Structure-from-motion photogrammetry of Antarctic polychaete reefs

This repository contains all the programming scripts and notebooks to process the orthomosaic and digital elevation raster files (.tiff) to retrieve benthic structural complexity metrics.

Encouragement to use, clone and cite the repository presented here. Scripts are presented in both R and Python, notebooks are presented in Python.

This is a repository corresponding to the publication:

Montes-Herrera, J.C., Hill, N., Cummings, V.J., Johnstone, G., Stark, J.S., Lucieer, V. 2023. Remote sensing of Antarctic polychaete reefs: Reproducible workflows for quantifying benthic structural complexity with action cameras, remotely operated vehicles, and structure-from-motion photogrammetry. Remote Sensing in Ecology and Conservation, 10: 72-90. https://doi.org/10.1002/rse2.358

Data availability

Orthomosaics and Digital Elevation Models available as raster files (.tiff) https://doi.org/10.5281/zenodo.7115132

Imagery was collected with a GoPro 5 at 2 Hz mounted on a remotely-operated vehicle in Ellis Fjord, Antarctica by the Australian Antarctic Division in 2019. Orthomosaics and concomitant digital elevation rasters were created in Metashape. A laser-scale of 10 cm was used.

Respectively, benthic biodiversity and structural complexity metrics were retrieved from the orthomosaic and its concomitant digital elevation raster ('3D model').

Project Data

• ROV imagery
  • Frontal ROV video
  • NADIR GoPro images & video
• Table of ROV depth & transect times
• Benthic cover annotations (.csv)
• Habitat structural metrics (.csv)

Sampling and processing methods

• Remotely Operated Vehicle
• Underwater cameras
• Structure from Motion photogrammetry
• Digital Elevation Model & GIS analysis
• R code developed by Fukunaga et al. (2019) https://doi.org/10.3390/jmse7020027
• Original Python & R code

Data acquisition

Australian Antarctic Division
2019

Geographic coverage

Ellis Fjord, Vestfold Hills, Antarctica

Taxonomic coverage

Serpula narconensis colonies
Associated fauna identified visually with ID guides and literature

Keywords

biogenic structure, underwater photogrammetry, structural Complexity, Digital Elevation Model, Remotely Operated Vehicle, benthos

Contact

J.C. Montes-Herrera
juancarlos.montesherrera@utas.edu.au
Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Australia