Benthic megafaunal assemblages from the Mayotte island outer slope: a case study illustrating workflow from annotation on images to georeferenced densities in sampling units

The Mayotte island outer slopes have been explored using a towed camera to describe the megabenthic communities in the bathyal domain. The present dataset focus on the eastern slope, at depths between 500 and 1100m. It is presented as a case study of workflow from annotations on images by using the Biigle online platform to georeferenced densities in standardized sampling units by the Adelie post-processing software. Data have been acquired during the Biomaglo cruise led by MNHN and Ifremer (Corbari, 2017). 

Workflow to obtain a density matrix from raw observation export

The file “1_dive05_raw” corresponds to the raw data export of the Biigle software for a specific dive.

This raw “csv” format contains one row for each annotation label. Since an annotation can have multiple labels, there may be multiple rows for a single annotation. The first row always contains the column headers. The columns are as follows:

  • 1: Annotation label ID (not the annotation ID)
  • 2 : Label ID
  • 3 : Label name
  • 4 : Label hierarchy (see the extended report on how to interpret a label hierarchy)
  • 5: ID of the user who created/attached the annotation label
  • 6 : User firstname
  • 7 : User lastname
  • 8 : Image ID
  • 9 : Image filename
  • 10 : Image longitude
  • 11 : Image latitude
  • 12 : Annotation shape ID
  • 13 : Annotation shape name
  • 14 : Annotation points. The annotation points are encoded as a JSON array of alternating x and y values (e.g. [x1,y1,x2,y2,...]). For circles, the third value of the points array is the radius of the circle.
  • 15 : Additional attributes of the image. The additional attributes of the image are encoded as a JSON object. The content may vary depending on the BIIGLE modules that are installed and the operations performed on the image (e.g. a laser point detection to calculate the area of an image).
  • 16 : Annotation ID

The file “2_dive05_biomaglo_taxo_abund.csv” corresponds to a «matrix of abundance» format after cleaning the dataset and reordering the columns and calculating the number of individuals per taxa per image in the R environment. This file is then formatted such as the file “3_dive05_biomaglo_taxo_abund_SIG.csv”. This third file corresponds to the format required by ADELIE (Ifremer software), used to calculate the density of taxa per sampling unit in the GIS. Taxon names are converted to “ID” because the software requires “.dbf” format files that truncate names beyond 10 characters.

From the ADELIE software, we perform a join between the abundance matrix and the “DIM” file of the dive which includes the georeferenced metadata of the images (latitude, longitude, altitude, filename). After the join, we proceed to the density calculation. The input files are the “join file” (i.e. georeferenced abundance matrix) and the navigation file which includes the altitude data (“NAV”).  The polygon area (sampling unit) must be specified (here 200m2).

The file “4_output_dive05.csv” is the output after calculating the abundance per sampling unit. Column « OBJECTID,N,9,0 » includes the polygon numbers.

This file is then cleaned in the R environment to obtain the file “5_dive05_density_final”: the value of the average surface image for the dive is added to the file, and from the number of replicates (images) per polygon, we standardize the abundance per polygon surface (~200m2). Taxon names are reassigned instead of the “ID”.


Fisheries and aquaculture


-10.822061N, -13.399857S, 47.991132E, 42.629804W


Camera of the SCAMPI towed camera system mounted in a downward configuration.

Annotations were computed on the Biigle 2.0 software (Langenkämper et al., 2017).

Densities were computed and georeferenced using the ADELIE software (internal dev. IFREMER/FOF; ArcGIS 10.7 plugin).

Please see the “Metadata and annotation protocols” and “workflow” files for further understanding on data formatting and handling.


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Metadata and Protocol
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How to cite
Hanafi-Portier Mélissa, Borremans Catherine, Soubigou Olivier, Samadi Sarah, Corbari Laure, Olu Karine (2023). Benthic megafaunal assemblages from the Mayotte island outer slope: a case study illustrating workflow from annotation on images to georeferenced densities in sampling units. SEANOE.

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