress tests. Additionally, it is crucial, as coral restoration becomes more commonplace, to establish practical guidelines and standardized methods of data collection that can be used across independent groups. Herein, we developed a streamlined workflow for growth rate quantification of live microfragmented corals using a structured-light 3D scanner to assess surface area measurements of live tissue over time. We then compared novel 3D and traditional 2D approaches to quantifying microfragment growth rates and assessed factors such as accuracy and speed. Compared to a more conventional 2D approach based on photography and ImageJ analysis, the 3D approach had comparable reliability, greater accuracy regarding absolute surface area quantification, high repeatability, and low variability between scans. However, the 2D approach accurately measured growth and proved to be faster and cheaper, factors not trivial when attempting to upscale for restoration efforts. Nevertheless, the 3D approach has greater capacity for standardization across dissimilar studies, making it a better tool for restoration practitioners striving for consistent and comparable data across users, as well as for those conducting networked experiments, meta-analyses, and syntheses. Furthermore, 3D scanning has the capacity to provide more accurate surface area measurements for rugose, mounding, or complex colony shapes. While each method has its advantages and disadvantages, disadvantages to a 3D approach based on speed and cost may diminish with time as interest and usage increase. As a resource for coral restoration practitioners and researchers, we provide a detailed 3D scanning protocol herein and discuss its potential limitations, applications, and future directions.


These data are both raw and corrected area data obtained both from 2D images processed in imageJ, as well as surface area estimates from a 3D Flex Scan scanner. The growth estimates were obtained by regressing the area at different time points as a function of d.since.start to obtain daily growth rate estimates.

Further methodological details can be found in the paper.

This file also includes the R script to reproduce all analyses.

Usage notes

To reproduce the figures and analysis in this paper please refer to the R script as part of this documentation.

The 'area.corr' column are the final data and should be used for all product generation, do not use the 'mean.area' column as these are raw data.  For any questions, please reach out to Dr. Rob Nowicki at


Mote Marine Laboratory and Aquarium, Award: Postdoctoral Research Fellowship

Deutsche Forschungsgemeinschaft, Award: 394448490

Mote Marine Laboratory and Aquarium, Award: Mote REU internship