Re-identification of individuals from images using spot constellations: a case study in Arctic charr (Salvelinus alpinus)

Ignacy T. Debicki, Elizabeth A. Mittell, Bjarni K. Kristjánsson, Camille A. Leblanc, Michael B. Morrissey, Kasim Terzić

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The ability to re-identify individuals is fundamental to the individual-based studies that are required to estimate many important ecological and evolutionary parameters in wild populations. Traditional methods of marking individuals and tracking them through time can be invasive and imperfect, which can affect these estimates and create uncertainties for population management. Here we present a photographic re-identification method that uses spot constellations in images to match specimens through time. Photographs of Arctic charr (Salvelinus alpinus) were used as a case study. Classical computer vision techniques were compared with new deep-learning techniques for masks and spot extraction. We found that a U-Net approach trained on a small set of human-annotated photographs performed substantially better than a baseline feature engineering approach. For matching the spot constellations, two algorithms were adapted, and, depending on whether a fully or semi-automated set-up is preferred, we show how either one or a combination of these algorithms can be implemented. Within our case study, our pipeline both successfully identified unmarked individuals from photographs alone and re-identified individuals that had lost tags, resulting in an approximately 4 our multi-step pipeline involves little human supervision and could be applied to many organisms.
Original languageEnglish
Article number201768
Number of pages19
JournalRoyal Society Open Science
Issue number7
Early online date21 Jul 2021
Publication statusPublished - Jul 2021


  • Capture-mark-recapture
  • Spot matching
  • Spot extraction
  • Deep-learning
  • Individual re-identification
  • Photo identification


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