Benthic Photo Survey Methods

Field methods have been developed to assess ecosystem health and for validation and calibration purposes. We focus on close range, and spectrometry.

Locations
Various

People
Chris Roelfsema, Josh Passenger, Eva Kovacs, Kathryn Markey, Kirsten Golding, Tiny Remmers

Collaborators
CSIRO, AIMS-ReefCloud, CoralNet

Timeframe
2000 - ongoing

Funding
Various

Summary

Benthic Photoquadrats

Briefly, benthic photoquadrats are photos of the sea floor collected along an imaginary transect at a set distance from the seabed, that represent a 1m2 footprint of the benthos. Photos are captured with a standard camera (e.g., Olympus TG 5,6,7, GoPro, iPhone) from the surface while snorkelling, or at depth by divers or underwater robots. A standard GPS (e.g., Garmin Etracks) in a drybag is towed at the surface and tracks the position of the person or robot.

Photos are assigned a GPS location by time synchronisation between GPS and camera using off the shelf software or custom-made software (i.e., GPS-Photo Linking).

Benthic information can be derived from the photos through manual annotation using Coral Point Count with excel extensions (Kohler et al 2006) or through automated photo analysis using CoralNet or ReefCloud. These methods have been used for collection of calibration and validation data for various habitat mapping projects, including the Allen Coral Atlas.

3D photogrammetry

Close-range underwater photogrammetry is rapidly emerging as a new standard in measuring and monitoring coral reefs, due to its potential to record colony- and habitat-scale metrics in two- and three-dimensions at sub-centimetre scales. Photogrammetry, a process of digitally reconstructing a large area 3D scene from multiple photographs, is being applied to extract structural information of the benthos.

Photos are collected by “lawn mowing” a set pattern over a benthic habitat with one or more cameras that capture overlapping pictures of the benthos.

A machine learning approach has been developed to quantify benthic community composition in coral reefs from the created orthomosaics (Remmers et al., in press), which requires no manual delineation of benthic constituents for training or implementation.

 

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Publications

Scientific journals

  • Remmers T, A Grech, CM Roelfsema, S Gordon, R Ferrari (2023) Close-range underwater photogrammetry for coral reef ecology: a systematic literature review. Coral Reefs. https://doi.org/10.1007/s00338-023-02445-w

  • Roelfsema, C. M., E. Kovacs, K. Markey, J. Vercelloni, A. Rodriguez-Ramirez, S. Lopez-Marcano, M. Gonzalez-Revero, O. Hoegh-Guldberg and R. S. Phinn (2021). "Benthic and coral reef community field data for Heron Reef, Southern Great Barrier Reef, Australia, 2002-2018." Scientific Data. https://www.nature.com/articles/s41597-021-00871-5

  • Leon J., C.M. Roelfsema, M.Saunders, and S.R.  Phinn (2015), Measuring coral reef terrain roughness using 'Structure-from-Motion' close-range photogrammetry. Geomorphology https://doi.org/10.1016/j.geomorph.2015.01.030    

  • Roelfsema, C.M., E. Kovacs, and S. Phinn (2015) “A Multi-date seagrass species and percentage cover field data set, derived from georeferenced photo transects for the Eastern Banks, Moreton Bay, Australia, 2004-2014” Nature Scientific Data. https://doi.org/10.1038/sdata.2015.40   

  • Roelfsema, C.M., and S.R. Phinn (2010) Calibration and Validation of Coral Reef Benthic Community Maps: Integration of Field Data with High Spatial Resolution Multi Spectral Satellite Imagery. Journal of Applied Remote Sensing, https://doi.org/10.1117/1.3430107

  • Roelfsema, C.M., Joyce, K. E., Phinn, S.R., (2006) Evaluation of Benthic Survey Techniques for Validating Remotely Sensed Images of Coral Reefs. Proceedings 10th International Coral Reef Symposium Okinawa.

Scientific data

See data scientific data journals

Scientific Software

  • GPS-Photo, Josh Passenger, Simple tool for positioning photos along GPS tracks using linear interpolation. GITHUB