Insights on back marking for the automated identification of animals

Automated pig monitoring is essential for assessing their health, behaviour, and welfare. To date, most pig monitoring solutions operate on the group-level, because individual-level monitoring requires reliable long-term identification and tracking of each animal. For domesticated pigs this remains challenging because pigs of the same breed often have highly uniform appearances. Moreover, research on pig monitoring is almost exclusively reported in top-down view camera settings, which considerably ease tracking, but are not always an option in practice. In this work, BMCTrack-d is presented, a novel tracking-by-detection approach that leverages unique back marks to enable robust pig re-identification and tracking in a challenging side-view camera setting, afflicted by rapidly moving pigs, severe occlusions and low resolution. The method first predicts the detected pigs' identities using a neural network-based back mark classifier. To improve re-identification reliability over time, two dedicated post-processing stages are introduced: a temporal prediction consistency check, which validates the identity assignments against the recent prediction history, and deduplication, which resolves conflicting identity assignments in each time step. By explicitly prioritising accurate, appearance-based re-identification over continuous tracking, the proposed approach addresses a key limitation of existing trackers for individual-level monitoring scenarios. On a demanding test set BMCTrack-d outperforms two strong baselines, BoT-SORT-ReID and TrackTrack-ReID, by 9.11% and 1.03%, respectively, in higher-order tracking accuracy. These results demonstrate the effectiveness of back mark-based re-identification and tracking for robust individual-level pig monitoring in challenging settings.

Foundation models (FM) are reshaping computer vision by reducing reliance on task-specific supervised learning and leveraging general visual representations learned at scale. In precision livestock farming, most pipelines remain dominated by supervised learning models that require extensive labeled data, repeated retraining, and farm-specific tuning. This study presents an FM-centered workflow for automated monitoring of group-housed nursery pigs, in which pretrained vision-language FM serve as general visual backbones and farm-specific adaptation is achieved through modular post-processing. Grounding-DINO was first applied to 1,418 annotated images to establish a baseline detection performance. While detection accuracy was high under daytime conditions, performance degraded under night-vision and heavy occlusion, motivating the integration of temporal tracking logic. Building on these detections, short-term video segmentation with Grounded-SAM2 was evaluated on 550 one-minute video clips; after post-processing, over 80% of 4,927 active tracks were fully correct, with most remaining errors arising from inaccurate masks or duplicated labels. To support identity consistency over an extended time, we further developed a long-term tracking pipeline integrating initialization, tracking, matching, mask refinement, re-identification, and post-hoc quality control. This system was evaluated on a continuous 132-minute video and maintained stable identities throughout. On 132 uniformly sampled ground-truth frames, the system achieved a mean region similarity (J) of 0.83, contour accuracy (F) of 0.92, J&F of 0.87, MOTA of 0.99, and MOTP of 90.7%, with no identity switches. Overall, this work demonstrates how FM prior knowledge can be combined with lightweight, task-specific logic to enable scalable, label-efficient, and long-duration monitoring in pig production.

In this paper, we explore deep learning techniques for individual identification of animals based on their skin patterns. Individual identification is crucial in biodiversity monitoring, since it enables analysis of decline or growth of populations, or intra-species interactions within populations. Models trained for the task of individual identification often do not focus on the skin pattern of animals, but on background details or body shape details. These characteristics are not individually specific, or can change drastically through time. We focus on techniques that will make machine learning models more responsive to skin pattern structure when extracting individual visual embeddings from images. For this, we explore image inpainting of task-specific masks as an auxiliary task to enhance ML-based individual identification from animal skin patterns. We propose a comparative analysis among four models as an encoder backbone for the individual identification task. We focus on the case study of zebrafish, which is a widely recognized biological model organism, and which exhibits individually identifying skin patterns. To evaluate encoder backbone performance, we present standard metrics for classification accuracy, embedding clustering metrics, and GradCAM visualizations.