DIPLOMAT: multi-animal tracking with efficient manual editing

Recent advances in computer vision have enabled the development of automated animal behavior observation tools. Several software packages currently exist for concurrently tracking pose in multiple animals; however, existing tools still face challenges in maintaining animal identities across frames and can demand extensive human oversight and editing. Here we report on DIPLOMAT, a <underline>D</underline>eep learning-based, <underline>I</underline>dentity-<underline>P</underline>reserving, <underline>L</underline>abeled-<underline>O</underline>bject <underline>M</underline>ulti-<underline>A</underline>nimal <underline>T</underline>racker, which implements automated algorithms to improve identity continuity, supplemented by an efficient human interface to help eliminate remaining errors. DIPLOMAT is designed to perform multi-animal tracking by building on the per-frame pose prediction models of two state-of-the-art tools, DeepLabCut and SLEAP, applying novel methods to tolerate occlusion and preserve animal identity across frames. Notable features include leveraging model-derived positional probabilities to compute independent maximum probability traces across frames of a video, use of video-specific skeletal constraints, and implementation of an efficient user interface for resolving errors. On the MABe mouse tracking benchmark, automated tracking with DIPLOMAT reduces body identity swaps by >75%, while remaining errors are easily eradicated with manual correction.