Redefining Instance Matching: A Unified Framework for Part-Aware Matching in Panoptic Segmentation Evaluation
Authors: Erik Großkopf, Soumya Snigdha Kundu, Hendrik Möller, Nicolas Münster, Mehdi Astaraki, Paula Tamara Buzduga, Kerstin Ritter, Benedikt Wiestler, +4 more
Abstract
The Panoptic Quality (PQ) metric is the standard for jointly evaluating instance and semantic segmentation. However, its original definition relies on a One-to-One matching between predicted and ground truth segments, which is only straightforward when the IoU threshold exceeds 0.5. Below 0.5, multiple matching strategies emerge in a poorly explored problem space. We systematically elucidate this space by recasting segment matching as a constrained bipartite assignment problem. Independently bounding the prediction- and ground-truth-side degrees yields four matching strategies: One-to-One, Many-to-One, One-to-Many, and Many-to-Many. We show that the first three are well-defined within the PQ framework, while Many-to-Many falls outside it. These strategies become relevant when instances are fragmented, adjacent objects are difficult to delineate, or annotations are noisy. Central to our framework is a vertex-based accounting of TP, FN, and FP, anchored to ground truth and predicted segments rather than to matching edges. We further show that the framework extends naturally to part-aware panoptic segmentation, and we explore part-aware evaluation on biomedical data. Across configurable case studies we report how different combinations of thresholds and matching strategies behave in practice. We release a unified open-source package built on Panoptica. It exposes Voronoi-based region-wise analysis, part-aware evaluation, and Area Under Threshold Curve computations as configurable options.
Reliable evaluation of instance segmentation models requires metrics that accurately and consistently reflect segmentation quality. However, the metrics most widely used in biological imaging carry fundamental mathematical weaknesses: hard Intersection-over-Union (IoU) thresholds that produce discontinuous, low sensitivity scoring; per-object normalization that distorts scores under object size variation; and greedy or one-to-many matching procedures that yield non-optimal, order-dependent correspondences. Together, these properties produce unintuitive and unreliable model rankings under common failure modes such as split cells, merged cells, and cell boundary imprecision. We propose Maximum Matching Accuracy (MMA), a threshold-free continuous metric that finds a globally optimal one-to-one matching between predicted and ground truth objects and aggregates total overlap using per-pixel normalization. We evaluate MMA against AP@50, PQ, SEG, and AJI across three experiments: synthetic failure cases, progressive corruption tests, and a model ranking comparison. MMA produces scores that are more stable, more sensitive, and more interpretable than existing alternatives, providing a principled foundation for fair instance segmentation benchmarking in biological cell imaging.
Kaden Stillwagon, Alexandra D. VandeLoo, Craig R. Forest
This paper presents the report of the URVIS 2026 challenge on adverse-to-extreme panoptic segmentation. As the first challenge of its kind, it attracted 17 registered participants and 47 submissions, with 4 teams reaching the final phase. The challenge is based on the MUSES dataset, a multi-sensor benchmark for panoptic segmentation in adverse-to-extreme weather, including RGB frame camera, LiDAR, radar, and event camera data. Weighted Panoptic Quality (wPQ) is designed and adopted as the official ranking metric for fair evaluation across weather conditions. In this report, we summarise the challenge setting and benchmark results, analyse the performance of the submitted methods, and discuss current progress and remaining challenges for robust multimodal panoptic segmentation. Link: https://urvis-workshop.github.io/challenge-Muses.html
Yiting Wang, Nolwenn Peyratout, Tim Brodermann +13
Evaluation metrics are central to binary target segmentation because they determine how progress is measured, compared, and interpreted. In this paper, target denotes the task-defined positive region to be segmented rather than a generic foreground object. It may be salient, camouflaged, transparent, glass-like, mirror-like, shadow-like, lesion-like, or defined by other application-specific semantics. We treat existing metrics as compositions of modular design choices rather than isolated formulas. The proposed framework decomposes each metric into five stages covering prediction representation, target extraction, target matching, score computation, and metric reporting. We use this framework to analyze representative metrics and show how newer metrics address specific limits in earlier protocols. The stage choices keep each metric's assumptions visible. We then discuss the design space opened by the framework and its implications for task-aware evaluation protocols. Reference code is available at https://github.com/lartpang/PySODMetrics.