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HabitatAnnotation

Habitat annotation of horizontally facing benthic imagery from baited and unbaited remote stereo-video deployments and diver swum stereo-video transects.

We have developed an simple approach to characterise the composition and complexity of habitats from horizontally facing benthic imagery, adapting existing standardised schema for benthic composition (CATAMI classification scheme1) and benthic complexity2, with the addition of a class to quantify the % of benthos versus open water within the horizontally facing image. The annotation approach is rapid and produces % composition and mean and standard deviation estimates of complexity which enable flexible modeling of habitat occurrence and habitat-fish relationships.

This annotation schema is described and included in a published paper3, please cite if you use it. However, please refer to this GitHub repository for uptodate versions of the annotation schema.

Parts of this annotation scheme have also been trailed in two further published papers so far4,5.

To simplify the annotation process and give the charateristic changing depth of field of view of horizontaly facing imagery we have gridded the images in 5 x 4 cells.

Each of the cells should be annotated for dominant Benthic Composition, Field of View and Relief.

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Tht annotation schema is made up of nested Benthic Composition classes taken direclty from the CATAMI schema and a Field of View and Relief class that are useful for characterising horizonatlly facing imagery. BROAD>MORPHOLOGY>TYPE/FieldOfView/Relief

For detailed information on the particaulr taxaonomic levels within BROAD>MORPHOLOGY>TYPE classifications please consult the CATAMI visual guide within this repository.

To the BROAD class, we have added additional levels of "Open Water", to calculate the % of benthos within each image, and "Unknown", to account for the frequent issues of limited visibility typical for forward facing imagery.

The FieldOfView class allows the qualification of the image quality within each cell and the "Limited" level is used where benthos or substrate obscurs the cell within ~1m of the camera (typically the length of the diode arm of stereo-video systems)

The Relief class uses a 0-5 quatification of relief 2 and includes and "Unknown" level to account for cells with limited visibility.

Recommended applications:

For a very rapid assement of Benthic Composition, Field of View and Relief we reccomend only using the: BROAD/FieldOfView/Relief classes An experienced analyst would be able to annotate this schema to over 200 images a day

For a more detailed assement of Benthic Composition (where coral bleaching or macrcoalga compostion was of interest), Field of View and Relief we reccomend using all the classes: BROAD>MORPHOLOGY>TYPE/FieldOfView/Relief classes An experienced analyst would be able to annotate this schema to over 120 images a day

The anntotaion schema has been applied using the TransectMeasure software from www.seagis.com.au and the configuration text file for uploading the schema to TransectMeasure is provided in this repository.

Bibliography

  1. Hill, N., Althaus, F., Rees, T., et al., 2014. CATAMI Classification Scheme for Scoring Marine Biota and Substrata in Underwater Imagery Version 1.4: December 2014

  2. Wilson, S. K., N. A. J. Graham, and N. V. C. Polunin. 2006. “Appraisal of Visual Assessments of Habitat Complexity and Benthic Composition on Coral Reefs.” Marine Biology 151 (3). Springer-Verlag: 1069–76.

  3. McLean, Dianne L., Tim J. Langlois, Stephen J. Newman, Thomas H. Holmes, Matthew J. Birt, Katrina R. Bornt, Todd Bond, et al. 2016. “Distribution, Abundance, Diversity and Habitat Associations of Fishes across a Bioregion Experiencing Rapid Coastal Development.” Estuarine, Coastal and Shelf Science 178 (September): 36–47.

  4. Collins, Danielle, Tim J. Langlois, Todd Bond, Thomas H. Holmes, Euan S. Harvey, Rebecca Fisher Dianne L. McLean. In press. “A novel stereo-video method to investigate fish-habitat relationships.” Methods in Ecology and Evolution.

  5. Katherine Bennett, Tim Langlois , George Shedrawi , Shaun Wilson, Dianne McLean. In press. “Can Diver Operated Stereo-Video Surveys for Fish Be Used to Collect Meaningful Data on Benthic Coral Reef Communities?” Limnology and Oceanography, Methods / ASLO.