The scripts in this repository accompany a protocol for color correcting digital underwater reef images obtained by the Connolly Lab.
The purpose of these scripts is to produce reef images free from water distortion. Inconsistent water conditions vary the color of coral, making it challenging to establish a standard color threshold for bleached coral. This protocol builds off of underwater colorimetry methods developed by the COLOR lab to correct water’s effect on reef colors and addresses this issue.
This repository was developed through a collaboration between the COLOR Lab and the Connolly Lab, combining scripts and methods developed by Richard Montes Lemus with resources and scripts adapted from Dr. Derya Akkaynak’s Underwater Colorimetry course.
- /code – main scripts for underwater color correction
- /agisoft_scripts – Agisoft Metashape automation scripts
For a detailed, step-by-step protocol that explains the use of this repository's scripts and folders, contact richard.montes.lemus@gmail.com
- R – mgcv, ggplot2, tidyr, dplyr, reshape2, plotly, glmmTMB, glue
- Python – Metashape, sys, os, csv
- Matlab – Image Processing Toolbox
For questions about this repository, please contact: