Annotation guide: benthic composition and relief for horizontally facing imagery
Updated: December 2023
Table of Contents
TransectMeasure - Standard Operating Procedure
1. Load images and attribute file
2. Setting and overlaying the annotation points and adding frame information
3. Classifying the benthic composition in an image
4. Classifying the relief of an image
5. Saving and exporting from TransectMeasure
Annotation summary and quality control
Examples of publications that have used this or earlier versions of this SOP
List of Figures
Figure 1: TransectMeasure initial opening screen.
Figure 2: Creating a new measurement file in TransectMeasure.
Figure 3: Setting the picture directory and loading the image in TransectMeasure.
Figure 4: Loading the attribute file in TransectMeasure.
Figure 5: Adding a new area of interest in TransectMeasure.
Figure 6: Setting the dot configuration in TransectMeasure.
Figure 7: Adding dots in TransectMeasure.
Figure 10: The ‘attribute editor’ window within TransectMeasure.
Figure 11: Setting the dot configuration in TransectMeasure.
Figure 12: Adding dots to an image in TransectMeasure.
Figure 13: Example of a stereo-BRUV image annotated for relief.
Figure 14: Example of a panoramic drop camera composite image annotated for relief.
Figure 15: The ‘attribute editor’ window within TransectMeasure.
Figure 16: Writing to file in TransectMeasure in order to save image observations.
Figure 17: The ‘batch text file output’ option in TransectMeasure.
Figure 18: Input and output file directory options for batch text file outputs in TransectMeasure.
Figure 19: Quality control visualisation of the habitat annotations.
Figure 20: Quality control visualisation of the relief annotations.
Figure 21: Quality control spatial visualisation of broad habitat classes annotated.
We have developed a simple approach to characterise benthic composition and complexity from horizontally facing imagery (including stereo-BRUVs and panoramic drop cameras), adapting existing standardised schema for benthic composition (CATAMI classification scheme) and benthic complexity as per Wilson et al. (2006).
The annotation approach is rapid and produces point annotation-level composition and mean and standard deviation estimates of complexity, which enable flexible modelling of habitat occurrence and fish-habitat relationships. A set of scripts to ensure quality assurance and quality control are also provided.
NOTE: To accurately overlay an area of interest over the lower 50% of the image, you can firstly overlay gridded dots with rectangles (“Measurements” > “Dot configuration ...”. Set accordingly: Gridded dots, ‘Dots across image’ = 1, ‘Dots down image’ = 2 and check the “Overlay rectangles” box) and use the border of the rectangles as a guide.
NOTE: To annotate composite imagery, multiple areas of interest will need to be added corresponding to the images contained in the composite image. For the first area of interest, points can be added following the steps detailed above. For the remaining images within the composite image, points can be added to the existing points by specifying a new area of interest, and then using “ctrl + right click + Add dots” > “Add to the existing points” (Fig. 9). For all subsequent images, “ctrl + shift + i” will overlay the last area of interest and add random dots to the image.
NOTE: This autofill information uses the filename structure that is automatically generated when exporting habitat images from EventMeasure (Right click > “Save as jpeg”. If you wish to use this feature, you must either export your images from EventMeasure, or name your images to match the following structure - ‘OpCode_Period_ImageName’. TransectMeasure will detect the first 2 underscores as separators and parse the information from these into the frame information fields.
Note: Zoom into an image to analyse the benthic composition more closely by adjusting the "Zoom" value at the top left of the window before holding down the ctrl key and hovering your cursor over the area that you would like to zoom to.
Annotation of relief will need to be annotated in a separate TransectMeasure file (.TMObs), which can be set up by following the same steps defined in ‘1. Load images and attribute file’. A separate schema for relief is available for download via CheckEM - ‘Schema downloads’.
NOTE: For composite imagery that consists of multiple images, gridded dot configuration can be changed to reflect multiple images. For panoramic drop camera imagery containing four images, we overlay 10 dots across the image and 8 dots down the image (Fig. 14).
NOTE: Any ‘rectangle’ that has some form of benthos/substrate visible should be classified for Relief (even if open water makes up the majority of the grid). The relief score for rectangles that are entirely composed of open water should be left blank.
NOTE: In order for ‘OpCode’ and ‘Period’ to be included in the final data outputs, you will need to select this option from … . You will only need to do this once per computer.
For standard (rapid) assessment of Benthic Composition and Relief we recommend using ONLY the: “BROAD” classification within the Benthic Composition and Relief. An experienced analyst would be able to annotate this schema to over 200 images a day.
OR
For detailed assessment of Benthic Composition (where coral bleaching or macroalgae composition was of interest) and Relief we recommend using all the classes in Benthic Composition (“BROAD” > “MORPHOLOGY” > “TYPE” and Relief. An experienced analyst would be able to annotate this schema to over 120 images a day.
All corrections should be made within the original annotation files to ensure data consistency over time. We recommend the following approaches to ensure quality control:
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2. McLean, D. L. et al. Using industry ROV videos to assess fish associations with subsea pipelines. Cont. Shelf Res. 141, 76–97 (2017).
3. Bond, T., Partridge, J. C., Taylor, M. D., Cooper, T. F. & McLean, D. L. The influence of depth and a subsea pipeline on fish assemblages and commercially fished species. PLoS One 13, e0207703 (2018).
4. Bond, T. et al. Fish associated with a subsea pipeline and adjacent seafloor of the North West Shelf of Western Australia. Mar. Environ. Res. (2018) doi:10.1016/j.marenvres.2018.08.003.
5. Bond, T. et al. Diel shifts and habitat associations of fish assemblages on a subsea pipeline. Fish. Res. 206, 220–234 (2018).
6. Lester, E. et al. Drivers of variation in occurrence, abundance, and behaviour of sharks on coral reefs. Sci. Rep. 12, 728 (2022).
7. Lester, E. K. et al. Relative influence of predators, competitors and seascape heterogeneity on behaviour and abundance of coral reef mesopredators. Oikos 130, 2239–2249 (2021).
8. Rolim, F. A. et al. Network of small no-take marine reserves reveals greater abundance and body size of fisheries target species. PLoS One 14, e0204970 (2019).
9. Rolim, F. A., Rodrigues, P. F. C. & Gadig, O. B. F. Baited videos to assess semi-aquatic mammals: occurrence of the neotropical otter Lontra longicaudis (Carnivora: Mustelidae) in a marine coastal island in São Paulo, Southeast Brazil. Mar. Biodivers. (2018) doi:10.1007/s12526-018-0868-7.
10. Haberstroh, A. J., McLean, D., Holmes, T. H. & Langlois, T. Baited video, but not diver video, detects a greater contrast in the abundance of two legal-size target species between no-take and fished zones. Mar. Biol. 169, (2022).
11. Piggott, C. V. H., Depczynski, M., Gagliano, M. & Langlois, T. J. Remote video methods for studying juvenile fish populations in challenging environments. J. Exp. Mar. Bio. Ecol. 532, 151454 (2020).
12. MacNeil, M. A. et al. Global status and conservation potential of reef sharks. Nature 583, 801–806 (2020).
13. Goetze, J. S. et al. Drivers of reef shark abundance and biomass in the Solomon Islands. PLoS One 13, e0200960 (2018).
14. Wilson, S. K., Graham, N. A. J., Pratchett, M. S., Jones, G. P. & Polunin, N. V. C. Multiple disturbances and the global degradation of coral reefs: are reef fishes at risk or resilient? Glob. Chang. Biol. 12, 2220–2234 (2006).