Image Thresholding: Understanding Bias of Evaluation Metrics towards Specific Evaluation Functions

Multilevel Image thresholding is an important preprocessing algorithm in computer vision applications nowadays. Since most common thresholding methods take the desired count of thresholds as input by the user, thresholding methods that automatically determines a suitable count of thresholds from the input image itself are advantageous. In this article, a novel thresholding method based on a dynamic programming algorithm and a modification of Minimum Error Thresholding (MET) criterion is thoroughly presented. An empirical statistical study is performed to pinpoint why this proposed method is superior. Moreover, an extended comparison between this proposed method and other state-of-the-art methods is performed on a comprehensive set of natural, satellite and medical test images. The numerical results show that the proposed MET-DP method takes much less time than traditional dynamic programming thresholding methods when the number of thresholds is high. The proposed method can detect a suitable count of thresholds for most of tested images of different types. However, traditional methods that take the count of thresholds as input produce thresholded images of higher structural similarity index measure (SSIM) and peak signal-to-noise ratio (PSNR) values than MET-DP. Source code can be found on https://w3id.org/met-dp/article1-code

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.

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.