idtracker.ai: tracking all individuals in small or large collectives of unmarked animals

Understanding of animal collectives is limited by the ability to track each individual. We describe an algorithm and software that extract all trajectories from video, with high identification accuracy for collectives of up to 100 individuals. idtracker.ai uses two convolutional networks: one that detects when animals touch or cross and another for animal identification. The tool is trained with a protocol that adapts to video conditions and tracking difficulty. The idtracker.ai software tracks freely moving animals in large groups of up to 100 individuals. The tool is versatile and has been applied to groups of fruit flies, zebrafish, medaka, ants and mice.