Uncertainty Quantification in Medical Image Segmentation: A Comprehensive Survey

Uncertainty quantification (UQ) in medical image segmentation is essential for ensuring the reliability and interpretability of deep learning models in clinical decision-making. While convolutional neural networks (CNNs) and transformer-based architectures have achieved remarkable segmentation performance, they often provide deterministic outputs without accounting for uncertainty, which can lead to overconfident predictions in ambiguous cases. This paper presents a comprehensive survey of UQ techniques in medical image segmentation, categorizing existing approaches into Bayesian methods, deep ensembles, deterministic methods, test-time data augmentation, and hybrid models, while treating foundation-model-based UQ as a separate cross-cutting category. We examine key methodologies, including Monte Carlo dropout, Bayesian neural networks, variational inference, and ensemble learning, discussing their advantages and limitations in addressing aleatoric and epistemic uncertainties. Additionally, we explore the clinical relevance of UQ by reviewing its applications in brain tumor segmentation, cardiac imaging, lung nodule detection, and other medical domains. The paper also highlights key evaluation metrics, such as calibration errors, uncertainty–error correlation, and visual interpretability, to assess the effectiveness of UQ methods. Finally, we discuss challenges and future research directions, emphasizing the need for scalable, interpretable, and clinically actionable uncertainty quantification strategies to improve trust in AI-assisted medical image analysis.