Easily accessible sensors, like drones with diverse onboard sensors, have greatly expanded studying animal behavior in natural environments. Yet, analyzing vast, unlabeled video data, often spanning hours, remains a challenge for machine learning, especially in computer vision. Existing approaches often analyze only a few frames. Our focus is on long-term animal behavior analysis. To address this challenge, we utilize classical probabilistic methods for state estimation, such as particle filtering. By incorporating recent advancements in semantic object segmentation, we enable continuous tracking of rapidly evolving object formations, even in scenarios with limited data availability. Particle filters offer a provably optimal algorithmic structure for recursively adding new incoming information. We propose a novel approach for tracking schools of fish in the open ocean from drone videos. Our framework not only performs classical object tracking in 2D, instead it tracks the position and spatial expansion of the fish school in world coordinates by fusing video data and the drone's on board sensor information (GPS and IMU). The presented framework for the first time allows researchers to study collective behavior of fish schools in its natural social and environmental context in a non-invasive and scalable way.