Pancakes: Consistent Multi-Protocol Image Segmentation Across Biomedical Domains

Marianne Rakic, Siyu Gai, Etienne Chollet, John Guttag, Adrian Dalca

Advances in Neural Information Processing Systems 38 Main Conference (NeurIPS 2025) Main Conference Track DOI: 10.52202/085713-1422

A single biomedical image can be segmented in multiple valid ways, depending on the application. For instance, a brain MRI may be divided according to tissue types, vascular territories, broad anatomical regions, fine-grained anatomy, or pathology. Existing automatic segmentation models typically either (1) support only a single protocol---the one they were trained on---or (2) require labor-intensive prompting to specify the desired segmentation. We introduce Pancakes, a framework that, given a new image from a previously unseen domain, automatically generates multi-label segmentation maps for multiple plausible protocols, while maintaining semantic consistency across related images. In extensive experiments across seven previously unseen domains, Pancakes consistently outperforms strong baselines, often by a wide margin, demonstrating its ability to produce diverse yet coherent segmentation maps on unseen domains.