Beyond Pixel Overlap: A Framework for Decomposing Segmentation Evaluation Metrics

Despite rapid advances in MIS, fair and reproducible comparisons of segmentation models remain challenging due to heterogeneous datasets, inconsistent evaluation protocols, and rapidly evolving architectures. In particular, comparisons often implicitly assume that model rankings are invariant to data partitioning, preprocessing, metric aggregation, uncertainty estimation, and computational constraints. The lack of extensible and unified evaluation frameworks further limits systematic investigation of new models, datasets, and training paradigms. We present MEDSEGBENCHMARKER (MSB), a configuration-driven framework for controlled benchmarking of 2D MIS. It integrates duplicate and near-duplicate image detection, group-aware data splitting, YAML study specifications, resumable training, hyperparameter optimization, cross-validation, and checkpoint-based evaluation. Rather than retaining only aggregate performance measures, MSB exports sample- and class-level pixel counts and predictions together with the evaluation context. These elementary artifacts enable post-hoc analyses without repeated inference. We demonstrate MSB in a case study involving three heterogeneous 2D datasets and multiple MIS and general-purpose vision models evaluated at 256- and 512-pixel input resolutions. Reaggregation of identical predictions changes the top-ranked architecture in three of six dataset-resolution settings, despite high rank correlations between aggregation strategies. Increasing input resolution produces model- and dataset-dependent performance gains and losses that must be considered alongside empirically measured inference complexity. These results show that seemingly minor choices in evaluation and experimental setup can affect benchmark conclusions. MSB, available at GitHub, provides a practical and extensible basis for making benchmark conditions and evaluation choices explicit and reproducible.

Progress in colonoscopy polyp segmentation is routinely reported through leaderboard comparisons on a small set of public benchmarks. We argue that this apparent progress is difficult to verify: a systematic audit of \textbf{27 papers} published between 2015 and 2026 reveals three structural problems in how the community evaluates models. \textbf{First}, 25 of 27 papers \textit{omit the Hausdorff distance}. Hausdorff distance is a boundary-accuracy metric with direct clinical relevance for detecting flat or small polyps, and is a standard in radiotherapy segmentation. \textbf{Second}, at least five \textit{incompatible train/test split protocols} co-exist across papers reporting results on the same two datasets (Kvasir-SEG and CVC-ClinicDB), making published Dice scores non-comparable even when they appear in the same leaderboard column. \textbf{Third}, 26 of 27 papers make \textit{performance claims without any statistical significance test}. Strikingly, four papers published \emph{after} the Metrics Reloaded framework~\cite{metricsreloaded2024} (Maier-Hein et al., \textit{Nature Methods} 2024) perpetuate these same problems, suggesting that general-purpose metric guidance has not yet reached the colonoscopy sub-community. To show these problems are not merely cosmetic, we re-evaluate five representative models under three controlled protocols with a single uniform scorer, and find that the reported metric conceals large boundary and recall failures, that the ``best'' model changes with the metric, and that near-tied rankings reverse across random splits. We propose a five-point \textbf{Polyp Segmentation Reporting Checklist}~(PSRC) as a lightweight, domain-adapted corrective.

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.