DOI: 10.5061/dryad.4b8gthtc1
title: 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

description: 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.
description: 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.<br> <br> Further methodological
 details can be found in the paper. This file also
 includes the R script to reproduce all analyses.
description: To reproduce the figures and analysis in this paper please refer
 to the R script as part of this documentation.<br> <br> 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
 rnowicki@mote.org.