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

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

Comparative population assessments of Nautilus sp. in the Philippines, Australia, Fiji, and American Samoa using baited remote underwater video systems

The extant species of Nautilus and Allonautilus (Cephalopoda) inhabit fore-reef slope environments across a large geographic area of the tropical western Pacific and eastern Indian Oceans. While many aspects of their biology and behavior are now well-documented, uncertainties concerning their current populations and ecological role in the deeper, fore-reef slope environments remain. Given the historical to current day presence of nautilus fisheries at various locales across the Pacific and Indian Oceans, a comparative assessment of the current state of nautilus populations is critical to determine whether conservation measures are warranted. We used baited remote underwater video systems (BRUVS) to make quantitative photographic records as a means of estimating population abundance of Nautilus sp. at sites in the Philippine Islands, American Samoa, Fiji, and along an approximately 125 km transect on the fore reef slope of the Great Barrier Reef from east of Cairns to east of Lizard Island, Australia. Each site was selected based on its geography, historical abundance, and the presence (Philippines) or absence (other sites) of Nautilus fisheries The results from these observations indicate that there are significantly fewer nautiluses observable with this method in the Philippine Islands site. While there may be multiple possibilities for this difference, the most parsimonious is that the Philippine Islands population has been reduced due to fishing. When compared to historical trap records from the same site the data suggest there have been far more nautiluses at this site in the past. The BRUVS proved to be a valuable tool to measure Nautilus abundance in the deep sea (300-400 m) while reducing our overall footprint on the environment.Gregory J. Barord, Frederick Dooley, Andrew Dunstan, Anthony Ilano, Karen N. Keister, Heike Neumeister, Thomas Preuss, Shane Schoepfer, Peter D. War

Comparative Population Assessments of Nautilus sp. in the Philippines, Australia, Fiji, and American Samoa Using Baited Remote Underwater Video Systems

The extant species of Nautilus and Allonautilus (Cephalopoda) inhabit fore-reef slope environments across a large geographic area of the tropical western Pacific and eastern Indian Oceans. While many aspects of their biology and behavior are now well-documented, uncertainties concerning their current populations and ecological role in the deeper, fore-reef slope environments remain. Given the historical to current day presence of nautilus fisheries at various locales across the Pacific and Indian Oceans, a comparative assessment of the current state of nautilus populations is critical to determine whether conservation measures are warranted. We used baited remote underwater video systems (BRUVS) to make quantitative photographic records as a means of estimating population abundance of Nautilus sp. at sites in the Philippine Islands, American Samoa, Fiji, and along an approximately 125 km transect on the fore reef slope of the Great Barrier Reef from east of Cairns to east of Lizard Island, Australia. Each site was selected based on its geography, historical abundance, and the presence (Philippines) or absence (other sites) of Nautilus fisheries The results from these observations indicate that there are significantly fewer nautiluses observable with this method in the Philippine Islands site. While there may be multiple possibilities for this difference, the most parsimonious is that the Philippine Islands population has been reduced due to fishing. When compared to historical trap records from the same site the data suggest there have been far more nautiluses at this site in the past. The BRUVS proved to be a valuable tool to measure Nautilus abundance in the deep sea (300–400 m) while reducing our overall footprint on the environment

How unique is unique? Quantifying geometric differences in stripe patterns of Cape mountain zebra, Equus zebra zebra (Perissodactyla: Equidae)

Please read abstract in the article.https://academic.oup.com/zoolinneanhj2022Mammal Research InstituteZoology and Entomolog

Marking techniques in the Marbled Newt (Triturus marmoratus): PIT-Tag and tracking device implant protocols

Individual marking has become essential for studying population dynamics and ecological requirements. However, marking small-bodied species such as amphibians is becoming a challenge in the last decades. Amphibian surveys may require to mark manually individuals, using toe clipping, polymers and pigments, or passive integrated transponders (PIT-tags). Even if ethics committees have recently recommend avoiding toe clipping in amphibians, the use of PIT-tags led to controversial results because low tag retention reported in some studies. Here, we describe a protocol of potentially life-long PIT-tag marking in a protected species, the marbled newt Triturus marmoratus. In addition, we also detailed a second procedure of surgery for the implantation of transmitters needed in radio-tracking surveys. During both procedures, we found that the newt phase (either aquatic or terrestrial) strongly affected the anesthesia duration. Indeed, newts in aquatic phase were more quickly anesthetized than newts under terrestrial phase. We then recommend to pay attention of this physiological particularity when performing this kind of procedure. Improving our knowledge on ecological requirements and population dynamics of this species is crucial for management and conservation plans, and could be extended to other large newts

Marking techniques in the Marbled Newt (<em>Triturus marmoratus</em>): PIT-Tag and tracking device implant protocols

Individual marking has become essential for studying population dynamics and ecological requirements. However, marking small-bodied species such as amphibians is becoming a challenge in the last decades. Amphibian surveys may require to mark manually individuals, using toe clipping, polymers and pigments, or passive integrated transponders (PIT-tags). Even if ethics committees have recently recommend avoiding toe clipping in amphibians, the use of PIT-tags led to controversial results because low tag retention reported in some studies. Here, we describe a protocol of potentially life-long PIT-tag marking in a protected species, the marbled newt Triturus marmoratus. In addition, we also detailed a second procedure of surgery for the implantation of transmitters needed in radio-tracking surveys. During both procedures, we found that the newt phase (either aquatic or terrestrial) strongly affected the anesthesia duration. Indeed, newts in aquatic phase were more quickly anesthetized than newts under terrestrial phase. We then recommend to pay attention of this physiological particularity when performing this kind of procedure. Improving our knowledge on ecological requirements and population dynamics of this species is crucial for management and conservation plans, and could be extended to other large newts

Divergent water requirements partition exposure risk to parasites in wild equids

For grazing herbivores, dung density in feeding areas is an important determinant of exposure risk to fecal- orally transmitted parasites. When host species share the same parasite species, a nonrandom distribution of their cumulative dung density and/or nonrandom ranging and feeding behavior may skew exposure risk and the relative selection pressure parasites impose on each host. The arid-adapted Grevy\u27s zebra ( Equus grevyi ) can range more widely than the water-dependent plains zebra ( Equus quagga ), with which it shares the same species of gastrointestinal nematodes. We studied how the spatial distribution of zebra dung relates to ranging and feeding behavior to assess parasite exposure risk in Grevy\u27s and plains zebras at a site inhabited by both zebra species. We found that zebra dung density declined with distance from water, Grevy\u27s zebra home ranges (excluding those of territorial males) were farther from water than those of plains zebras, and plains zebra grazing areas had higher dung density than random points while Grevy\u27s zebra grazing areas did not, suggest - ing a greater exposure risk in plains zebras associated with their water dependence. Fecal egg counts increased with home range proximity to water for both species, but the response was stronger in plains zebras, indicating that this host species may be particularly vulnerable to the elevated exposure risk close to water. We further ran experiments on microclimatic effects on dung infectivity and showed that fewer nematode eggs embryonated in dung in the sun than in the shade. However, only 5% of the zebra dung on the landscape was in shade, indicating that the microclimatic effects of shade on the density of infective larvae is not a major influence on exposure risk dynamics. Ranging constraints based on water requirements appear to be key mediators of nematode parasite exposure in free-ranging equids