Combining feature aggregation and geometric similarity for re-identification of patterned animals

Image-based re-identification of animal individuals allows gathering of information such as migration patterns of the animals over time. This, together with large image volumes collected using camera traps and crowdsourcing, opens novel possibilities to study animal populations. For many species, the re-identification can be done by analyzing the permanent fur, feather, or skin patterns that are unique to each individual. In this paper, we address the re-identification by combining two types of pattern similarity metrics: 1) pattern appearance similarity obtained by pattern feature aggregation and 2) geometric pattern similarity obtained by analyzing the geometric consistency of pattern similarities. The proposed combination allows to efficiently utilize both the local and global pattern features, providing a general re-identification approach that can be applied to a wide variety of different pattern types. In the experimental part of the work, we demonstrate that the method achieves promising re-identification accuracies for Saimaa ringed seals and whale sharks.Comment: Camera traps, AI, and Ecology, 3rd International Worksho

Elu ääre peal: sisemerede hülged muutuvas kliimas

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Miljonite aastate jooksul on mereimetajad asustanud kogu Maa geograafiliste ja klimaatilised piirkondade mitmekesisuse, paljud tänapäevased hülgeliigid on levinud ühtlaselt kogu polaarmerede ulatuses. Samas on jääaja järgne maatõus või teised muutused vangistanud mitmed hülgeasurkonnas osaliselt või täiesti maailmameredest eraldatud veekogudesse kus nad on kohastunud elama aastaajaliselt väga laialt vahelduvates tingimustes. Ühest küljest pakub selline olukord mitmekesiseid elupaiku kuid teisalt esitab tõsise väljakutse nende hüljeste kohastumisvõimele. Käesolevas väitekirjas analüüsitakse kliimamuutuste võimalikke mõjusid Läänemere hallhülgele (Halichoerus grypus), viigerhülge (Pusa hispida botnica) ning Kaspia hülge (Pusa caspica) kohasusele ja elujäämisvõimalustele. Väitekirja osaks olevad neli teaduspublikatsiooni moodustavad sellele analüüsile tugeva põhja, kuna nendes uuringutes on kaetud ajalisel, ruumiliselt või sisuliselt mitmed kliimamuutustega seotud võtmeteemad. Võimaliku üleilmse soojenemise jätkudes pakuvad nad viiteid aegadesse kui see muutus end veel ei ilmutanud (II, III, IV) või keskenduvad ökoloogilistele väljakutsetele mis Maa soojenedes jõudu koguvad (I, ka II-IV). Kõik käsitletud hülged on enamal või vähemal määral jääga seotud, kuna nende levilad külmuvad talvekuudel täielikult või osaliselt. Jää moodustab uuritud liikidele ajutise kuid kriitiliselt olulise elupaiga. Käesolevas töös on hüljeste levikut, sigimisstrateegiaid ja edukust käsitletud talve karmuse ning selle võimalike muutuste valguses. Tänapäevane looduslik tasakaal on kujundatud pikaajaliste keskmiste ökoloogiliste tingimuste poolt, samas näitavad kliimamudelid lähiajal temperatuuri tõusu. Jääolude muutused soojenevas kliimas toovad kaasa kriitilise olukorra Läänemere lõunapoolsetele viigerhüljestele ja kaspia hüljestele. Jääpuudus suunab hüljeste leviku aladele kus keskkonnatingimused, mõõdetuna nii füüsiliste kui ka bioloogiliste näitajate kaudu, on praegusest ebasoodsamad. Hüljeste sigimisalad surutakse kokku ning konservatiivne, jääga seotud sigimisstrateegia võib osutuda oluliseks negatiivseks teguriks kiirete, vaid mõnd põlvkonda hõlmavate muutuste keerises. Hallhüljes võib tänu oma paindlikumale poegimisviisile olla vähem mõjutatud kuid ka nende puhul ahendab jää puudumine ning merepinna tõus selle liigi tänast poegimisaegset levikuala. Kõigile kolmele vaadeldud hülgeliigile mõjub pärssivalt jää ebastabiilsusega kaasnev järglaste madalam kvaliteet. Jääpindala kahanemine teeb hülged haavatavaks ka maismaakiskjate ja rööveluviisiliste lindude poolt. Kliimast tulenevaid keskkonnamuutusi võimendavad inimtekkelised tegurid, näiteks reostus, intensiivne kalapüük ning häirimine. Lisandudes keskkonnast johtuvale stressile kahandab inimtegevus oluliselt sisemeredes elavate loivaliste tulevikuväljavaateid.Over the millions of years marine mammals have explored the full range of climatic and geographic latitudes of the Earth, at present several seal species show circumpolar distribution ranges. Post-glacial rebounds or other geo-morphological changes during have locked several seal populations into fully or partly isolated water bodies where they are adapted to live in seasonally widely fluctuating environments which in one hand provide diverse habitat but in the other hand challenge the adaptivity of the seals. This thesis is discussing the landlocked seals in their captive habitats and ecological implications therein. In this thesis the possible impacts of climate change on the fitness and survival of the land-locked grey seal (Halichoerus grypus) and ringed seal (Pusa hispida botnica) in the Baltic Sea and the Caspian seal (Pusa caspica), inhabiting the Caspian Sea are analyzed. The four original publications form a firm basis to approach this analysis, as they are covering spatially, temporally or topically several key aspects relevant to the climate change. In the context of probably ongoing global warming they provide reference to the times when the change was not expressed yet (II, III, IV) or focus on ecological challenges which will gather force with warming Earth (I, also II-IV). All the involved species and subspecies are to greater or lesser extent ice-related as their distribution ranges freeze over partially or wholly during the winter months. Ice forms a temporary critical habitat to the study species so winter severity and its potential changes are discussed in the context of seal distribution, breeding strategy and success. The current ecological balance is determined by long term average ecological conditions while climatic models show increasing temperatures in close future. Change of the ice conditions in warming climate would bring about critical conditions for the southern populations of the Baltic Ringed seal and the Caspian seals. Deficit of ice will lead to change of seal distribution to areas where the habitat quality, measured by both physical and biological parameters is lower compared to the present situation. The seals’ breeding area will become restricted and thus the conservative, ice related breeding strategy of the seals appears to become a major negative factor during current changes which take place during only some generations. The grey seal would be less affected due to plasticity in breeding strategies, but loss of the ice platform and access to several current land breeding sites would also restrict the breeding range of the species, all the three species would lose in breeding success through reduced offspring quality on unstable ice. The reduced ice cover makes the seals vulnerable to terrestrial and avian predation. Climatic changes in the environment are amplified by the anthropogenic factors like pollution, intensive fishing and disturbance which add to the environmental stress and challenge further the survival of the land-locked seal populations

Rasvahappojen kerrostuminen itämerennorpan traanissa ja sen merkitys kudoksen rasvahappokostumukseen perustuvassa ravintokohteiden arvioinnissa

Työssä tutkittiin rasvahappojen kerrostumista itämerennorpan (Phoca hispida botnica) traanissa ja tämän merkitystä rasvahappokoostumukseen perustuvassa ravintokohteiden arvioinnissa. Vertaamalla sisätraanin rasvahappokoostumusta plasman ja maksan rasvahappokoostumuksiin pyrittiin selvittämään siirtyvätkö jotkut tietyt ravinnon rasvahapot toisia tehokkaammin traanin sisäosiin, eli heijastelevatko jotkut sisätraanin rasvahapoista ravinnon rasvahappokoostumusta toisia paremmin. Itämerennorpan traanin eri kerrosten rasvahappokoostumusta verrattiin myös sen tärkeimmän ravintokalan, Itämeren silakan rasvahappokoostumukseen, jotta nähtäisiin minkä kerroksen koostumus muistuttaa eniten ravinnon rasvahappokoostumusta. Vertailun vuoksi työssä tutkittiin myös makeassa vedessä elävän saimaannorpan (Phoca hispida saimensis) traanin ja maksan rasvahappokoostumuksia. Lisäksi määritettiin plasma- ja maksanäytteiden kuljettaman tai lyhytaikaisesti varastoiman varastorasvan määrät. Tutkimuksessa käytettiin Perämerellä ammutuista itämerennorpista kerättyjä traani-, maksa- ja plasmanäytteitä, sekä kuolleina löydetyistä saimaannorpista kerättyjä traani- ja maksanäytteitä. Kudosnäytteiden rasvahappokoostumusten määritys tehtiin analysoimalla niistä valmistettuja rasvahappojen metyyliesteriseoksia kaasukromatografisesti (GC). Lipidiluokkakoostumukset puolestaan määritettiin korkean erotuskyvyn ohutlevykromatografialla (HPTLC). Analyysien tuloksia käsiteltiin tilastollisesti pääkomponenttianalyysin (PCA) ja sen tuloksia ohjatusti luokittelevan menetelmän (SIMCA) avulla, regressioanalyysillä, sekä laskemalla koostumusten euklidisia etäisyyksiä eri näytteiden välillä. Jokaisen yksilön traanille luotiin vertikaalinen rasvahappoprofiili toisiaan nahasta lihakseen seuraavien osanäytteiden rasvahappokoostumuksen perusteella. Itämerennorpan traanin kerrostuneisuutta tutkittiin nyt ensimmäistä kertaa ja sen havaittiin olevan rakenteeltaan kerrostunut, kuten on havaittu myös aiemmin tutkituilla kahdella norpan alalajilla. Aiemmista tutkimustuloksista poiketen keskitraani ei kuitenkaan eronnut rasvahappokoostumukseltaan merkitsevästi muista traanikerroksista. Sisä- ja ulkotraanin väliset rasvahappokoostumuksen erot olivat sen sijaan merkitseviä. Traanikerroksista sisätraani muistutti eniten itämerennorpan tärkeän saalislajin, silakan, rasvahappokoostumusta. Itämerennorpan kudosten rasvahappokoostumus erosi selvästi saimaannorpan kudosten rasvahappokoostumuksista. Näiden kahden alalajin ulkotraanit kuitenkin muistuttivat toisiaan rasvahappokoostumukseltaan sisätraaneja enemmän, mikä viittaa siihen, että niiden ulkotraanin koostumusta säätelevät samankaltaiset lämmönsäätelyyn liittyvät geneettisesti määräytyvät tekijät. Rasvahappokoostumusten alalajikohtaisista eroista huolimatta traanin rasvahappojen kerrostumistapa oli samanlainen molemmilla tutkituista alalajeista. Traanin vertikaaliset rasvahappoprofiilit olivat kuitenkin hyvin yksilöllisiä. Useiden rasvahappojen suhteelliset määrät plasmassa ja sisätraanissa korreloivat tilastollisesti merkitsevästi keskenään. Tämä tulos vahvistaa oletuksen, että viimeaikaisella ravinnolla on vaikutusta erityisesti sisätraanin rasvahappokoostumukseen ja, että sen perusteella voidaan saada tietoa eläimen ravinnosta. On kuitenkin huomattava, että tietyt sisätraanin rasvahapot ilmentävät ravinnon rasvahappokoostumusta toisia paremmin. Vaikka traanien vertikaaliset rasvahappoprofiilit antavat mitä ilmeisimmin yksilökohtaista tietoa eläinten ravinnosta ja aineenvaihdunnasta, niitä ei ole pystytty tulkitsemaan aiemmissa tutkimuksissa kovinkaan syvällisesti. Nämä tulokset voivatkin osaltaan auttaa tulkitsemaan traanin vertikaalisia rasvahappoprofiileja tulevaisuudessa. Saatuja tuloksia voidaan lisäksi hyödyntää myös hylkeiden ravintokohteiden arvioinnissa käytettävien näytteenottoprotokollien suunnitteluun ja kehittämiseen

Automatic Individual Identification of Patterned Solitary Species Based on Unlabeled Video Data

The manual processing and analysis of videos from camera traps is time-consuming and includes several steps, ranging from the filtering of falsely triggered footage to identifying and re-identifying individuals. In this study, we developed a pipeline to automatically analyze videos from camera traps to identify individuals without requiring manual interaction. This pipeline applies to animal species with uniquely identifiable fur patterns and solitary behavior, such as leopards (Panthera pardus). We assumed that the same individual was seen throughout one triggered video sequence. With this assumption, multiple images could be assigned to an individual for the initial database filling without pre-labeling. The pipeline was based on well-established components from computer vision and deep learning, particularly convolutional neural networks (CNNs) and scale-invariant feature transform (SIFT) features. We augmented this basis by implementing additional components to substitute otherwise required human interactions. Based on the similarity between frames from the video material, clusters were formed that represented individuals bypassing the open set problem of the unknown total population. The pipeline was tested on a dataset of leopard videos collected by the Pan African Programme: The Cultured Chimpanzee (PanAf) and achieved a success rate of over 83% for correct matches between previously unknown individuals. The proposed pipeline can become a valuable tool for future conservation projects based on camera trap data, reducing the work of manual analysis for individual identification, when labeled data is unavailable

Optimizing the automated recognition of individual animals to support population monitoring

Reliable estimates of population size and demographic rates are central to assessing the status of threatened species. However, obtaining individual-based demographic rates requires long-term data, which is often costly and difficult to collect. Photographic data offer an inexpensive, noninvasive method for individual-based monitoring of species with unique markings, and could therefore increase available demographic data for many species. However, selecting suitable images and identifying individuals from photographic catalogs is prohibitively time-consuming. Automated identification software can significantly speed up this process. Nevertheless, automated methods for selecting suitable images are lacking, as are studies comparing the performance of the most prominent identification software packages. In this study, we develop a framework that automatically selects images suitable for individual identification, and compare the performance of three commonly used identification software packages; Hotspotter, I3S-Pattern, and WildID. As a case study, we consider the African wild dog, Lycaon pictus, a species whose conservation is limited by a lack of cost-effective large-scale monitoring. To evaluate intraspecific variation in the performance of software packages, we compare identification accuracy between two populations (in Kenya and Zimbabwe) that have markedly different coat coloration patterns. The process of selecting suitable images was automated using convolutional neural networks that crop individuals from images, filter out unsuitable images, separate left and right flanks, and remove image backgrounds. Hotspotter had the highest image-matching accuracy for both populations. However, the accuracy was significantly lower for the Kenyan population (62%), compared to the Zimbabwean population (88%). Our automated image preprocessing has immediate application for expanding monitoring based on image matching. However, the difference in accuracy between populations highlights that population-specific detection rates are likely and may influence certainty in derived statistics. For species such as the African wild dog, where monitoring is both challenging and expensive, automated individual recognition could greatly expand and expedite conservation efforts

Towards Automatic Honey Bee Flower-Patch Assays with Paint Marking Re-Identification

In this paper, we show that paint markings are a feasible approach to automatize the analysis of behavioral assays involving honey bees in the field where marking has to be as lightweight as possible. We contribute a novel dataset for bees re-identification with paint-markings with 4392 images and 27 identities. Contrastive learning with a ResNet backbone and triplet loss led to identity representation features with almost perfect recognition in closed setting where identities are known in advance. Diverse experiments evaluate the capability to generalize to separate IDs, and show the impact of using different body parts for identification, such as using the unmarked abdomen only. In addition, we show the potential to fully automate the visit detection and provide preliminary results of compute time for future real-time deployment in the field on an edge device.Comment: Paper 17, workshop "CV4Animals: Computer Vision for Animal Behavior Tracking and Modeling", in conjunction with Computer Vision and Pattern Recognition (CVPR 2023), June 18, 2023, Vancouver, Canad

Biotransformation and endocrine disruptive effects of contaminants in ringed seals - implications for monitoring and risk assessment

Marine mammals are exposed to persistent organic pollutants (POPs), which may be biotransformed to metabolites some of which are highly toxic. Both POPs and their metabolites may lead to adverse health effects, which have been studied using various biomarkers. Changes in endocrine homeostasis have been suggested to be sensitive biomarkers for contaminant-related effects. The overall objective of this doctoral thesis was to investigate biotransformation capacity of POPs and their potential endocrine disruptive effects in two contrasting ringed seal populations from the low contaminated Svalbard area and from the highly contaminated Baltic Sea. Biotransformation capacity was studied by determining the relationships between congener-specific patterns and concentrations of polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), polybrominated diphenyl ethers (PBDEs) and their hydroxyl (OH)- and/or methylsulfonyl (MeSO2)-metabolites, and catalytic activities of hepatic xenobiotic-metabolizing phase I and II enzymes. The results suggest that the biotransformation of PCBs, PBDEs and toxaphenes in ringed seals depends on the congener-specific halogen-substitution pattern. Biotransformation products detected in the seals included OH-PCBs, MeSO2-PCBs and –DDE, pentachlorophenol, 4-OHheptachlorostyrene, and to a minor extent OH-PBDEs. The effects of life history state (moulting and fasting) on contaminant status and potential biomarkers for endocrine disruption, including hormone and vitamin homeostasis, were investigated in the low contaminated ringed seal population from Svalbard. Moulting/fasting status strongly affected thyroid, vitamin A and calcitriol homeostasis, body condition and concentrations of POPs and their OH-metabolites. In contrast, moulting/fasting status was not associated with variations in vitamin E levels. Endocrine disruptive effects on multiple endpoints were investigated in the two contrasting ringed seal populations. The results suggest that thyroid, vitamin A and calcitriol homeostasis may be affected by the exposure of contaminants and/or their metabolites in the Baltic ringed seals. Complex and non-linear relationships were observed between the contaminant levels and the endocrine variables. Positive relationships between circulating free and total thyroid hormone concentration ratios and OH-PCBs suggest that OH-PCBs may mediate the disruption of thyroid hormone transport in plasma. Species differences in thyroid and bone-related effects of contaminants were studied in ringed and grey seals from low contaminated references areas and from the highly contaminated Baltic Sea. The results indicate that these two species living at the same environment approximately at the same trophic level respond in a very different way to contaminant exposure. The results of this thesis suggest that the health status of the Baltic ringed seals has still improved during the last decade. PCB and DDE levels have decreased in these seals and the contaminant-related effects are different today than a decade ago. The health of the Baltic ringed seals is still suggested to be affected by the contaminant exposure. At the present level of the contaminant exposure the Baltic ringed seals seem to be at a zone where their body is able to compensate for the contaminant-mediated endocrine disruption. Based on the results of this thesis, several recommendations that could be applied on monitoring and assessing risk for contaminant effects are provided. Circulating OH-metabolites should be included in monitoring and risk assessment programs due to their high toxic potential. It should be noted that endogenous variables may have complex and highly variable responses to contaminant exposure including non-linear responses. These relationships may be further confounded by life history status. Therefore, it is highly recommended that when using variables related to endocrine homeostasis to investigate/monitor or assess the risk of contaminant effects in seals, the life history status of the animal should be carefully taken into consideration. This applies especially when using thyroid, vitamin A or calcitriolrelated parameters during moulting/fasting period. Extrapolations between species for assessing risk for contaminant effects in phocid seals should be avoided.Siirretty Doriast

Remote Camera Technology and its Role in Grey Seal Haul-out Assessment

Remote cameras can permit non-invasive monitoring of marine species and habitats. Using automated time-lapse cameras in combination with human observations and an infrared visitor counter, this project collected data on the daily maximum number of grey seals (Halichoerus grypus) hauled-out and daily numbers of visitors at a major grey seal haul-out location in Cornwall, south west England between August 2013 and December 2017. This project assesses the uses of data captured by time-lapse cameras to quantify seasonal patterns of grey seal haul-out abundance and how haul-out patterns might be influenced by environmental conditions, as well as quantifying counts of pups (as pup positive days) during the grey seal pupping season (Chapter 1). Using this knowledge, the project combines data from human-led surveys with time-lapse cameras to quantify the effects of human disturbance at a grey seal haul-out (Chapter 2). The peak in grey seal haul-out abundance occurred in March and April with median daily maximum grey seal haul-out counts of 103 seals (± 52.00 IQR, range 52 to 188) and 83 seals (± 46.00 IQR, range 25 to 239) respectively. The largest range in daily visitor numbers occurred in April (range 23 to 743) coinciding within the peak period in grey seal abundance but the peak period for visitor numbers at the site occurred in August in 2014 and 2015 with median daily visitor counts of 381 (± 102.00 IQR, range 77-471). Grey seal white-coated pups were observed on a total of 99 days during three seasons of monitoring (2013, 2014, 2017) with the highest number of pup positive days occurring in September (median 15 ± pup positive days 4.00 IQR) and October (median 13 pup positive days ± 2.50 IQR) each year. ‘People on cliff’ disturbances were more likely to disturb grey seals into the sea than other stimuli and as such, reduced the number of grey seals hauled-out on the beach during a disturbance event. This project concludes with a discussion of the potential impacts of disturbance at the haul-out site, with the findings highlighting the value of using time-lapse camera technology in effectively monitoring a pinniped population for a prolonged period and the implications of disturbance and the need for management action