Coral Morphometrics using Metashape
This repository contains files that supported analysis for Curtis et al. (2023), "3D photogrammetry improves measurement of growth and biodiversity patterns in branching corals", now published in Coral Reefs (https://doi.org/10.1007/s00338-023-02367-7)
This project compares traditional field measurements of Pocillopora coral heads with 3D models constructed from digital images of the same coral using Agisoft Metashape software. We are interested in (1) creating a workflow utilizing best practices for photo acquistion and photogrammetry models of individual corals (2) comparing information gained or lost from photogrammetry vs. in-field manual measurements and (3) the ecological relevance of using photogrammetric measurements as a predictor for invertebrate communities within the coral. Data was collected in Moorea, French Polynesia on August 2019 for a project funded by the National Science Foundation (NSF).
Note: Project models and photos are stored in a Google Drive folder and are available upon request.
This repository was updated following publication (August 2, 2023) and is no longer actively maintained. For requests regarding this repository, please contact Joseph Curtis (University of Otago) or Dr. Adrian Stier (UCSB)
/morphometric_data Folder containing coral photogrammetry and field data
| file name | description |
|---|---|
| branchwidth_data.csv | Measurements of distances between coral branches including the average distance for each coral |
| photogrammetry_data_v3_2020_9_10_final.csv | Photogrammetric measurements from colonies imaged in August 2019 |
| field_experiment_colony_measurements_moorea_summer2019.csv | Measurements taken in the field in August 2019 |
| field_experiment_colony_measurements_moorea_december2019_v2.csv | Measurements taken in the field in December |
| maatea_experiment_photo_measurements_december_JC_2020_7_8.csv | Photogrammetric measurements from colonies imaged in December 2019 |
/cafi_data Folder containing coral associated fish and invertebrate data
| file name | description |
|---|---|
| cafi_data_w_taxonomy_summer2019_2020_5_21_final.csv | contains most up to date and thorough taxonomy data |
/code
| file name | description |
|---|---|
| photogrammetry_CAFI_figs_v5_2022_11_25.Rmd | Code for figures and stats analysis comparing photogrammetry and traditional measurements used in publication |
| photogrammetry_stats_aggregated_final_2023.R | Additional statistical analyses comparing photogrammetry and traditional measurements used in publication |
| source_data_cleanup_2022_11_25.R | Data tidying and management prior to use for figure creation and statistical analysis |
| /figures | Subfolder with figures generated by "photogrammetry_CAFI_figs_v5_2022_11_25.Rmd", formatting may slightly differ from published versions |
/notes
| file name | description |
|---|---|
| ORL_Photogrammetry_Protocol_Working.docx | Detailed manual explaining methodology and process for generating photogrammetric measurements from still images using Metashape |
Matthew Gottleib, a UCSB alumni, developed Python code for the Ocean Recoveries lab that can facilitate photogrammetry processing of multiple files by enabling Alignment and 3D model creation of batches of files without user input. Those files are stored and maintained on Matthew's GitHub: https://github.com/Mgla96/OceanRecoveryLabScripts
Note: any subfolder /old contains previous versions of files for analysis and visualization that we saved separately from version control for ease of access. These older files have not been adjusted for changes in file path or source code, and may need adjustment to function in their entirety