MORI-Seg: Learning Morphological Geometry for Instance Segmentation without Instance Annotations
Authors: Leiyue Zhao, Tianyu Shi, Daniel Reisenbuchler, Xinzi He, Junchao Zhu, Tianyuan Yao, Yuechen Yang, Yanfan Zhu, +7 more
Abstract
Instance-level quantification of kidney functional units is essential for morphometric analysis, yet most publicly available pathology datasets provide only semantic segmentation annotations, where adjacent structures of the same class are merged into single regions. This prevents reliable instance-level analysis and limits downstream quantitative studies. Existing heuristic post-processing methods often yield suboptimal instance separation, particularly in crowded and adherent regions, while deep learning-based instance segmentation approaches typically require intensive instance-level annotations that are costly and labor-intensive to obtain. We propose MORI-Seg, a deep learning framework that enables instance segmentation without requiring instance-level annotations. Instead of heuristic splitting or instance supervision, MORI-Seg learns morphology-aware geometric representations directly from semantic masks by jointly modeling object-centric distance fields and boundary-band representations to encode interior structure and contact interfaces. A class-conditioned feature disentanglement module further promotes intra-instance coherence and inter-instance separation. Under semantic-only supervision, MORI-Seg decomposes connected semantic regions into distinct instance masks in an end-to-end manner. Experiments demonstrate improved instance separation accuracy and more reliable morphometric quantification compared with classical post-processing pipelines and representative semantic-to-instance learning approaches. The official implementation is publicly available at https://github.com/ddrrnn123/MORI-Seg.
Accurate foreground masks can still form an incorrect surgical-instrument instance set: duplicate, fragmented, merged, missed, or empty-frame predictions may preserve favorable pixel overlap while violating object identity and count. Final query selection is therefore a relational, variable-cardinality problem rather than a collection of independent candidate decisions. We evaluate topology-aware query selection, which represents the nonempty candidates of a fixed Mask2Former as a complete graph, learns relational candidate and pair representations, predicts set cardinality, and solves an exact structured subset problem. The formal comparison is the complete relational path versus a node-feature-matched path; it evaluates the combined effect of pairwise geometry, message passing, and the additional relational-path capacity, not an isolated component. On the sealed 22-case source test, all three discovery seeds supported instance-set performance improvement with segmentation fidelity and predefined technical-safety preservation: instance F1 increased by 0.0504--0.0612 and positive-frame set-failure rate decreased by 0.0848--0.1060. Direct ROBUST-MIPS transfer reproduced the complete result in all three seeds. Endoscapes supported only one of three seeds and therefore did not establish stable direct transfer. Taken together, the results support a bounded conclusion: the evaluated complete path improved coherent instance-set construction from fixed Mask2Former candidates in specified native-instance contracts, while stable cross-domain transfer and component-specific effects remain unestablished.
Current instance segmentation models achieve high performance on average predictions, but lack principled uncertainty quantification: their outputs are not calibrated, and there is no guarantee that a predicted mask is close to the ground truth. To address this limitation, we introduce a conformal prediction algorithm to generate adaptive confidence sets for instance segmentation. Given an image and a pixel coordinate query, our algorithm generates a confidence set of instance predictions for that pixel, with a provable guarantee for the probability that at least one of the predictions has high Intersection-Over-Union (IoU) with the true object instance mask. We apply our algorithm to instance segmentation examples in agricultural field delineation, cell segmentation, and vehicle detection. Empirically, we find that our prediction sets vary in size based on query difficulty and attain the target coverage, outperforming baselines (naive best parameter and morphological dilation-based methods). We provide versions of the algorithm with asymptotic and finite sample guarantees. Our work is the first to capture structural uncertainty in instance segmentation by constructing confidence sets of diverse segmentation predictions.
Accurate pulmonary vessel segmentation remains challenging due to the sparse, tortuous, and multi-scale nature of vascular structures, where small branches are easily lost and topology integrity is difficult to preserve under voxel-wise supervision. Existing deep segmentation models primarily optimize binary masks, lacking explicit geometric constraints, thus struggling to recover continuous tubular morphology and fine vascular connectivity. In this study, we introduce MorVess, a morphology-aware segmentation framework that integrates differentiable geometric priors with large-scale foundation model adaptation to achieve fine-grained vascular parsing. MorVess jointly predicts vessel masks, distance maps, and thickness maps, providing explicit supervision for vascular boundaries, centerline consistency, and smooth diameter transitions. A lightweight 2.5D adapter bridges 3D spatial context and 2D SAM representations, while a global-local fusion block aggregates multi-level semantics and geometric cues for high-fidelity topology reconstruction. Across two challenging pulmonary CT benchmarks, MorVess delivers superior Dice, clDice, and HD95 scores, substantially improving small-vessel recovery and global connectivity. These results demonstrate that embedding geometric intelligence into pretrained vision models offers a principled and scalable pathway toward precise vessel analysis and clinically reliable structural quantification. Our source code is available at https://github.com/MaoFuyou/MorVess.