Medical Image Segmentation

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Overview

Medical image segmentation assigns labels to pixels or voxels to outline structures such as tumors, organs, vessels, and surgical instruments, enabling quantitative analysis and clinical workflows. Common approaches include U-Net-style convolutional networks, transformers and state-space models, and promptable foundation models; work also uses anatomical and topological priors, text guidance, and generative models. To reduce reliance on dense expert labels, researchers study self-supervised pretraining, semi- and weakly supervised learning, synthetic data, and interactive annotation, while domain adaptation addresses differences across scanners, hospitals, and modalities. A central challenge is making models reliable beyond their training data: high overlap scores can conceal boundary, connectivity, small-lesion, or subgroup failures, so external validation, uncertainty estimates, and clinically relevant metrics remain important.

Latest papers

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788 papers62 papers in the last four weeks, down 29% on the four weeks before. 0.4% of all new papers.

Mar 10, 2026

CLoE: Expert Consistency Learning for Robust Missing Modality Segmentation

Multimodal medical image segmentation often faces missing modalities at inference, which induces disagreement among modality experts and makes fusion unstable, particularly on small foreground structures. We propose Consistency Learning of Experts (CLoE), a consistency-driven framework for missing-modality segmentation that preserves strong performance when all modalities are available. CLoE formulates robustness as decision-level expert consistency control and introduces a dual-branch Expert Consistency Learning objective. Modality Expert Consistency enforces global agreement among expert predictions to reduce case-wise drift under partial inputs, while Region Expert Consistency emphasizes agreement on clinically critical foreground regions to avoid background-dominated regularization. We further map consistency scores to modality reliability weights using a lightweight gating network, enabling reliability-aware feature recalibration before fusion. Extensive experiments on BraTS 2020 and MSD Prostate demonstrate that CLoE outperforms state-of-the-art methods in incomplete multimodal segmentation, while exhibiting strong cross-dataset generalization and improving robustness on clinically critical structures.

Xinyu Tong, Meihua Zhou, Bowu Fan +1

University of Chinese Academy Sciences · School of Medicine, Southeast University · Zhejiang University

Missing-Modality Medical Image SegmentationMedical Image SegmentationMissing-Modality LearningMultimodal RobustnessMultimodal FusionConsistency Regularization
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Mar 10, 2026

TubeMLLM: A Foundation Model for Topology Knowledge Exploration in Vessel-like Anatomy

Modeling medical vessel-like anatomy is challenging due to its intricate topology and sensitivity to dataset shifts. Consequently, task-specific models often suffer from topological inconsistencies, including artificial disconnections and spurious merges. Motivated by the promise of multimodal large language models (MLLMs) for zero-shot generalization, we propose TubeMLLM, a unified foundation model that couples structured understanding with controllable generation for medical vessel-like anatomy. By integrating topological priors through explicit natural language prompting and aligning them with visual representations in a shared-attention architecture, TubeMLLM significantly enhances topology-aware perception. Furthermore, we construct TubeMData, a pionner multimodal benchmark comprising comprehensive topology-centric tasks, and introduce an adaptive loss weighting strategy to emphasize topology-critical regions during training. Extensive experiments on fifteen diverse datasets demonstrate our superiority. Quantitatively, TubeMLLM achieves state-of-the-art out-of-distribution performance, substantially reducing global topological discrepancies on color fundus photography (decreasing the β0β_{0} number error from 37.42 to 8.58 compared to baselines). Notably, TubeMLLM exhibits exceptional zero-shot cross-modality transferring ability on unseen X-ray angiography, achieving a Dice score of 67.50% while significantly reducing the β0β_{0} error to 1.21. TubeMLLM also maintains robustness against degradations such as blur, noise, and low resolution. Furthermore, in topology-aware understanding tasks, the model achieves 97.38% accuracy in evaluating mask topological quality, significantly outperforming standard vision-language baselines.

Yaoyu Liu, Minghui Zhang, Xin You +2

Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, China · Department of Automation, Shanghai Jiao Tong University, Shanghai, China

Medical VLMsTopology-Preserving Image SegmentationMedical Image SegmentationCross-Modality Medical Image SegmentationVLM Robustness
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Mar 10, 2026

Transformer-Based Multi-Region Segmentation and Radiomic Analysis of HR-pQCT Imaging for Osteoporosis Classification

Osteoporosis is a skeletal disease typically diagnosed using dual-energy X-ray absorptiometry (DXA), which quantifies areal bone mineral density but overlooks bone microarchitecture and surrounding soft tissues. High-resolution peripheral quantitative computed tomography (HR-pQCT) enables three-dimensional microstructural imaging with minimal radiation. However, current analysis pipelines largely focus on mineralized bone compartments, leaving much of the acquired image data underutilized. We introduce a fully automated framework for binary osteoporosis classification using radiomics features extracted from anatomically segmented HR-pQCT images. To our knowledge, this work is the first to leverage a transformer-based segmentation architecture, i.e., the SegFormer, for fully automated multi-region HR-pQCT analysis. The SegFormer model simultaneously delineated the cortical and trabecular bone of the tibia and fibula along with surrounding soft tissues and achieved a mean F1 score of 95.36%. Soft tissues were further subdivided into skin, myotendinous, and adipose regions through post-processing. From each region, 939 radiomic features were extracted and dimensionally reduced to train six machine learning classifiers on an independent dataset comprising 20,496 images from 122 HR-pQCT scans. The best image level performance was achieved using myotendinous tissue features, yielding an accuracy of 80.08% and an area under the receiver operating characteristic curve (AUROC) of 0.85, outperforming bone-based models. At the patient level, replacing standard biological, DXA, and HR-pQCT parameters with soft tissue radiomics improved AUROC from 0.792 to 0.875. These findings demonstrate that automated, multi-region HR-pQCT segmentation enables the extraction of clinically informative signals beyond bone alone, highlighting the importance of integrated tissue assessment for osteoporosis detection.

Mohseu Rashid Subah, Mohammed Abdul Gani Zilani, Thomas L. Nickolas +3

Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA · Division of Bone and Mineral Diseases, Washington University Medicine, St. Louis, MO, USA · Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN, USA +1

RadiomicsMedical Image SegmentationComputed Tomography
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Mar 9, 2026

Weakly Supervised Teacher-Student Framework with Progressive Pseudo-mask Refinement for Gland Segmentation

Background and objectives: Colorectal cancer histopathological grading depends on accurate segmentation of glandular structures. Current deep learning approaches rely on large scale pixel level annotations that are labor intensive and difficult to obtain in routine clinical practice. Weakly supervised semantic segmentation offers a promising alternative. However, class activation map based methods often produce incomplete pseudo masks that emphasize highly discriminative regions and fail to supervise unannotated glandular structures. We propose a weakly supervised teacher student framework that leverages sparse pathologist annotations and an Exponential Moving Average stabilized teacher network to generate refined pseudo masks. Methods: The framework integrates confidence based filtering, adaptive fusion of teacher predictions with limited ground truth, and curriculum guided refinement to progressively segment unannotated glandular regions. The method was evaluated on an institutional colorectal cancer cohort from The Ohio State University Wexner Medical Center consisting of 60 hematoxylin and eosin stained whole slide images and on public datasets including the Gland Segmentation dataset, TCGA COAD, TCGA READ, and SPIDER. Results: On the Gland Segmentation dataset the framework achieved a mean Intersection over Union of 80.10 and a mean Dice coefficient of 89.10. Cross cohort evaluation demonstrated robust generalization on TCGA COAD and TCGA READ without additional annotations, while reduced performance on SPIDER reflected domain shift. Conclusions: The proposed framework provides an annotation efficient and generalizable approach for gland segmentation in colorectal histopathology.

Hikmat Khan, Wei Chen, Muhammad Khalid Khan Niazi

Department of Pathology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA

Histopathology Image SegmentationMedical Image SegmentationWeakly Supervised Semantic SegmentationPseudo-LabelingTeacher-Student Learning
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Mar 9, 2026

Structure and Progress Aware Diffusion for Medical Image Segmentation

Medical image segmentation is crucial for computer-aided diagnosis, which necessitates understanding both coarse morphological and semantic structures, as well as carving fine boundaries. The morphological and semantic structures in medical images are beneficial and stable clues for target understanding. While the fine boundaries of medical targets (like tumors and lesions) are usually ambiguous and noisy since lesion overlap, annotation uncertainty, and so on, making it not reliable to serve as early supervision. However, existing methods simultaneously learn coarse structures and fine boundaries throughout the training process. In this paper, we propose a structure and progress-aware diffusion (SPAD) for medical image segmentation, which consists of a semantic-concentrated diffusion (ScD) and a boundary-centralized diffusion (BcD) modulated by a progress-aware scheduler (PaS). Specifically, the semantic-concentrated diffusion introduces anchor-preserved target perturbation, which perturbs pixels within a medical target but preserves unaltered areas as semantic anchors, encouraging the model to infer noisy target areas from the surrounding semantic context. The boundary-centralized diffusion introduces progress-aware boundary noise, which blurs unreliable and ambiguous boundaries, thus compelling the model to focus on coarse but stable anatomical morphology and global semantics. Furthermore, the progress-aware scheduler gradually modulates noise intensity of the ScD and BcD forming a coarse-to-fine diffusion paradigm, which encourage focusing on coarse morphological and semantic structures during early target understanding stages and gradually shifting to fine target boundaries during later contour adjusting stages.

Siyuan Song, Guyue Hu, Chenglong Li +3

School of Artificial Intelligence, Anhui University, 230601, Hefei, China · State Key Laboratory of Opto-Electronic Information Acquisition and Protection Technology, Anhui University, Hefei, 230601, China · Anhui Provincial Key Laboratory of Security Artificial Intelligence, Anhui University, Hefei, 230601, China +2

Diffusion Models for Medical Image SegmentationMedical Image SegmentationBoundary-Aware Segmentation
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Mar 8, 2026

RPG-SAM: Reliability-Weighted Prototypes and Geometric Adaptive Threshold Selection for Training-Free One-Shot Polyp Segmentation

Training-free one-shot segmentation offers a scalable alternative to expert annotations where knowledge is often transferred from support images and foundation models. But existing methods often treat all pixels in support images and query response intensities models in a homogeneous way. They ignore the regional heterogeity in support images and response heterogeity in query.To resolve this, we propose RPG-SAM, a framework that systematically tackles these heterogeneity gaps. Specifically, to address regional heterogeneity, we introduce Reliability-Weighted Prototype Mining (RWPM) to prioritize high-fidelity support features while utilizing background anchors as contrastive references for noise suppression. To address response heterogeneity, we develop Geometric Adaptive Selection (GAS) to dynamically recalibrate binarization thresholds by evaluating the morphological consensus of candidates. Finally, an iterative refinement loop method is designed to polishes anatomical boundaries. By accounting for multi-layered information heterogeneity, RPG-SAM achieves a 5.56% mIoU improvement on the Kvasir dataset. Code will be released.

Weikun Lin, Yunhao Bai, Yan Wang

Shanghai Key Laboratory of Multidimensional Information Processing, East China Normal University

Image SegmentationPolyp SegmentationMedical Image Segmentation
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Mar 7, 2026

LightMedSeg: Lightweight 3D Medical Image Segmentation with Learned Spatial Anchors

Accurate and efficient 3D medical image segmentation is essential for clinical AI, where models must remain reliable under stringent memory, latency, and data availability constraints. Transformer-based methods achieve strong accuracy but suffer from excessive parameters, high FLOPs, and limited generalization. We propose LightMedSeg, a modular UNet-style segmentation architecture that integrates anatomical priors with adaptive context modeling. Anchor-conditioned FiLM modulation enables anatomy-aware feature calibration, while a local structural prior module and texture-aware routing dynamically allocate representational capacity to boundary-rich regions. Computational redundancy is minimized through ghost and depthwise convolutions, and multi-scale features are adaptively fused via a learned skip router with anchor-relative spatial position bias. Despite requiring only 0.48M parameters and 14.64~GFLOPs, LightMedSeg achieves segmentation accuracy within a few Dice points of heavy transformer baselines. Therefore, LightMedSeg is a deployable and data-efficient solution for 3D medical image segmentation. Code will be released publicly upon acceptance.

Kavyansh Tyagi, Vishwas Rathi, Puneet Goyal

National Institute of Technology Kurukshetra, India · Indian Institute of Technology Ropar, India

Medical Image Segmentation3D Medical Image SegmentationU-Net
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Mar 7, 2026

DDS-UDA: Dual-Domain Synergy for Unsupervised Domain Adaptation in Joint Segmentation of Optic Disc and Optic Cup

Convolutional neural networks (CNNs) have achieved exciting performance in joint segmentation of optic disc and optic cup on single-institution datasets. However, their clinical translation is hindered by two major challenges: limited availability of large-scale, high-quality annotations and performance degradation caused by domain shift during deployment across heterogeneous imaging protocols and acquisition platforms. While unsupervised domain adaptation (UDA) provides a way to mitigate these limitations, most existing approaches do not address cross-domain interference and intra-domain generalization within a unified framework. In this paper, we present the Dual-Domain Synergy UDA (DDS-UDA), a novel UDA framework that comprises two key modules. First, a bi-directional cross-domain consistency regularization module is enforced to mitigate cross-domain interference through feature-level semantic information exchange guided by a coarse-to-fine dynamic mask generator, suppressing noise propagation while preserving structural coherence. Second, a frequency-driven intra-domain pseudo label learning module is used to enhance intra-domain generalization by synthesizing spectral amplitude-mixed supervision signals, which ensures high-fidelity feature alignment across domains. Implemented within a teacher-student architecture, DDS-UDA disentangles domain-specific biases from domain-invariant feature-level representations, thereby achieving robust adaptation to heterogeneous imaging environments. We conduct a comprehensive evaluation of our proposed method on two multi-domain fundus image datasets, demonstrating that it outperforms several existing UDA based methods and therefore providing an effective way for optic disc and optic cup segmentation.

Yusong Xiao, Yuxuan Wu, Li Xiao +3

MoE Key Laboratory of Brain-Inspired Intelligence Perception and Cognition, University of Science and Technology of China, Hefei 230052, China · Department of Biomedical Engineering, Tulane University, New Orleans, LA 70118, USA · School of Mathematics and Computer Sciences, Nanchang University, Nanchang 330031, China

Medical Image SegmentationUnsupervised Domain AdaptationPseudo-Labeling
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Mar 6, 2026

CLoPA: Continual Low Parameter Adaptation of Interactive Segmentation for Medical Image Annotation

Interactive segmentation enables clinicians to guide annotation, but existing zero-shot models like nnInteractive fail to consistently reach expert-level performance across diverse medical imaging tasks. Because annotation campaigns produce a growing stream of task-specific labelled data, online adaptation of the segmentation model is a natural complement to zero-shot inference. We propose CLoPA, a continual adaptation strategy that tunes a small fraction of nnInteractive's parameters on the annotation cache, triggered by lightweight episode scheduling. CLoPA requires no new parameters or changes to the inference pipeline, and operates entirely within the existing annotation workflow. Across eight Medical Segmentation Decathlon tasks spanning diverse anatomical targets and imaging characteristics, CLoPA rapidly elevates performance to expert-level, even for tasks where nnInteractive previously failed, with the majority of gains realised after a single training episode. We show that the benefits of tuning different parameter groups depends on task characteristics and data regimes. Also, that for targets with complex geometries (e.g., hepatic vessels), instance normalisation and low-level feature tuning saturates, suggesting a need for deeper feature-representation alignment in the most challenging scenarios.

Parhom Esmaeili, Chayanin Tangwiriyasakul, Eli Gibson +2

School of Biomedical Engineering and Imaging Sciences, KCL, UK · Siemens Healthineers, Princeton NJ, USA

Medical Image SegmentationInteractive Medical Image SegmentationContinual LearningParameter-Efficient Fine-Tuning
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Mar 6, 2026

Prompt Group-Aware Training for Robust Text-Guided Nuclei Segmentation

Foundation models such as Segment Anything Model 3 (SAM3) enable flexible text-guided medical image segmentation, yet their predictions remain highly sensitive to prompt formulation. Even semantically equivalent descriptions can yield inconsistent masks, limiting reliability in clinical and pathology workflows. We reformulate prompt sensitivity as a group-wise consistency problem. Semantically related prompts are organized into prompt groups sharing the same ground-truth mask, and a prompt group-aware training framework is introduced for robust text-guided nuclei segmentation. The approach combines (i) a quality-guided group regularization that leverages segmentation loss as an implicit ranking signal, and (ii) a logit-level consistency constraint with a stop-gradient strategy to align predictions within each group. The method requires no architectural modification and leaves inference unchanged. Extensive experiments on multi-dataset nuclei benchmarks show consistent gains under textual prompting and markedly reduced performance variance across prompt quality levels. On six zero-shot cross-dataset tasks, our method improves Dice by an average of 2.16 points. These results demonstrate improved robustness and generalization for vision-language segmentation in computational pathology.

Yonghuang Wu, Zhenyang Liang, Wenwen Zeng +2

Fudan University, Shanghai, China

Text-Guided Image SegmentationMedical Image SegmentationVLM RobustnessHistopathology Image SegmentationZero-Shot Medical Image SegmentationConsistency Regularization
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Mar 6, 2026

CORE-Seg: Reasoning-Driven Segmentation for Complex Lesions via Reinforcement Learning

Medical image segmentation is undergoing a paradigm shift from conventional visual pattern matching to cognitive reasoning analysis. Although Multimodal Large Language Models (MLLMs) have shown promise in integrating linguistic and visual knowledge, significant gaps remain: existing general MLLMs possess broad common sense but lack the specialized visual reasoning required for complex lesions, whereas traditional segmentation models excel at pixel-level segmentation but lack logical interpretability. In this paper, we introduce ComLesion-14K, the first diverse Chain-of-Thought (CoT) benchmark for reasoning-driven complex lesion segmentation. To accomplish this task, we propose CORE-Seg, an end-to-end framework integrating reasoning with segmentation through a Semantic-Guided Prompt Adapter. We design a progressive training strategy from SFT to GRPO, equipped with an adaptive dual-granularity reward mechanism to mitigate reward sparsity. Our Method achieves state-of-the-art results with a mean Dice of 37.06% (14.89% higher than the second-best baseline), while reducing the failure rate to 18.42%. Project Page: https://xyxl024.github.io/CORE-Seg.github.io/

Yuxin Xie, Yuming Chen, Yishan Yang +5

School of Computer Science and Engineering, Southeast University, Nanjing, 211189, China. · School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China. · Zhongda Hospital, Southeast University, Nanjing, 210009, China. +1

Medical Image SegmentationReasoning Segmentation
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Mar 6, 2026

Shifting Adaptation from Weight Space to Memory Space: A Memory-Augmented Agent for Medical Image Segmentation

Medical image segmentation is fundamental to clinical workflows, yet models trained on a single dataset often fail to generalize across institutions, scanners, or patient populations. While vision foundation models have shown great promise in addressing this challenge, their deployment typically requires task-specific fine-tuning, which introduces substantial communication overhead in federated learning and prevents continuous knowledge evolution during deployment. In this work, we propose a memory-augmented segmentation agent (MemSeg-Agent) that shifts adaptation from weight space to memory space, enabling few-shot learning, federated supervised learning, and test-time adaptation within a unified architecture. MemSeg-Agent conditions a fixed backbone with lightweight static, few-shot, and test-time working memories, which are dynamically composed by an agentic controller. In federated settings, we update compact memory units instead of model parameters, substantially reducing communication overhead. Experiments on four public datasets demonstrate strong performance and robustness to domain shift: Static memory alone matches or surpasses strong supervised baselines with high parameter efficiency, and test-time working memory further improves in-domain and cross-domain performance without fine-tuning. Overall, MemSeg-Agent introduces a new paradigm for scalable and adaptive medical image segmentation in the era of agentic AI.

Bowen Chen, Qiaohui Gao, Shaowen Wan +6

Department of Electrical and Computer Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA · College of Engineering, Northeastern University, Boston, MA 02115, USA · Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA +4

Medical Image SegmentationFew-Shot Medical Image SegmentationMemory-Augmented Neural NetworksDomain GeneralizationTest-Time Adaptation
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Mar 5, 2026

Exploiting Intermediate Reconstructions in Optical Coherence Tomography for Test-Time Adaption of Medical Image Segmentation

Primary health care frequently relies on low-cost imaging devices, which are commonly used for screening purposes. To ensure accurate diagnosis, these systems depend on advanced reconstruction algorithms designed to approximate the performance of high-quality counterparts. Such algorithms typically employ iterative reconstruction methods that incorporate domain-specific prior knowledge. However, downstream task performance is generally assessed using only the final reconstructed image, thereby disregarding the informative intermediate representations generated throughout the reconstruction process. In this work, we propose IRTTA to exploit these intermediate representations at test-time by adapting the normalization-layer parameters of a frozen downstream network via a modulator network that conditions on the current reconstruction timescale. The modulator network is learned during test-time using an averaged entropy loss across all individual timesteps. Variation among the timestep-wise segmentations additionally provides uncertainty estimates at no extra cost. This approach enhances segmentation performance and enables semantically meaningful uncertainty estimation, all without modifying either the reconstruction process or the downstream model.

Thomas Pinetz, Veit Hucke, Hrvoje Bogunovic

Institute of Artificial Intelligence, Center for Medical Data Science, Medical University of Vienna, Austria

Medical Image SegmentationTest-Time AdaptationOptical Coherence TomographySegmentation Uncertainty Estimation
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Mar 5, 2026

Tell2Adapt: A Unified Framework for Source Free Unsupervised Domain Adaptation via Vision Foundation Model

Source Free Unsupervised Domain Adaptation (SFUDA) is critical for deploying deep learning models across diverse clinical settings. However, existing methods are typically designed for low-gap, specific domain shifts and cannot generalize into a unified, multi-modalities, and multi-target framework, which presents a major barrier to real-world application. To overcome this issue, we introduce Tell2Adapt, a novel SFUDA framework that harnesses the vast, generalizable knowledge of the Vision Foundation Model (VFM). Our approach ensures high-fidelity VFM prompts through Context-Aware Prompts Regularization (CAPR), which robustly translates varied text prompts into canonical instructions. This enables the generation of high-quality pseudo-labels for efficiently adapting the lightweight student model to target domain. To guarantee clinical reliability, the framework incorporates Visual Plausibility Refinement (VPR), which leverages the VFM's anatomical knowledge to re-ground the adapted model's predictions in target image's low-level visual features, effectively removing noise and false positives. We conduct one of the most extensive SFUDA evaluations to date, validating our framework across 10 domain adaptation directions and 22 anatomical targets, including brain, cardiac, polyp, and abdominal targets. Our results demonstrate that Tell2Adapt consistently outperforms existing approaches, achieving SOTA for a unified SFUDA framework in medical image segmentation. Code are avaliable at https://github.com/derekshiii/Tell2Adapt.

Yulong Shi, Shijie Li, Ziyi Li +1

College of Medicine and Biological Information Engineering, Northeastern University · Engineering Research Center of Medical Imaging and Intelligent Analysis, Ministry of Education · Key Laboratory of Medical Image Computing, Ministry of Education, Northeastern University

Source-Free Domain AdaptationMedical Image SegmentationVision Foundation Model Adaptation
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Mar 5, 2026

Meta-D: Metadata-Aware Architectures for Brain Tumor Analysis and Missing-Modality Segmentation

We present Meta-D, an architecture that explicitly leverages categorical scanner metadata such as MRI sequence and plane orientation to guide feature extraction for brain tumor analysis. We aim to improve the performance of medical image deep learning pipelines by integrating explicit metadata to stabilize feature representations. We first evaluate this in 2D tumor detection, where injecting sequence (e.g., T1, T2) and plane (e.g., axial) metadata dynamically modulates convolutional features, yielding an absolute increase of up to 2.62% in F1-score over image-only baselines. Because metadata grounds feature extraction when data are available, we hypothesize it can serve as a robust anchor when data are missing. We apply this to 3D missing-modality tumor segmentation. Our Transformer Maximizer utilizes metadata-based cross-attention to isolate and route available modalities, ensuring the network focuses on valid slices. This targeted attention improves brain tumor segmentation Dice scores by up to 5.12% under extreme modality scarcity while reducing model parameters by 24.1%.

SangHyuk Kim, Daniel Haehn, Sumientra Rampersad

University of Massachusetts Boston

Missing-Modality Medical Image SegmentationMedical Image AnalysisBrain Tumor SegmentationMedical Image Segmentation3D Medical Image Segmentation
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Mar 5, 2026

LAW & ORDER: Adaptive Spatial Weighting for Medical Diffusion and Segmentation

Medical image analysis depends on accurate segmentation and controllable synthesis, but both tasks face severe spatial imbalance: lesions occupy small regions against large backgrounds. We study adaptive spatial weighting as a task-level design principle and instantiate it in two adapters. LAW learns per-pixel loss weights for mask-conditioned diffusion by modulating a ratio prior with a feature-dependent delta map, with normalization, clamping, and Dice regularization for stability. ORDER improves lightweight segmentation by adding selective bidirectional skip attention with stage-wise confidence gating. On held-out diffusion test sets, LAW lowers FID from 158.13±\pm0.15 to 108.43±\pm0.71 on Polyps, from 144.13±\pm0.31 to 89.51±\pm0.96 on KiTS19, and from 139.22±\pm0.38 to 112.58±\pm0.68 on BRISC, while improving held-out mask-recovery Dice from 0.681±\pm0.013 to 0.825±\pm0.003 on Polyps. When the resulting images are added to nnUNet training, downstream Polyps mDice rises from 71.7±\pm0.4 to 74.1±\pm0.8. On the cleaned Polyps segmentation protocol, the reported ORDER configuration reaches 76.3±\pm1.9 mDice and 67.2±\pm2.0 mIoU at 42K parameters and 0.11 GFLOPs, versus 70.3±\pm1.5 mDice and 59.9±\pm1.7 mIoU for matched MK-UNet. On BRISC under the same training recipe, ORDER reaches 77.4±\pm0.8 mDice and 68.1±\pm0.7 mIoU. These results position adaptive spatial weighting as a practical design idea for both medical diffusion and efficient segmentation.

Anugunj Naman, Ayushman Singh, Gaibo Zhang +1

Elmore Family School of Electrical and Computer Engineering Purdue University, West Lafayette, USA · Sesame AI, New York, USA · Department of Computer Science Purdue University, West Lafayette, USA +1

Image SegmentationHealthcareAdaptive Loss WeightingDiffusion-Based Image GenerationMedical Image SegmentationMedical Image Synthesis
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Mar 5, 2026

MADCrowner: Margin Aware Dental Crown Design with Template Deformation and Refinement

Dental crown restoration is one of the most common treatment modalities for tooth defect, where personalized dental crown design is critical. While computer-aided design (CAD) systems have notably enhanced the efficiency of dental crown design, extensive manual adjustments are still required in the clinic workflow. Recent studies have explored the application of learning-based methods for the automated generation of restorative dental crowns. Nevertheless, these approaches were challenged by inadequate spatial resolution, noisy outputs, and overextension of surface reconstruction. To address these limitations, we propose \totalframework, a margin-aware mesh generation framework comprising CrownDeformR and CrownSegger. Inspired by the clinic manual workflow of dental crown design, we designed CrownDeformR to deform an initial template to the target crown based on anatomical context, which is extracted by a multi-scale intraoral scan encoder. Additionally, we introduced \marginseg, a novel margin segmentation network, to extract the cervical margin of the target tooth. The performance of CrownDeformR improved with the cervical margin as an extra constraint. And it was also utilized as the boundary condition for the tailored postprocessing method, which removed the overextended area of the reconstructed surface. We constructed a large-scale intraoral scan dataset and performed extensive experiments. The proposed method significantly outperformed existing approaches in both geometric accuracy and clinical feasibility.

Linda Wei, Chang Liu, Wenran Zhang +9

3D Mesh ReconstructionDeformable Shape ReconstructionMedical Image Segmentation
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Mar 4, 2026

Self-Supervised Multi-Stage Domain Unlearning for White-Matter Lesion Segmentation

Inter-scanner variability of magnetic resonance imaging has an adverse impact on the diagnostic and prognostic quality of the scans and necessitates the development of models robust to domain shift inflicted by the unseen scanner data. Review of recent advances in domain adaptation showed that efficacy of strategies involving modifications or constraints on the latent space appears to be contingent upon the level and/or depth of supervision during model training. In this paper, we therefore propose an unsupervised domain adaptation technique based on self-supervised multi-stage unlearning (SSMSU). Building upon the state-of-the-art segmentation framework nnU-Net, we employ deep supervision at deep encoder stages using domain classifier unlearning, applied sequentially across the deep stages to suppress domain-related latent features. Following self-configurable approach of the nnU-Net, the auxiliary feedback loop implements a self-supervised backpropagation schedule for the unlearning process, since continuous unlearning was found to have a detrimental effect on the main segmentation task. Experiments were carried out on four public datasets for benchmarking white-matter lesion segmentation methods. Five benchmark models and/or strategies, covering passive to active unsupervised domain adaptation, were tested. In comparison, the SSMSU demonstrated the advantage of unlearning by enhancing lesion sensitivity and limiting false detections, which resulted in higher overall segmentation quality in terms of segmentation overlap and relative lesion volume error. The proposed model inputs only the FLAIR modality, which simplifies preprocessing pipelines, eliminates the need for inter-modality registration errors and harmonization, which can introduce variability. Source code is available on https://github.com/Pubec/nnunetv2-unlearning.

Domen Preložnik, Žiga Špiclin

University of Ljubljana, Faculty of Electrical Engineering, Slovenia

Unsupervised Domain AdaptationMedical Image SegmentationMachine UnlearningSelf-Supervised Learning
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Mar 4, 2026

Volumetric Directional Diffusion: Anchoring Uncertainty Quantification in Anatomical Consensus for Ambiguous Medical Image Segmentation

Ambiguous 3D medical image segmentation often involves boundaries where different expert delineations are non-identical yet clinically plausible. Modeling such inter-observer variability requires a careful balance between diversity and anatomical fidelity: deterministic models preserve coherent volumetric structures but collapse expert disagreement into a single mask, while stochastic generative models can produce diverse samples but may introduce disconnected components or slice-to-slice inconsistency when generating full 3D masks from unstructured noise. We propose Volumetric Directional Diffusion (VDD), a prior-anchored diffusion framework that shifts stochastic generation from full-mask synthesis to residual boundary exploration. VDD uses a coarse consensus prediction as an anatomical anchor and learns a directional diffusion process to generate plausible boundary variations around ambiguous regions while preserving stable volumetric topology. Experiments on three multi-rater datasets, including LIDC-IDRI, KiTS21, and ISBI 2015, show that VDD improves uncertainty distribution alignment while maintaining competitive segmentation accuracy and 3D structural consistency. These results suggest that prior-anchored residual diffusion can model clinically plausible expert disagreement without sacrificing anatomical fidelity.

Chao Wu, Mahesh Bhosale, Kangxian Xie +3

Department of Computer Science and Engineering University at Buffalo, SUNY Buffalo, NY, USA

Diffusion Models for Medical Image SegmentationMedical Image Segmentation3D Medical Image SegmentationSegmentation Uncertainty Estimation
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Mar 4, 2026

ProFound: A moderate-sized vision foundation model for multi-task prostate imaging

Many diagnostic and therapeutic clinical tasks for prostate cancer increasingly rely on multi-parametric MRI. Automating these tasks is challenging because they necessitate expert interpretations, which are difficult to scale to capitalise on modern deep learning. Although modern automated systems achieve expert-level performance in isolated tasks, their general clinical utility remains limited by the requirement of large task-specific labelled datasets. In this paper, we present ProFound, a domain-specialised vision foundation model for volumetric prostate mpMRI. ProFound is pre-trained using several variants of self-supervised approaches on a diverse, multi-institutional collection of 5,000 patients, with a total of over 22,000 unique 3D MRI volumes (over 1,800,000 2D image slices). We conducted a systematic evaluation of ProFound across a broad spectrum of 1111 downstream clinical tasks on over 3,000 independent patients, including prostate cancer detection, Gleason grading, lesion localisation, gland volume estimation, zonal and surrounding structure segmentation. Experimental results demonstrate that finetuned ProFound consistently outperforms or remains competitive with state-of-the-art specialised models and existing medical vision foundation models trained/finetuned on the same data.

Yipei Wang, Yinsong Xu, Weixi Yi +11

UCL Hawkes Institute, University College London, London, UK · Department of Medical Physics and Biomedical Engineering, University College London, London, UK · School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China +11

Medical Imaging Foundation ModelsMedical Image Representation LearningMagnetic Resonance ImagingMedical Image SegmentationMedical Image Localization
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Mar 3, 2026

ProSMA-UNet: Decoder Conditioning for Proximal-Sparse Skip Feature Selection

Medical image segmentation commonly relies on U-shaped encoder-decoder architectures such as U-Net, where skip connections preserve fine spatial detail by injecting high-resolution encoder features into the decoder. However, these skip pathways also propagate low-level textures, background clutter, and acquisition noise, allowing irrelevant information to bypass deeper semantic filtering -- an issue that is particularly detrimental in low-contrast clinical imaging. Although attention gates have been introduced to address this limitation, they typically produce dense sigmoid masks that softly reweight features rather than explicitly removing irrelevant activations. We propose ProSMA-UNet (Proximal-Sparse Multi-Scale Attention U-Net), which reformulates skip gating as a decoder-conditioned sparse feature selection problem. ProSMA constructs a multi-scale compatibility field using lightweight depthwise dilated convolutions to capture relevance across local and contextual scales, then enforces explicit sparsity via an ℓ1\ell_1 proximal operator with learnable per-channel thresholds, yielding a closed-form soft-thresholding gate that can remove noisy responses. To further suppress semantically irrelevant channels, ProSMA incorporates decoder-conditioned channel gating driven by global decoder context. Extensive experiments on challenging 2D and 3D benchmarks demonstrate state-of-the-art performance, with particularly large gains (≈20\approx20%) on difficult 3D segmentation tasks. Project page: https://math-ml-x.github.io/ProSMA-UNet/

Chun-Wun Cheng, Yanqi Cheng, Peiyuan Jing +4

Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK · School of Engineering, Zurich University of Applied Sciences, CH · Bioengineering Department and ImperialX, Imperial College London, UK +2

U-NetMedical Image Segmentation3D Medical Image SegmentationSparse AttentionMulti-Scale Attention
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Mar 3, 2026

Gated Differential Linear Attention: A Linear-Time Decoder for High-Fidelity Medical Segmentation

Medical image segmentation requires models that preserve fine anatomical boundaries while remaining practical for clinical deployment. Transformers capture long-range dependencies but incur quadratic attention cost, whereas CNNs are efficient but less effective at global reasoning. Linear attention offers O(N)\mathcal{O}(N) scaling, but often produces diffuse feature aggregation that weakens boundary-sensitive prediction. We introduce a gated differential linear-attention mixer for medical image segmentation. Its global path, Gated Differential Linear Attention (GDLA), performs differential subtraction between two kernelized attention branches over complementary query/key subspaces to suppress redundant responses, and employs a data-dependent gate for token refinement. A parallel local token-mixing branch with depthwise convolution strengthens neighborhood interactions for better refinement, and the two branches are fused while preserving O(N)\mathcal{O}(N) complexity. When instantiated in a pretrained Pyramid Vision Transformer (PVT)-based encoder--decoder model, \name achieves state-of-the-art results on the evaluated 2D medical segmentation benchmarks spanning CT, MRI, ultrasound, and dermoscopy, with a favorable accuracy--efficiency trade-off over closely related baselines. The code is publicly available at https://github.com/xmindflow/gdla.

Hongbo Zheng, Afshin Bozorgpour, Dorit Merhof +1

University of Illinois Urbana-Champaign · University of Regensburg

Medical Image SegmentationLinear AttentionGated AttentionBoundary-Aware SegmentationHybrid CNN-Transformer Architectures
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Mar 2, 2026

A Detection-Gated Pipeline for Robust Glottal Area Waveform Extraction and Clinical Pathology Assessment

We present a fully automated, two-stage modular glottal area segmentation framework for high-speed videoendoscopy (HSV) designed for accuracy, generalizability, and real-time playback. Our detection-gated pipeline combines a YOLOv8n glottis localizer with a U-Net segmenter; the localizer defines a tight crop to ensure a consistent field of view and gates the output to reduce spurious segmentations during glottal closure. The models were trained on the GIRAFE (N=600) and BAGLS (N=55,750) datasets. Cross-dataset portability was evaluated by benchmarking GIRAFE-trained models on the BAGLS test set without fine-tuning. In these evaluations, the pipeline achieved a Dice Similarity Coefficient (DSC) of 0.745 (87% of the in-domain ceiling). On in-distribution test sets, the system achieved DSCs of 0.81 (GIRAFE) and 0.856 (BAGLS), outperforming or competing with state-of-the-art methods. An exploratory clinical study of 40 subjects demonstrated that the glottal area Coefficient of Variation (CV distinguished healthy from pathological function (p=0.006). The system processes ~35 frames per second on commodity hardware, enabling interactive clinical review. This design supports uniform extraction of laryngeal kinematic measures across varying acquisition settings. Code, weights, and software are available at https://github.com/hari-krishnan/openglottal.

Harikrishnan Unnikrishnan, Rita Patel

¹Orchard Robotics, San Francisco, California, USA. · ²Department of Speech, Language, and Hearing Sciences, Indiana University, Bloomington, Indiana, USA. · ³Department of Otolaryngology–Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, Indiana, USA.

Medical Image SegmentationEndoscopy
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Mar 1, 2026

The MAMA-MIA Challenge: Advancing Generalizability and Fairness in Breast MRI Tumor Segmentation and Treatment Response Prediction

Breast cancer is the most frequently diagnosed malignancy among women worldwide and a leading cause of cancer-related mortality. Dynamic contrast-enhanced magnetic resonance imaging plays a central role in tumor characterization and treatment monitoring, particularly in patients receiving neoadjuvant chemotherapy. However, existing artificial intelligence models for breast magnetic resonance imaging are typically developed and evaluated using heterogeneous datasets, study populations, and assessment protocols, making direct comparison difficult and limiting understanding of model robustness across institutions and clinically relevant patient subgroups. The MAMA-MIA Challenge was designed to address these challenges by providing a standardized benchmark for the joint evaluation of primary tumor segmentation and prediction of pathologic complete response using pre-treatment magnetic resonance imaging only. The training cohort comprised 1,506 patients from multiple institutions in the United States, while evaluation was conducted on an external test set of 574 patients from three independent European centers to assess cross-continental and cross-institutional generalization. A unified scoring framework combined predictive performance with subgroup consistency across age, menopausal status, and breast density. Twenty-six international teams participated in the final evaluation phase. Results demonstrate substantial performance variability under a common external evaluation framework and reveal trade-offs between overall accuracy and subgroup fairness. The challenge provides standardized datasets, evaluation protocols, and public resources to promote the development of robust and equitable artificial intelligence systems for breast cancer imaging.

Lidia Garrucho, Smriti Joshi, Kaisar Kushibar +43

Medical Image SegmentationMedical Image BenchmarksClinical Outcome PredictionAlgorithmic Fairness
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Mar 1, 2026

LUMOS: Latent Universal Medical Priors for Segmentation

General vision foundation models (VFMs) have been primarily developed on natural images, and their utility for medical image segmentation is therefore often considered to depend on costly adaptation or domain-specific fine-tuning. In this paper, we revisit this assumption from a different perspective: rather than requiring VFM segmentors to relearn visual regularities, we investigate whether the low-level visual priors necessary for anatomical delineation already lie dormant within general VFMs. We observe that frozen VFMs, despite lacking medical supervision, encode transferable visual regularities. These properties are not exclusive to natural images but are also fundamental to medical image understanding. Motivated by this observation, we propose Latent Universal Medical PriOrs for Segmentation (LUMOS), a novel framework that amplifies general VFM priors to conventional medical segmentors. LUMOS consists of two key components: (1) Pathfinder that distills visual cues from a frozen vision foundation model, and (2) Inspiror that sparks the conventional medical networks with spatial guidance from distilled visual regularities. In this way, the segmentor is relieved from learning complex visual regularities entirely from limited medical annotations and can instead focus on task-specific anatomical delineation. Across diverse medical datasets and token-based VFMs, LUMOS shows that general VFMs can serve as spatial prior generators when their frozen token spaces preserve patch-level pattern relevance. DINO provides stable matched-backbone gains, while SigLIP exposes VFM-specific sensitivity caused by its different token granularity and representation objective.

Zhuonan Liang, Wei Guo, Jie Gan +4

The University of Sydney, Sydney, NSW 2006, Australia. · Biological System & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. · Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Medical Image SegmentationTransfer LearningVision Foundation Model Adaptation
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Mar 1, 2026

GroundedSurg: A Multi-Procedure Benchmark for Language-Conditioned Surgical Tool Segmentation

Clinically reliable perception of surgical scenes is essential for advancing intelligent, context-aware intraoperative assistance such as instrument handoff guidance, collision avoidance, and workflow-aware robotic support. Existing surgical tool benchmarks primarily evaluate category-level segmentation, requiring models to detect all instances of predefined instrument classes. However, real-world clinical decisions often require resolving references to a specific instrument instance based on its functional role, spatial relation, or anatomical interaction capabilities not captured by current evaluation paradigms. We introduce GroundedSurg, the first language-conditioned, instance-level surgical grounding benchmark. Each instance pairs a surgical image with a natural-language description targeting a single instrument, accompanied by structured spatial grounding annotations including bounding boxes and point-level anchors. The dataset spans ophthalmic, laparoscopic, robotic, and open procedures, encompassing diverse instrument types, imaging conditions, and operative complexities. By jointly evaluating linguistic reference resolution and pixel-level localization, GroundedSurg enables a systematic and realistic evaluation of vision-language models in clinically realistic multi-instrument scenes. Extensive experiments demonstrate substantial performance gaps across modern segmentation and VLMs, highlighting the urgent need for clinically grounded vision-language reasoning in surgical AI systems. Code and data are publicly available at https://github.com/gaash-lab/GroundedSurg

Tajamul Ashraf, Abrar Ul Riyaz, Wasif Tak +4

King Abdullah University of Science and Technology (KAUST), Saudi Arabia · Gaash Research Lab, National Institute of Technology Srinagar, India · Thapar Institute of Engineering and Technology, India +1

Medical Image GroundingReferring Image SegmentationMedical Image BenchmarksMedical VLMsMedical Image Segmentation
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Mar 1, 2026

Fake It Right: Injecting Anatomical Logic into Synthetic Supervised Pre-training for Medical Segmentation

Vision Transformers (ViTs) excel in 3D medical segmentation but require massive annotated datasets. While Self-Supervised Learning (SSL) mitigates this using unlabeled data, it still faces strict privacy and logistical barriers. Formula-Driven Supervised Learning (FDSL) offers a privacy-preserving alternative by pre-training on synthetic mathematical primitives. However, a critical semantic gap limits its efficacy: generic shapes lack the morphological fidelity, fixed spatial layouts, and inter-organ relationships of real anatomy, preventing models from learning essential global structural priors. To bridge this gap, we propose an Anatomy-Informed Synthetic Supervised Pre-training framework unifying FDSL's infinite scalability with anatomical realism. We replace basic primitives with a lightweight shape bank with de-identified, label-only segmentation masks from 5 subjects. Furthermore, we introduce a structure-aware sequential placement strategy to govern the patch synthesis process. Instead of random placement, we enforce physiological plausibility using spatial anchors for correct localization and a topological graph to manage inter-organ interactions (e.g., preventing impossible overlaps). Extensive experiments on BTCV and MSD datasets demonstrate that our method significantly outperforms state-of-the-art FDSL baselines and SSL methods by 1.74% and up to 1.66%, while exhibiting a robust scaling effect where performance improves with increased synthetic data volume. This provides a data-efficient, privacy-compliant solution for medical segmentation. The code will be made publicly available upon acceptance.

Jiaqi Tang, Mengyan Zheng, Shu Zhang +2

Peking University · Beihang University · Deepwise Ltd.

Medical Image SegmentationSynthetic Data Pretraining3D Medical Image Segmentation3D ViTs
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Feb 28, 2026

Efficient Conformal Volumetry for Template-Based Segmentation

Template-based segmentation, a widely used paradigm in medical imaging, propagates anatomical labels via deformable registration from a labeled atlas to a target image, and is often used to compute volumetric biomarkers for downstream decision-making. While conformal prediction (CP) provides finite-sample valid intervals for scalar metrics, existing segmentation-based uncertainty quantification (UQ) approaches either rely on learned model features, often unavailable in classic template-based pipelines, or treat the registration process as a black box, resulting in overly conservative intervals when applied directly in output space. We introduce ConVOLT, a CP framework that achieves efficient volumetric UQ by conditioning calibration on properties of the estimated deformation field from template-based segmentation. ConVOLT calibrates a learned volumetric scaling factor from deformation space features. We evaluate ConVOLT on template-based segmentation tasks involving global, regional, and label volumetry across multiple datasets and registration methods. ConVOLT achieves target coverage while producing substantially tighter intervals than output-space conformal baselines. Our work paves way to exploit the registration process for efficient UQ in medical imaging pipelines.

Matt Y. Cheung, Ashok Veeraraghavan, Guha Balakrishnan

Department of Electrical & Computer Engineering Rice University Houston, TX 77005, USA

Segmentation Uncertainty EstimationMedical Image AnalysisConformal PredictionMedical Image Segmentation
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Feb 28, 2026

Explainable Continuous-Time Mask Refinement with Local Self-Similarity Priors for Medical Image Segmentation

Accurate semantic segmentation of foot ulcers is essential for automated wound monitoring, yet boundary delineation remains challenging due to tissue heterogeneity and poor contrast with surrounding skin. To overcome the limitations of standard intensity-based networks, we present LSS-LTCNet:an ante-hoc explainable framework synergizing deterministic structural priors with continuous-time neural dynamics. Our architecture departs from traditional black-box models by employing a Local Self-Similarity (LSS) mechanism that extracts dense, illumination-invariant texture descriptors to explicitly disentangle necrotic tissue from background artifacts. To enforce topological precision, we introduce a Liquid Time-Constant (LTC) refinement module that treats boundary evolution as an ODEgoverned dynamic system, iteratively refining masks over continuous time-steps. Comprehensive evaluation on the MICCAI FUSeg dataset demonstrates that LSS-LTCNet achieves state-of-the-art boundary alignment, securing a peak Dice score of 86.96% and an exceptional 95th percentile Hausdorff Distance (HD95) of 8.91 pixels. Requiring merely 25.70M parameters, the model significantly outperforms heavier U-Net and transformer baselines in efficiency. By providing inherent visual audit trails alongside high-fidelity predictions, LSS-LTCNet offers a robust and transparent solution for computer-aided diagnosis in mobile healthcare (mHealth) settings.

Rajdeep Chatterjee, Sudip Chakrabarty, Trishaani Acharjee

School of Computer Engineering, Kalinga Institute of Industrial Technology, Bhubaneswar, India · AmygdalaAI-India Lab, Bhubaneswar, India

Medical Image SegmentationBoundary-Aware SegmentationExplainable Medical Image Analysis
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Feb 27, 2026

Extending 2D foundational DINOv3 representations to 3D segmentation of neonatal brain MR images

Precise volumetric delineation of hippocampal structures is essential for quantifying neurodevelopmental trajectories in pre-term and term infants, where subtle morphological variations may carry prognostic significance. While foundation encoders trained on large-scale visual data offer discriminative representations, their 2D formulation is a limitation with respect to the 33D organization of brain anatomy. We propose a volumetric segmentation strategy that reconciles this tension through a structured window-based disassembly-reassembly mechanism: the global MRI volume is decomposed into non-overlapping 3D windows or sub-cubes, each processed via a separate decoding arm built upon frozen high-fidelity features, and subsequently reassembled prior to a ground-truth correspendence using a dense-prediction head. This architecture preserves constant a decoder memory footprint while forcing predictions to lie within an anatomically consistent geometry. Evaluated on the ALBERT dataset for hippocampal segmentation, the proposed approach achieves a Dice score of 0.65 for a single 3D window. The method demonstrates that volumetric anatomical structure could be recovered from frozen 2D foundation representations through structured compositional decoding, and offers a principled and generalizable extension for foundation models for 3D medical applications.

Annayah Usman, Behraj Khan, Tahir Qasim Syed

Institute of Business Administration Karachi

Medical Image Segmentation3D Medical Image SegmentationMedical Imaging Foundation ModelsTransfer Learning
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