Multi-view Tracking, Re-ID, and Social Network Analysis of a Flock of Visually Similar Birds in an Outdoor Aviary

The ability to capture detailed interactions among individuals in a social group is foundational to our study of animal behavior and neuroscience. Recent advances in deep learning and computer vision are driving rapid progress in methods that can record the actions and interactions of multiple individuals simultaneously. Many social species, such as birds, however, live deeply embedded in a three-dimensional world. This world introduces additional perceptual challenges such as occlusions, orientation-dependent appearance, large variation in apparent size, and poor sensor coverage for 3D reconstruction, that are not encountered by applications studying animals that move and interact only on 2D planes. Here we introduce a system for studying the behavioral dynamics of a group of songbirds as they move throughout a 3D aviary. We study the complexities that arise when tracking a group of closely interacting animals in three dimensions and introduce a novel dataset for evaluating multi-view trackers. Finally, we analyze captured ethogram data and demonstrate that social context affects the distribution of sequential interactions between birds in the aviary.

3D Bird Reconstruction: a Dataset, Model, and Shape Recovery from a Single View

Automated capture of animal pose is transforming how we study neuroscience and social behavior. Movements carry important social cues, but current methods are not able to robustly estimate pose and shape of animals, particularly for social animals such as birds, which are often occluded by each other and objects in the environment. To address this problem, we first introduce a model and multi-view optimization approach, which we use to capture the unique shape and pose space displayed by live birds. We then introduce a pipeline and experiments for keypoint, mask, pose, and shape regression that recovers accurate avian postures from single views. Finally, we provide extensive multi-view keypoint and mask annotations collected from a group of 15 social birds housed together in an outdoor aviary. The project website with videos, results, code, mesh model, and the Penn Aviary Dataset can be found at https://marcbadger.github.io/avian-mesh.