Re-identification of individuals from images using spot constellations:a case study in Arctic charr ( Salvelinus alpinus )
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, whic...
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2021
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Online Access: | https://risweb.st-andrews.ac.uk/portal/en/researchoutput/reidentification-of-individuals-from-images-using-spot-constellations(11d97fd3-9793-423f-b28a-95adc0692b7d).html https://doi.org/10.1098/rsos.201768 https://research-repository.st-andrews.ac.uk/bitstream/10023/23658/1/Debicki_2021_RSOS_Re_identification_individual_CC.pdf |
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ftunstandrewcris:oai:risweb.st-andrews.ac.uk:publications/11d97fd3-9793-423f-b28a-95adc0692b7d 2023-05-15T14:25:33+02:00 Re-identification of individuals from images using spot constellations:a case study in Arctic charr ( Salvelinus alpinus ) Debicki, Ignacy T. Mittell, Elizabeth A. Kristjánsson, Bjarni K. Leblanc, Camille A. Morrissey, Michael B. Terzić, Kasim 2021-07 application/pdf https://risweb.st-andrews.ac.uk/portal/en/researchoutput/reidentification-of-individuals-from-images-using-spot-constellations(11d97fd3-9793-423f-b28a-95adc0692b7d).html https://doi.org/10.1098/rsos.201768 https://research-repository.st-andrews.ac.uk/bitstream/10023/23658/1/Debicki_2021_RSOS_Re_identification_individual_CC.pdf eng eng info:eu-repo/semantics/openAccess Debicki , I T , Mittell , E A , Kristjánsson , B K , Leblanc , C A , Morrissey , M B & Terzić , K 2021 , ' Re-identification of individuals from images using spot constellations : a case study in Arctic charr ( Salvelinus alpinus ) ' , Royal Society Open Science , vol. 8 , no. 7 , 201768 . https://doi.org/10.1098/rsos.201768 Capture-mark-recapture Spot matching Spot extraction Deep-learning Individual re-identification Photo identification article 2021 ftunstandrewcris https://doi.org/10.1098/rsos.201768 2021-12-26T14:38:55Z 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. Article in Journal/Newspaper Arctic Arctic charr Arctic Salvelinus alpinus University of St Andrews: Research Portal Arctic Royal Society Open Science 8 7 201768 |
institution |
Open Polar |
collection |
University of St Andrews: Research Portal |
op_collection_id |
ftunstandrewcris |
language |
English |
topic |
Capture-mark-recapture Spot matching Spot extraction Deep-learning Individual re-identification Photo identification |
spellingShingle |
Capture-mark-recapture Spot matching Spot extraction Deep-learning Individual re-identification Photo identification Debicki, Ignacy T. Mittell, Elizabeth A. Kristjánsson, Bjarni K. Leblanc, Camille A. Morrissey, Michael B. Terzić, Kasim Re-identification of individuals from images using spot constellations:a case study in Arctic charr ( Salvelinus alpinus ) |
topic_facet |
Capture-mark-recapture Spot matching Spot extraction Deep-learning Individual re-identification Photo identification |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Debicki, Ignacy T. Mittell, Elizabeth A. Kristjánsson, Bjarni K. Leblanc, Camille A. Morrissey, Michael B. Terzić, Kasim |
author_facet |
Debicki, Ignacy T. Mittell, Elizabeth A. Kristjánsson, Bjarni K. Leblanc, Camille A. Morrissey, Michael B. Terzić, Kasim |
author_sort |
Debicki, Ignacy T. |
title |
Re-identification of individuals from images using spot constellations:a case study in Arctic charr ( Salvelinus alpinus ) |
title_short |
Re-identification of individuals from images using spot constellations:a case study in Arctic charr ( Salvelinus alpinus ) |
title_full |
Re-identification of individuals from images using spot constellations:a case study in Arctic charr ( Salvelinus alpinus ) |
title_fullStr |
Re-identification of individuals from images using spot constellations:a case study in Arctic charr ( Salvelinus alpinus ) |
title_full_unstemmed |
Re-identification of individuals from images using spot constellations:a case study in Arctic charr ( Salvelinus alpinus ) |
title_sort |
re-identification of individuals from images using spot constellations:a case study in arctic charr ( salvelinus alpinus ) |
publishDate |
2021 |
url |
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/reidentification-of-individuals-from-images-using-spot-constellations(11d97fd3-9793-423f-b28a-95adc0692b7d).html https://doi.org/10.1098/rsos.201768 https://research-repository.st-andrews.ac.uk/bitstream/10023/23658/1/Debicki_2021_RSOS_Re_identification_individual_CC.pdf |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Arctic charr Arctic Salvelinus alpinus |
genre_facet |
Arctic Arctic charr Arctic Salvelinus alpinus |
op_source |
Debicki , I T , Mittell , E A , Kristjánsson , B K , Leblanc , C A , Morrissey , M B & Terzić , K 2021 , ' Re-identification of individuals from images using spot constellations : a case study in Arctic charr ( Salvelinus alpinus ) ' , Royal Society Open Science , vol. 8 , no. 7 , 201768 . https://doi.org/10.1098/rsos.201768 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1098/rsos.201768 |
container_title |
Royal Society Open Science |
container_volume |
8 |
container_issue |
7 |
container_start_page |
201768 |
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1766297986949709824 |