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

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.