Topology-Aware Query Selection for Surgical Instrument Instance Segmentation

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.

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.

Open-vocabulary 3D instance segmentation is a core capability for robotics and AR/VR, but prior methods trade one bottleneck for another: multi-stage 2D+3D pipelines aggregate foundation-model outputs at hundreds of seconds per scene, while pseudo-labeled end-to-end approaches rely on fragmented masks and external region proposals. We present SpaCeFormer, a proposal-free space-curve transformer that runs in 0.12--0.30 seconds per scene across standard benchmarks, 2--3 orders of magnitude faster than multi-stage 2D+3D pipelines. We pair it with SpaCeFormer-3M, the largest open-vocabulary 3D instance segmentation dataset (3.0M multi-view-consistent captions over 604K instances from 7.4K scenes) built through multi-view mask clustering and multi-view VLM captioning; it reaches 21$\times$ higher mask recall than prior single-view pipelines (54.3% vs 2.5% at IoU$>$0.5). SpaCeFormer combines spatial window attention with Morton-curve serialization for spatially coherent features, and uses a RoPE-enhanced decoder to predict instance masks directly from learned queries without external proposals. On ScanNet200 we achieve 11.1 zero-shot mAP, a 2.8$\times$ improvement over the prior best proposal-free method; on ScanNet++ and Replica, we reach 22.9 and 24.1 mAP, surpassing all prior methods including those using multi-view 2D inputs.