Identificación no supervisada de fauna marina mediante procesamiento de imágenes fotográficas

Las técnicas de procesamiento inteligente de imágenes han experimentado en la última década un desarrollo muy importante, debido a la conjunción de varios factores tecnológicos. Por un lado, se han propuesto técnicas y metodologías de estimación robusta de los parámetros geométricos relevantes en fotografías oblicuas (y por lo tanto una reconstrucción 3D plausible de las mismas), por otro lado, se han desarrollado nuevos modelos de reconocimiento de patrones e identificación no supervisada, aplicados con éxito en una gran variedad de contextos y áreas de intervención. Estos avances permiten construir la hipótesis fundamental de esta línea de trabajo, según la cual es posible investigar y desarrollar técnicas y metodologías de procesamiento inteligente de imágenes para la identificación de individuos de fauna marina. En el caso particular de los cetáceos, en los que las muescas en aletas dorsales son utilizadas para realizar la identificación individual, es necesario el procesamiento de imágenes fotográficas oblicuas. Una solución de este tipo poseería un sinnúmero de ventajas. Por un lado, la intervención no es directa y por lo tanto no es traumática para los individuos bajo estudio. Por otro lado es de aplicación masiva, es decir puede utilizarse para resolver problemas similares en distintas especies.Eje: Computación Gráfica, Imágenes y Visualización.Red de Universidades con Carreras en Informática (RedUNCI

The impact of health and environmental factors on a population of Mekong River Irrawaddy dolphins (Orcaella brevirostris) in Cambodia

Background The critically endangered Mekong River Irrawaddy dolphin (MRID) (Orcaella brevirostris) population, estimated to comprise 85 individuals in 2010, is at risk of extirpation due to a high level of mortality, particularly in calves, and a very low recruitment level (<1%) into the population; however existing studies have failed to identify the causes of mortality in this population. In this study, a retrospective study was conducted to better understand the causes of mortality in different age classes, so that potentially mortality levels can be mitigated and recruitment rates improved. Methods Mortality data from 2001-2010 were analysed to identify mortality trends in 102 MRIDs. Samples were also collected from 41 necropsied dolphins and subjected to microbiological, histopathological, genetic and toxicological analyses to identify and quantify the threats to this population. Additionally, a study of skin lesions using photo-identification data of live MRIDs from 2007 to 2010 was conducted. Results In this study, significantly high levels of immuno-toxic pollutants, particularly DDT and mercury; genetic factors, specifically genetic drift and outbreeding depression; and disease and immunosuppression; were all contributing towards the population’s decline. Dead calves were 15 times (95%CI 2.4, 88.1, p=0.001) more likely to have a localised gangrenous, blue/black neck lesion than dead adult dolphins. These lesions were clinically, pathologically and microbiologically similar to necrotising fasciitis of humans. In contrast, adults were 17 times (95%CI of 1.8, 166.1, p=0.006) more likely to have evidence of interaction with fishery activities than juveniles and calves. The incidence of mortality in adults over a three year period when gillnets were used was 18.3% (95%CI 11.6, 26.9), and this reduced to 6.7% (95%CI 2.5, 14.1) when restrictions on the use of gillnets were introduced. The risk of dying during the three years with gillnets was 2.7 times (95%CI 1.1, 6.5) higher than the period when gillnet use was restricted (p=0.016). In contrast, there was no significant difference in mortality for calves for years with and without gillnet restrictions (p=0.39). Skin lesions were common in live MRIDs being detected in 35 of 84 individuals observed (41.6%; 95%CI 31.1, 52.2) over a three year period. However, the mean prevalence of MRIDs photographed with skin lesions during 11 surveys was 7% (95%CI 1.9, 16.7), with a significant difference found in the prevalence of skin lesions in MRIDs from pools 1 and 9 (Fisher’s exact test p=0.002). In necropsied MRIDs (n=8), significantly more calves 100% (95%CI 47.8, 100) had neck lesions and associated neck swelling with wet gangrenous musculature than adults (0%; 95%CI 0.0, 70.8) (p=0.018). The three most frequent bacteria cultured in 13 dolphins examined with neck lesions were Aeromonas hydrophila (54%, 95%CI 25.1, 80.8), Plesiomonas shigelloides (46%, 95%CI 19.2, 74.9), and ß-haemolytic Group C Streptococcus spp. (23%, 95%CI 5, 53.8). Toxicological analysis in a larger sample set (n=20), revealed that the levels of mercury (Hg) and methylmercury (MeHg) were significantly higher in the adult dolphins sampled than in calves (11.21μg/g vs. 1.51μg/g, p=0.019; 7.23μg/g vs. 0.72, p=0.033, respectively). In contrast, calves had significantly higher levels of liver copper (Cu) than adults (40.72μg/g vs. 3.49μg/g, p=0.0005). Adults also had a significantly higher level of Hg (11.21 μg/g vs. 0.91 μg/g, p=0.026) and MeHg (7.23 μg/g vs. 0.17 μg/g, p=0.006) than juveniles. The mean molar selenium:mercury ratio was significantly higher in calves (2.27, p=0.039) and juveniles (2.94, p=0.007) than in adults (0.95). The level of zinc (Zn) in the liver of adults with neck lesions (28.7μg/g) was significantly lower (p=0.049) than that of adults without evidence of neck lesions (65.17μg/g). The concentrations of organochlorines in the blubber of MRID decreased in the order of DDTs > PCBs > CHLs > HCB > PBDEs > Dioxins > OC. The level of ΣDioxins was significantly higher in adults (2.27TEQ) than in calves (1.15TEQ, p=0.004), and also significantly higher in juveniles (3.57TEQ) than in calves (p=0.0094). The levels of PCBs in adults (346.9ng/g) and in juveniles (705.4ng/g) were significantly higher than in calves (142.75ng/g) (p=0.019, p=0.012, respectively). Adult females had higher ΣDioxin levels (61.3pg/g; 2.27TEQ) than female (3.7pg/g, p=0.0017; 1.15 TEQ p=0.02) and male calves (2.8pg/g, p=0.003; 0.99 TEQ, p=0.01). Juvenile females had significantly higher ΣDioxins (3.57TEQ) and ΣPCBs (705.4ng/g) than female (1.15TEQ, p=0.02; 163.2ng/g, p=0.016) and male calves (0.99TEQ, p=0.01; 142.8ng/g, p=0.03) respectively. Adult males had significantly higher PCB levels (606.8ng/g) than female (163.2ng/g, p=0.01) and male calves (142.8 ng/g, p=0.03). The levels of ΣPBDE, ΣCHLDs, ΣDDT and ΣHCB were all significantly higher in MRIDs than in the Chilika Lake Irrawaddy dolphins from the study of Kannan et al. (2005) (p=0.0007). Phylogenetically the MRIDs appear to be an evolutionary significant unit (ESU), with six new haplotypes identified in this study. The average nucleotide diversity (π) was 0.001 ( SD 0.0001) and the average haplotype diversity (h) was 0.812 ( SD 0.333). 34% (n=11) of the necropsied MRIDs had Infrequent/Rare (I/R) alleles, with an excess found in the adults compared to the calves, indicating a strong likelihood of genetic drift occurring. Paternity tests suggested reproductive failure, as only a few dolphins were breeding in the population and breeding females were genetically related. Conclusions It is concluded that two principal factors are driving the population decline. Firstly, the interaction of adults with commercial fishery activities and secondly, necrotising fasciitis associated with neck lesions in the calves. Furthermore, reproductive failure is a major contributing factor limiting recruitment into the population and ultimately affecting the population stability. This study highlights the need for urgent attention to save this population from certain extirpation

Etude des processus métaboliques, écologiques et biogéochimiques contrôlant le fractionnement isotopique du Hg chez les mammifères marins de l'Arctique

Depuis la découverte de processus de dépôts massifs de Hg (AMDE), l'Arctique est devenue une région clé dans la compréhension du cycle global du Hg. L'impact sur la santé humaine de ce polluant dépend non seulement de sa concentration mais aussi et surtout de sa forme chimique. En particulier, le monométhylmercure (MMHg) est une puissante neurotoxine qui atteint des concentrations élevées chez les prédateurs de l'Arctique du fait de ses propriétés de bioaccumulation et de bioamplification dans la chaine alimentaire. La compréhension des mécanismes à l'origine de la formation du MMHg (méthylation) et de sa dégradation (déméthylation) est primordiale pour caractériser son devenir et son impact dans les milieux aquatiques. Nous présentons ici une étude environnementale effectuée sur des tissus biologiques prélevés sur trois espèces emblématiques de l'Arctique : le phoque annelé (Pusa hispida), la baleine beluga (Delphinapterus leucas) et l'ours polaire (Ursus Maritimus). L'analyse de leurs compositions isotopiques en Hg montre simultanément un fractionnement dépendant (MDF, d202Hg) et indépendant de la masse (MIF, delta199Hg). Alors que les variations en d202Hg semblent largement expliquées par des processus métaboliques internes de détoxification/accumulation, la tendance temporelle (1988-2002, Pusa hispida) et le gradient latitudinal (60°N-71°N, Delphinapterus leucas) observés pour le delta199Hg reflètent vraisemblablement l'influence de l'évolution et de la distribution de la banquise sur le cycle biogéochimique du Hg en Arctique. Dans la seconde partie de cette thèse de doctorat, nous développons une approche moléculaire novatrice et prometteuse permettant de déterminer pour la première fois la composition isotopique des atomes de Hg et de carbone contenus dans la molécule de MMHg pour les échantillons biologiques. Ces premières mesures offrent des perspectives prometteuses pour tracer l'origine du MMHg dans les milieux aquatiques.Since the discovery of atmospheric Hg depletion events (AMDE) in the Arctic, the Polar Regions have become key in understanding the Hg global cycle. The impact of Hg on human health depends on both Hg concentration and chemical form. In particular, monomethylmercury (MMHg) is a potent neurotoxin. High MMHg concentrations are observed in Arctic top predators due to bioaccumulation and biomagnification processes in the food webs. Hence, the characterization of the transformations leading to the formation (methylation) and the degradation (demethylation) of MMHg is of great concern to assess its fate and impact in aquatic ecosystems. In this context, we present an environmental study on three Arctic bio-indicators: the ringed seal (Pusa hispida), the beluga whale (Delphinaperus leucas) and the polar bear (Ursus maritimus). Hg isotope analysis of the bio-indicator liver tissues show both mass dependent isotope fractionation (MDF, delta202Hg) and mass independent fractionation (MIF, delta199Hg). While the changes in d202Hg are widely linked to in vivo metabolic processes, the time trend (1988-2002, Pusa hispida) and the latitudinal gradient (60°N-71°N, Delphinaperus leucas) observed for ?199Hg signatures suggests the influence of sea ice cover on the Arctic biogeochemical Hg cycle. In a second part of this dissertation, we propose a novel and promising molecular approach with the first measurements of the isotopic compositions of Hg and carbon on the MMHg molecule in biological samples. These results are very promising for tracing MMHg origin in aquatic environments

(Automatic) detection, poses determination and identification of horses with methods of 2D and 3D image processing using biometrics

Die Identifikation von Individuen beim Menschen anhand von Gesichtsaufnahmen wurde bereits in zahlreichen Arbeiten behandelt. Dagegen umfasst die Literatur nur wenige Arbeiten, welche entsprechende Ansätze der Gesichtserkennung beim Menschen zur Unterscheidung von Nutztieren untersuchen. Zudem konnten keine Arbeiten ausgemacht werden, die eine Detektion der Köpfe von Tieren (Nutztiere wie Rind, Pferd und Schaf) mit seitlich am Kopf ausgerichteten Augen behandeln. Ein entsprechendes System zur Identifikation von Nutztieren anhand ihrer Gesichter per Kamera stellt eine Alternative zur Erkennung durch am Tier befestigte RFID-Transponder zum Monitoring der Tiere in der Präzisionstierhaltung (PLF) dar. Das Hauptziel der vorliegenden Arbeit war die Entwicklung und Anwendung von Methoden, die es weitestgehend automatisch ermöglichen Individuen bei Pferden anhand von Kameradaten der Gesichter zu unterscheiden. Dazu wurde ein Bilderfassungssystem aufgebaut, um unter realen Bedingungen in einer Futterstation, neben den Grauwertdaten zweier Industriekameras, die Tiefendaten der Szene zu erfassen. In dem Pferdestall wurde eine Datenbank der Besuche von Pferden mit insgesamt 587k Frames erstellt. Die Methoden zur Detektion und Posennormalisierung der Pferdeköpfe in den Bilddaten sind speziell für die Pferde angepasst und entwickelt worden. Die Detektion der Pferdeköpfe arbeitet ausschließlich auf den Tiefendaten, um unabhängig von Fellfarbe und -zeichnung der Tiere zu sein, und erreicht auf den Vergleichsdaten eine Treffergenauigkeit von 97,4%. Die Identifikation von Individuen aus einer Gruppe von neun Pferden erreicht mit dem hier angewendeten Verfahren der Eigengesichter bereits mit geringer Auflösung und einem Lernanteil von 12,5% der Bilddaten eine Treffergenauigkeit von 97%. Diese Arbeit zeigt somit einen erfolgreichen Weg zur weitestgehend automatischen Identifikation von Pferden unter Verwendung der biometrischen Merkmale im Gesicht der Tiere auf.The recognition of human individuals based on facial images is a wide spreaded topic within research literature. Whereas there’s only very limited literature/research on the adaptation of methods to recognize individuals in livestock. Additionally no sound scientific literature deals with the detection of those animals’ heads in livestock (e.g. cattle, horse or sheep), whose eyes are placed laterally on their heads. An appropriate system being able to do animal identification on face images is a true alternative to current systems using radio-frequency identification (RFID) transponders for animal monitoring in precision livestock farming (PFL). The main objective of the current research work was to develop and apply methods to identify individual horses only based on facial camera data, which should run at the greatest possible extent automatically. To achieve this goal a device has been developed that allows the capturing of depth data of the scene in addition to grey scale data of two industrial cameras under real-life conditions within a feeding station for horses. A database of horses has been created during their visits to an automatic feeding station inside the housing. Altogether 587k frames have been captured. Special methods were developed and/or adapted to detect the individual heads of the horses and to normalize their pose in the image data automatically. The detection of the horses’ heads is based exclusively on the depth data, in order to be independent of color and pattern on the animal’s coat. It achieves an accuracy (ACC) of 97,4% on the comparative data. Identification has been performed with the method of eigenfaces on a group of nine horses reaching an accuracy (ACC) of 97% using low image resolution and 12,5% of the image data for training. The current research work was successful in showing a way for an almost completely automatic detection and identification of horses by utilizing the biometric features within the animals’ faces