Higher-Order Cell Tracking Transformer
HOCT is an edge-centric transformer that links cell detections across time via 3D geometric attention, achieving state-of-the-art tracking without pretrained encoders and reducing errors 59% with minimal annotations.
Published 2026Sydney Poster Session 4 · Wed, Dec 9, 5:00 PM–8:00 PM local time · Hall 1-4arXiv ↗OpenReview ↗
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Abstract
Reconstructing lineages from live-imaging microscopy requires linking cell detections across time, including through cell divisions. A common approach is to construct a candidate graph and associate cell segmentations (nodes) across frames. However, these and other existing methods overlook two structural obstacles in candidate tracking graphs: (i) cell divisions entangle distinct lineage paths in the node embedding space, and (ii) edges sharing a node have near-random label agreement, so the candidate-graph topology carries no useful information for graph neural networks to aggregate. We propose the \textbf{Higher-Order Cell Tracking Transformer} (HOCT), an edge-centric architecture in which candidate cell links attend to one another under a 3D geometric prior, resolving both issues. Evaluated on the Cell Tracking Challenge and a bacteria division benchmark, HOCT achieves state-of-the-art results without deep pre-trained image encoders. Moreover, the proposed approach is easier to fine-tune, quickly reducing tracking errors by 59% with 400 annotations in a human-in-the-loop setting, outperforming LoRA fine-tuning of competing transformer baselines (6.75% improvement).