APHIS: A new software for photo-matching in ecological studies

Moya, Óscar; Mansilla, Pep-Luis; Madrazo, Sergio; Igual, José Manuel; Rotger, Andreu; Romano, Antonio; Tavecchia, Giacomo

doi:10.1016/j.ecoinf.2015.03.003

Cited by 55 publications

(48 citation statements)

References 22 publications

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“…Together with specification of whole-animal traits (e.g., sex, age class), this considerably reduced the number of images to be compared visually. Alternatively, automatic pattern recognition by image comparison software (e.g., Bolger et al, 2012;Hartog & Reijns, 2014;Moya et al, 2015) could be used. However, application of this method to reptile scalation patterns requires the digitization of reference points on each photograph (Sacchi, Scali, Mangiacotti, Sannolo, & Zuffi, 2016;Sacchi et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

“…Photographs are stored in a (digital) library to facilitate cross-matching of the images. Potential matches of the individually unique natural marks can be detected and evaluated by eye or by photo-identification software (e.g., Van Tienhoven, Den Hartog, & Reijns, 2007;Sacchi et al, 2010;Bolger, Morrison, Vance, Lee, & Farid, 2012;Hartog & Reijns, 2014;Moya et al, 2015). Photographic identification by natural markings is especially appropriate when live animals are difficult to capture (e.g., large marine and terrestrial mammals), or when capture and handling cause severe stress to the study organisms.…”

Section: Introductionmentioning

confidence: 99%

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Genotyping validates photo‐identification by the head scale pattern in a large population of the European adder (Vipera berus)

Bauwens

Claus

Mergeay

2018

Ecology and Evolution

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Capture‐mark‐recapture procedures are a basic tool in population studies and require that individual animals are correctly identified throughout their lifetime. A method that has become more and more popular uses photographic records of natural markings, such as pigmentation pattern and scalation configuration. As with any other marking tool, the validity of the photographic identification technique should be evaluated thoroughly. Here, we report on a large‐scale double‐marking study in which European adders (Vipera berus) were identified by both microsatellite genetic markers and by the pattern of head scalation. Samples that were successfully genotyped for all nine loci yielded 624 unique genotypes, which matched on a one‐to‐one basis with the individual assignments based on the head scalation pattern. Thus, adders considered as different individuals by their genotypes were also identified as different individuals by their head scalation pattern, and vice versa. Overall, variation in the numbers, shape, and arrangement of the head scales enabled us to distinguish among 3200+ photographed individual snakes. Adders that were repeatedly sequenced genetically over intervals of 2–3 years showed no indication whatsoever for a change in the head scale pattern. Photographic records of 900+ adders that were recaptured over periods of up to 12 years showed a very detailed and precise match of the head scale characteristics. These natural marks are thus robust over time and do not change during an individual's lifetime. With very low frequency (0.3%), we detected small changes in scalation that were readily discernible and could be attributed to physical injury or infection. Our study provides a conclusive validation for the use of photo‐identification by head scale patterns in the European adder.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genotyping validates photo‐identification by the head scale pattern in a large population of the European adder (Vipera berus)

Bauwens

Claus

Mergeay

2018

Ecology and Evolution

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“…to camera‐based wildlife assessment may represent a paradigm change in the current technological era. For example, photo identification (Moya et al., ) may become the input for spatial capture–recapture models (Chandler & Royle, ). Concerning marine wildlife assessment, conventional methods (e.g.…”

Section: Introductionmentioning

confidence: 99%

A camera‐based method for estimating absolute density in animals displaying home range behaviour

Campos-Candela

Palmer

Balle

et al. 2018

Journal of Animal Ecology

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The measurement of animal density may take advantage of recent technological achievements in wildlife video recording. Fostering the theoretical links between the patterns depicted by cameras and absolute density is required to exploit this potential. We explore the applicability of the Hutchinson-Waser's postulate (i.e. when animal density is stationary at a given temporal and spatial scale, the absolute density is given by the average number of animals counted per frame), which is a counter-intuitive statement for most ecologists and managers who are concerned with counting the same individual more than once. We aimed to reconcile such scepticism for animals displaying home range behaviour. The specific objectives of this paper are to generalize the Hutchinson-Waser's postulate for animals displaying home range behaviour and to propose a Bayesian implementation to estimate density from counts per frame using video cameras. Accuracy and precision of the method was evaluated by means of computer simulation experiments. Specifically, six animal archetypes displaying well-contrasted movement features were considered. The simulation results demonstrate that density could be accurately estimated after an affordable sampling effort (i.e. number of cameras and deployment time) for a great number of animals across taxa. The proposed method may complement other conventional methods for estimating animal density. The major advantages are that identifying an animal at the individual level and precise knowledge on how animals move are not needed, and that density can be estimated in a single survey. The method can accommodate conventional camera trapping data. The major limitations are related to some implicit assumptions of the underlying model: the home range centres should be homogeneously distributed, the detection probability within the area surveyed by the camera should be known, and animals should move independently to one another. Further improvements for circumventing these limitations are discussed.

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“…Tags however, may cause problems associated with physical or behavioural disruptions of normal processes (Speed et al, ). As an alternative or supplement to conventional methods, photo‐identification (photo‐ID) using natural markings, morphological features or scars offer a non‐invasive way to collect individual data (Speed et al, ; van Tienhoven et al, ; Moya et al, ; Barría et al, ). Despite some limitations related to its technical application, photo‐ID has been increasingly used in elasmobranch studies (Castro & Rosa, ; van Tienhoven et al, ; Holmberg et al, ; Luiz et al, ).…”

mentioning

confidence: 99%

“…(c)]. The second aspect that makes this photo‐ID method useful is that the user visually chooses the matching individual among different options suggested by the algorithm at the end of the process, reducing potential errors if the match is provided automatically by the software (van Tienhoven et al, ; Moya et al, ).…”

mentioning

confidence: 99%

Photo‐identification as a tool to study small‐spotted catshark Scyliorhinus canicula

Navarro

Pérez-Grueso

Barría

et al. 2018

Journal of Fish Biology

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Photo-identification (photo-ID) was tested as a means to identify individual small-spotted catsharks Scyliorhinus canicula. The spotting pattern of the caudal region of S. canicula was used for the tests and revealed that photo-ID is an efficient method to identify individuals. Photo-ID is logistically simple, making it a potential alternative to traditional tagging to provide information on the distribution patterns and population dynamics of S. canicula and related species.

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APHIS: A new software for photo-matching in ecological studies

Cited by 55 publications

References 22 publications

Genotyping validates photo‐identification by the head scale pattern in a large population of the European adder (Vipera berus)

Genotyping validates photo‐identification by the head scale pattern in a large population of the European adder (Vipera berus)

A camera‐based method for estimating absolute density in animals displaying home range behaviour

Photo‐identification as a tool to study small‐spotted catshark Scyliorhinus canicula

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