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.

May 19, 2026

Pixel Wised Lesion Prediction on COVID-19 CT Imagery: A Comparative Analysis of Automated Image Segmentation Architectures

In recent years, there has been a notable increase in the level of attention that is given to algorithms based on deep learning in the context of medical image segmentation. Nevertheless, the reliability of the field has been hindered due to the absence of a standardized methodology for performance analysis and the utilization of different datasets in previous research. The primary objective of the research is to comprehensively evaluate contemporary segmentation frameworks combined with state-of-the-art pre-trained backbones in order to accurately predict COVID-19 lesions in CT images. Moreover, this evaluation can serve as a point of reference for the segmentation of images in various other imaging scenarios. In order to accomplish this, we integrate four distinct deep learning architectures, namely Unet, PSPNet, Linknet, and FPN, with six pre-trained encoders, including VGG 19, DenseNet 121, Inception ResNet V2, MobileNet V2, SeresNet 101, and EfficientNet B0. This approach enables the development of diverse testing architectures. In the context of image segmentation, our research encompassed both binary and multi-class experimentation. The findings derived from our analysis of three distinct COVID-19 CT segmentation datasets indicate that deep learning architectures yield precise and efficient segmentation outcomes. Significantly, a maximum F1-Score of 98% was attained for binary class segmentation, while multi-class segmentation yielded F1-Scores of 75% and 77% across two separate datasets. The utilization of artificial intelligence and deep learning enhances the diagnostic process for pandemic diseases across multiple dimensions.

Sarmad Khan, Arslan Shaukat, Umer Asgher +1

Department of Computer & Software Engineering National University of Sciences & Technology Islamabad, Pakistan · School of Computing & Information Systems University of Melbourne Melbourne, Australia

Medical Image SegmentationConvolutional Neural Networks
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May 19, 2026

ELEMENT: Multi-Modal Retinal Vessel Segmentation Based on a Coupled Region Growing and Machine Learning Approach

Vascular structures in the retina contain important information for the detection and analysis of ocular diseases, including age-related macular degeneration, diabetic retinopathy and glaucoma. Commonly used modalities in diagnosis of these diseases are fundus photography, scanning laser ophthalmoscope (SLO) and fluorescein angiography (FA). Typically, retinal vessel segmentation is carried out either manually or interactively, which makes it time consuming and prone to human errors. In this research, we propose a new multi-modal framework for vessel segmentation called ELEMENT (vEsseL sEgmentation using Machine lEarning and coNnecTivity). This framework consists of feature extraction and pixel-based classification using region growing and machine learning. The proposed features capture complementary evidence based on grey level and vessel connectivity properties. The latter information is seamlessly propagated through the pixels at the classification phase. ELEMENT reduces inconsistencies and speeds up the segmentation throughput. We analyze and compare the performance of the proposed approach against state-of-the-art vessel segmentation algorithms in three major groups of experiments, for each of the ocular modalities. Our method produced higher overall performance, with an overall accuracy of 97.40%, compared to 25 of the 26 state-of-the-art approaches, including six works based on deep learning, evaluated on the widely known DRIVE fundus image dataset. In the case of the STARE, CHASE-DB, VAMPIRE FA, IOSTAR SLO and RC-SLO datasets, the proposed framework outperformed all of the state-of-the-art methods with accuracies of 98.27%, 97.78%, 98.34%, 98.04% and 98.35%, respectively.

Erick O. Rodrigues, Aura Conci, Panos Liatsis

Academic Department of Informatics, Universidade Tecnologica Federal do Parana (UTFPR), Pato Branco 80230-901, Brazil · Department of Computer Science, Universidade Federal Fluminense (UFF), Niteroi 24220-900, Brazil · Department of Electrical Engineering and Computer Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates

Image SegmentationMedical ImagingRetinal Vessel SegmentationMedical Image SegmentationFundus Imaging
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May 19, 2026

Disentangling Sampling from Training Budget in Class-Imbalanced CT Body Composition Segmentation

Class imbalance is a fundamental challenge in medical image segmentation, where frequent classes typically dominate training at the expense of rare classes. Loss-based approaches mitigate imbalance by reweighting the per-pixel loss within the batch, while sampling strategies control which images enter the batch. Yet neither explicitly controls which classes appear within the batch, leaving rare-class exposure only partially rebalanced. In this work, we adopt episodic sampling from few-shot learning to promote class-balanced batch construction in a fully supervised setting. We decouple episodic sampling from its conventional metric-learning context and evaluate it in body composition segmentation in CT. We compare episodic sampling against random and weighted sampling on nine muscle and adipose tissues, derived from 210 scans of the public SAROS dataset. Training is performed under full- and low-data regimes, with additional comparisons under matched training iteration budgets. Under full-data training, all three strategies performed comparably (mean Dice 0.882 for episodic, 0.878 for random and weighted). Under low-data training, episodic sampling outperformed random and weighted (0.787 vs. 0.758 and 0.762), driven by a 12-fold difference in training iterations. Under matched training budgets, random and weighted overfit earlier, while episodic improved for approximately three times more iterations before plateauing. Our findings identify the training iteration budget as under-recognized confound in sampling strategies, motivating iteration-aware evaluation protocols for small datasets. Furthermore, the residual advantage of episodic sampling is consistent with an implicit regularization effect of class-balanced batches, offering a low-cost, model-agnostic strategy for class-imbalanced medical image segmentation. Code is available at https://github.com/iasonsky/episodic-sampling.

Iason Skylitsis, Dimitrios Karkalousos, Ivana Išgum

Department of Biomedical Engineering & Physics Amsterdam University Medical Center Amsterdam, The Netherlands · Informatics Institute, Faculty of Science University of Amsterdam Amsterdam, The Netherlands · Department of Radiology Mayo Clinic Rochester, United States

Class-Imbalanced LearningImage SegmentationMedical Image Segmentation
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May 19, 2026

X-Ray cardiac angiographic vessel segmentation based on pixel classification using machine learning and region growing

This work proposes a pixel-classification approach for vessel segmentation in x-ray angiograms. The proposal uses textural features such as anisotropic diffusion, features based on the Hessian matrix, mathematical morphology and statistics. These features are extracted from the neighborhood of each pixel. The approach also uses the ELEMENT methodology, which consists of creating a pixel-classification controlled by region-growing where the result of the classification affects further classifications of pixels. The Random Forests classifier is used to predict whether the pixel belongs to the vessel structure. The approach achieved the best accuracy in the literature (95.48%) outperforming unsupervised state-of-the-art approaches.

E O Rodrigues, L O Rodrigues, J J Lima +6

Department of Academic Informatics (DAINF), Universidade Tecnologica Federal do Parana (UTEPR), Pato Branco, Parana, Brazil · Graduate Program of Applied Sciences to Health Products, Universid ade Federal Fluminense(UFF), Niteroi, Rio de Janeiro, Brazil · Primary Health Care, Pato Branco Prefecture, Parana, Brazil +1

Image SegmentationMedical ImagingMedical Image SegmentationCoronary Artery SegmentationSemantic Segmentation
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May 19, 2026

Cardiac fat segmentation using computed tomography and an image-to-image conditional generative adversarial neural network

In recent years, research has highlighted the association between increased adipose tissue surrounding the human heart and elevated susceptibility to cardiovascular diseases such as atrial fibrillation and coronary heart disease. However, the manual segmentation of these fat deposits has not been widely implemented in clinical practice due to the substantial workload it entails for medical professionals and the associated costs. Consequently, the demand for more precise and time-efficient quantitative analysis has driven the emergence of novel computational methods for fat segmentation. This study presents a novel deep learning-based methodology that offers autonomous segmentation and quantification of two distinct types of cardiac fat deposits. The proposed approach leverages the pix2pix network, a generative conditional adversarial network primarily designed for image-to-image translation tasks. By applying this network architecture, we aim to investigate its efficacy in tackling the specific challenge of cardiac fat segmentation, despite not being originally tailored for this purpose. The two types of fat deposits of interest in this study are referred to as epicardial and mediastinal fats, which are spatially separated by the pericardium. The experimental results demonstrated an average accuracy of 99.08% and f1-score 98.73 for the segmentation of the epicardial fat and 97.90% of accuracy and f1-score of 98.40 for the mediastinal fat. These findings represent the high precision and overlap agreement achieved by the proposed methodology. In comparison to existing studies, our approach exhibited superior performance in terms of f1-score and run time, enabling the images to be segmented in real time.

Guilherme Santos da Silva, Dalcimar Casanova, Jefferson Tales Oliva +1

Academic Department of Informatics, Universidade Tecnoldgica Federal do Parand (UTFPR), Pato Branco, 85503-390, Brasil · Graduate Program of Production and Systems Engineering, Universidade Tecnológica Federal do Parand (UTFPR), Pato Branco, 85503-390, Brazil

Medical Image Segmentation
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May 19, 2026

WoundFormer: Multi-Scale Spatial Feature Fusion for Multi-Class Wound Tissue Segmentation

Chronic wounds such as diabetic foot ulcers and pressure injuries require accurate tissue-level assessment to guide treatment planning and monitor healing progression. While deep learning methods have advanced automated wound analysis, most existing approaches focus on binary segmentation and inadequately model heterogeneous tissue composition due to high intra-class variability and limited annotated data. Multi-class wound tissue segmentation, therefore, remains a challenging and clinically relevant problem. We propose WoundFormer, a transformer-based framework that enhances hierarchical spatial feature fusion for multi-class wound tissue segmentation. Specifically, we replace the standard SegFormer decoder with a spatially-preserving multi-scale aggregation head that maintains feature topology during cross-scale integration and strengthens contextual interactions through convolutional fusion. This design improves boundary localization and discrimination between visually similar tissue categories while preserving transformer efficiency. We evaluate WoundFormer on the WoundTissueSeg dataset (147 images, six tissue classes) and a second benchmark (DFUTissue dataset). The proposed method achieves an overall Dice score of 81.9%, outperforming strong CNN- and transformer-based baselines by up to 4.3 Dice points on the WoundTissueSeg benchmark, with consistent improvements across minority tissue classes. These results indicate that explicit modeling of hierarchical spatial interactions enhances transformer representations for heterogeneous wound tissue segmentation and supports more reliable quantitative wound assessment.

Muhammad Ashad Kabir, Rabin Dulal

School of Computing, Mathematics and Engineering, Charles Sturt University, NSW, Australia

Multi-Scale Feature FusionMedical Image Segmentation
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May 19, 2026

MedCRP-CL: Continual Medical Image Segmentation via Bayesian Nonparametric Semantic Modality Discovery

Medical image segmentation faces a fundamental challenge in continual learning: data arrives sequentially from heterogeneous sources, yet effective continual learning requires discovering which tasks share sufficient structure to benefit from joint learning. Existing methods either apply uniform constraints across all tasks, causing catastrophic forgetting when tasks conflict, or require predefined task groupings that cannot anticipate future task diversity. We introduce MedCRP-CL, a framework that performs online task structure discovery and structure-aware continual learning. Leveraging the Chinese Restaurant Process (CRP), our method dynamically infers task groupings from clinical text prompts as tasks arrive, without requiring predefined cluster counts or access to future tasks. We term these discovered groupings semantic modalities, as they capture finer-grained structure than physical imaging modalities by integrating anatomical region and pathological context. Guided by this discovered structure, we maintain semantic modality-specific LoRA adapters regularized by intra-modality EWC, ensuring parameter isolation across dissimilar task groups while facilitating knowledge transfer within similar ones. The framework is also replay-free, storing only aggregate statistics rather than raw patient data. Experiments on 16 medical segmentation tasks across four imaging modalities demonstrate that MedCRP-CL achieves 73.3% Dice score with only 4.1% forgetting, outperforming the best baseline by 8.0% while requiring 6×\times fewer parameters. Code is available at https://github.com/zygao930/MedCRP-CL.

Ziyuan Gao

University College London, London, United Kingdom

Interactive Medical Image SegmentationImage SegmentationMedical Image Segmentation
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May 19, 2026

WBCAtt+: Fine-Grained Pixel-Level Morphological Annotations for White Blood Cell Images

The microscopic examination of white blood cells (WBCs) plays a fundamental role in pathology and is essential for diagnosing blood disorders such as leukemia and anemia. To support further research on WBC images, multiple datasets have been proposed. However, they mainly annotate cell categories, and lack detailed morphological characteristics that pathologists use to explain their interpretations of cells. To address this gap, we introduce WBCAtt+, a novel dataset of WBC images densely annotated with 11 morphological attributes and five pixel-level cell components. With 113k image-level labels and 10k segmentation maps, WBCAtt+ is the first to provide comprehensive annotations for WBC images. Leveraging this dataset, we provide baseline models for attribute recognition and semantic segmentation. We also design an attribute recognition model to incorporate compositional structure of cells, further improving the recognition performance. Lastly, we showcase various applications enabled by our dataset, such as explainable AI models, including counterfactual example generation. \revision{The dataset and code are publicly available\footnote{https://doi.org/10.57967/hf/8143}}.

Satoshi Tsutsui, Winnie Pang, Shuting He +1

Rapid-Rich Object Search (ROSE) Lab, School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore · Shanghai University of Finance and Economics, Shanghai, China

Medical Image AnalysisMedical Image SegmentationMedical Image Benchmarks
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May 18, 2026

MedFM-Robust: Benchmarking Robustness of Medical Foundation Models

Medical foundation models have achieved remarkable clinical performance, yet their robustness under real-world perturbations remains underexplored. We present a robustness benchmark comprising 40 perturbation types (12 base, 28 medical-specific) across eight imaging modalities, evaluating five VLMs (LLaVA-Med, MedGemma, MedGemma-1.5, Gemini-2.5-flash and GPT-4o-mini) on VQA, visual grounding, and captioning, alongside two segmentation models (MedSAM, SAM-Med2D) with five fine-tuning strategies. Our findings reveal: (1) Fine-tuning strategy dominates robustness, with LoRA exhibiting nearly double the degradation of full fine-tuning, while SAM-Med2D's Adapter offers favorable efficiency-robustness trade-off. (2) Medical-specific perturbations disproportionately damage segmentation, with 9 of 15 top corruptions being domain-specific. (3) LoRA-tuned visual grounding drops over 40 points, whereas zero-shot captioning remains stable (<7% drop). Zero-shot VQA shows model-dependent robustness--medical models drop under 20% while Gemini-2.5-flash drops 54%. General-purpose VLMs achieve higher VQA accuracy but fail on grounding; among medical VLMs, MedGemma demonstrates the best overall stability. These results provide deployment guidelines and underscore the necessity of domain-specific robustness evaluation for medical AI. Our code is available at: https://abnerai.github.io/MedFM-Robust.

Xiangxiang Cui, Tianjin Huang, Yifang Wang +2

Beijing Normal University, China · University of Exeter, United Kingdom · University College London, United Kingdom +2

Multimodal RobustnessNeural Network RobustnessVision Foundation Model AdaptationMedical VLMsMedical Image SegmentationMedical Image Benchmarks
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May 18, 2026

Speech-Guided Multimodal Learning for Vocal Tract Segmentation in Real-Time MRI

Segmenting vocal tract articulators in real-time MRI (rtMRI) is a challenging dynamic image segmentation problem characterized by low contrast, rapid motion, and limited spatial resolution. However, while rtMRI acquisitions may provide synchronized acoustic signals, existing methods discard this information, and the few multimodal approaches that incorporate audio cannot be deployed when audio is unavailable. We propose a three-stage framework that leverages acoustic and phonological supervision during training while requiring only the rtMRI image at inference: phonological representations are converted into spatial bounding-box priors for articulator localization, visual and acoustic encoders are aligned via dual-level cross-modal contrastive pretraining, and the learned representations are fused through a cross-attention decoder, effectively transferring multimodal knowledge into a single-modality inference pipeline. Evaluated on 75-Speaker~Annot-16 and USC-TIMIT datasets, our method outperforms existing unimodal and multimodal methods, demonstrating that multimodal supervision provides transferable benefits for precise and clinically deployable vocal tract segmentation.

Daiqi Liu, Lukas Mulzer, Md Hasan +11

Pattern Recognition Lab, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany · Smart Imaging Lab, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany · Harvard Medical School / Massachusetts General Hospital, Boston, USA +3

Cross-Modality Medical Image SegmentationMagnetic Resonance ImagingMedical Image SegmentationMultimodal Fusion
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May 18, 2026

Lost in the Folds: When Cross-Validation Is Not a Deep Ensemble for Uncertainty Estimation

Ensemble disagreement is widely used as a proxy for epistemic uncertainty in medical image segmentation. In practice, many studies form ensembles via K-fold cross-validation (CV), yet refer to them as ``deep ensembles'' (DE). Because CV members are trained on different data subsets, their disagreement mixes seed-driven variability with data-exposure effects, which can change how uncertainty should be interpreted. We audit recent segmentation uncertainty studies and find that terminology--implementation mismatches are common. We then compare a standard 5-fold CV ensemble to a 5-member DE (fixed training set, different random seeds) under otherwise identical configurations on three multi-rater segmentation datasets spanning three modalities. We evaluate uncertainty for calibration, failure detection, ambiguity modeling, and robustness under distribution shift. DE match segmentation accuracy while improving calibration and failure detection, whereas CV ensembles sometimes correlate more strongly with inter-rater variability on the studied datasets. Thus, ensemble construction should be chosen to match the research question: DE for reliability-oriented use (e.g., selective referral/failure detection) and CV ensembles as a proxy for ambiguity. We provide a lightweight nnU-Net modification enabling DE training within the default pipeline.

Tristan Kirscher, Markus Bujotzek, Yannick Kirchhoff +5

ICube, Institut Strauss, DKFZ · ICube Laboratory, CNRS UMR-7357, University of Strasbourg, Strasbourg, France · CLCC Institut-Strauss, Strasbourg, France +6

Deep EnsemblesMedical Image SegmentationSegmentation Uncertainty EstimationUncertainty CalibrationCross-Validation
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May 18, 2026

Patch-MoE Mamba: A Patch-Ordered Mixture-of-Experts State Space Architecture for Medical Image Segmentation

CNN- and Transformer-based architectures have achieved strong performance in medical image segmentation, but CNNs are limited in modeling long-range dependencies, while Transformers often suffer from quadratic computational and memory complexity. State space models, especially Mamba-based networks, offer an efficient alternative with linear sequence complexity. However, existing Mamba segmentation models still face two limitations: pixel-wise directional scanning can disrupt local 2D spatial structure, and simple summation-based fusion of scan directions cannot adapt well to diverse object sizes, shapes, and boundaries. To address these issues, we propose Patch-MoE Mamba, a patch-ordered mixture-of-experts state space architecture for medical image segmentation. It introduces a hierarchical patch-ordered scanning mechanism that preserves local spatial neighborhoods while capturing multi-scale context, and an MoE-based directional fusion module that adaptively combines multiple Mamba scanner outputs using four directional experts, a learnable concatenation expert, and residual directional aggregation. Experiments on five public polyp segmentation benchmarks and the ISIC 2017/2018 skin lesion segmentation datasets demonstrate the effectiveness and generality of Patch-MoE Mamba.

Diego Adame, Fabian Vazquez, Jose A. Nunez +7

University of Texas Rio Grande Valley, Edinburg, TX 78539, USA

MambaImage SegmentationPolyp SegmentationMedical Image SegmentationSkin Lesion SegmentationMixture-of-Experts Models
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May 17, 2026

VISTA: Variance-Gated Inter-Sequence Test-Time Adaptation for Multi-Sequence MRI Segmentation

Deploying multi-sequence magnetic resonance imaging (MRI) segmentation models to new clinical environments is challenging due to variations in scanners and acquisition protocols. Although existing TTA methods handle basic per-modality shifts, they often fail under a fundamental dual-shift problem, as their adaptation signals fail to capture modality-interaction shifts that disrupt inter-sequence consistency. To address this, we propose Variance-gated Inter-Sequence Test-time Adaptation (VISTA), a source-free framework that tackles modality-interaction shifts. First, we design an Inter-Sequence Intervention Generator (ISIG) that generates a set of consistency probes by swapping low-frequency spectra and entropy-localized patches across sequences, preserving anatomical semantics while challenging inter-sequence dependencies. Second, we introduce Cross-View Disagreement-Aware Pseudo Labeling (CDPL), which establishes a voxel-wise reliability metric using cross-view disagreement variance to dynamically gate self-training and enforce interventional consistency, encouraging the network to rely on robust anatomical semantics. Extensive experiments adapting from standard adult MRI (BraTS-GLI-Pre) to African low-field (BraTS-SSA) and pediatric (BraTS-PED) cohorts show improved performance over competing methods under clinical shifts, achieving absolute Dice improvements of +1.89% (SSA) and +2.82% (PED) over the source model. The code is available at https://github.com/dzp2095/VISTA.

Zhipeng Deng, Jiale Zhou, Wenhan Jiang +4

Westlake University, Hangzhou, China · Hokkaido University, Sapporo, Japan · The Chinese University of Hong Kong, Hong Kong SAR, China +1

Multi-View ConsistencyTest-Time AdaptationMagnetic Resonance ImagingMedical Image Segmentation
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May 17, 2026

RadGenome-Anatomy: A Large-Scale Anatomy-Labeled Chest Radiograph Dataset via Physically Grounded Volumetric Projection

Anatomical structure labels for chest radiographs are essential for medical image segmentation and a broad range of downstream diagnostic tasks. However, annotating anatomy directly on 2D chest radiographs is labor-intensive and intrinsically ambiguous, as 3D anatomical structures are projected onto a single 2D plane where boundaries may overlap, be occluded, or appear only partially visible. Consequently, existing anatomy-labeled chest radiograph datasets remain limited in scale, anatomy coverage, and label reliability. To address these limitations, we introduce RadGenome-Anatomy, the largest anatomy-labeled chest radiograph dataset, containing over 10 million segmentation masks across 210 anatomical structures in 25,692 studies. It is constructed by projecting large-scale 3D anatomical masks from CT volumes into 2D radiographic space through canonical radiographic geometry. This shifts annotation from directly tracing uncertain 2D boundaries to defining anatomy in volumetric space, where structures that overlap or become partially invisible in radiographs remain spatially separable. As a result, each 2D mask represents the physically grounded projected footprint of a volumetrically defined structure. The scale and broad anatomical coverage of RadGenome-Anatomy, including structures that are overlapping, partially visible, or difficult to delineate directly, enable research on geometric measurements as explicit evidence for chest radiograph interpretation. We demonstrate this by training XAnatomy to predict structure-specific masks and derive clinically relevant measurements, achieving diagnostic accuracies of 96.4%, 95.6%, and 89.2% for cardiomegaly, kyphosis, and scoliosis, respectively.

Shuchang Ye, Mingyuan Meng, Hao Wang +2

The University of Sydney · Zhongguancun Academy · Shanghai Jiao Tong University +1

Medical ImagingMedical Image SegmentationMedical Image Benchmarks
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May 15, 2026

TriALS: Triphasic-Aided Liver Lesion Segmentation Benchmark in Non-Contrast CT

Automated segmentation of liver lesions on non-contrast computed tomography (NCCT) is clinically important but fundamentally challenging, particularly in low-resource settings across Africa and Asia where contrast agents are frequently unavailable. Progress has been limited by the absence of annotated NCCT benchmarks. Here we describe the TriALS challenge for automated liver lesion segmentation under contrast-limited conditions, supported by a multi-centre dataset of 150 cases with four-phase CT acquisitions (600 volumes) from Egyptian and Chinese institutions. Algorithms were evaluated on 70 cases from three institutions, including an independent external cohort. The top-performing method achieved a mean venous-phase Dice of 0.754, consistent with human-level performance, yet dropped to 0.57 on NCCT. On external validation, the leading method outperformed off-the-shelf models by up to 28% in Dice on NCCT. Algorithm performance was most strongly predicted by training data scale and pre-training strategy. A cross-year comparison exposed a persistent perceptual barrier on NCCT that scaling pre-training alone cannot overcome. Data, annotations, and code are available at https://github.com/xmed-lab/TriALS.

Marawan Elbatel, Mohamed Ghonim, Jiaji Mao +62

Image SegmentationMedical Image SegmentationComputed TomographyMedical Image Benchmarks
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May 15, 2026

DepthPolyp: Pseudo-Depth Guided Lightweight Segmentation for Real-Time Colonoscopy

Accurate polyp segmentation in colonoscopy is essential for early colorectal cancer detection, yet real-world clinical environments pose persistent challenges such as motion blur, specular reflections, and illumination instability. Most existing methods are optimized on clean benchmark images and suffer noticeable performance degradation when deployed in authentic surgical scenarios. We propose DepthPolyp, a lightweight and robust segmentation framework based on pseudo-depth-guided multi-task learning and efficient feature modulation. The architecture combines hierarchical Ghost factorization for compact feature generation, Interleaved Shuffle Fusion for low-cost cross-scale interaction, and Dynamic Group Gating for adaptive group-wise feature weighting. Extensive experiments demonstrate that DepthPolyp achieves strong cross-dataset generalization when trained on degraded data and evaluated on both clean and noisy target domains, consistently outperforming lightweight baselines and remaining competitive with substantially larger models. In real surgical video evaluation on PolypGen, DepthPolyp achieves better segmentation performance than models up to 20×20\times larger while preserving real-time inference speed. With only 3.57M parameters and 0.86 GMACs, the proposed method runs at over 180 FPS on mobile devices, making it well suited for real-time deployment in resource-constrained clinical environments. Code and pretrained weights are available at: https://github.com/ReaganWu/DepthPolyp/

Zhuoyu Wu, Wenhui Ou, Lexi Zhang +5

CyPhi AI Lab, Monash University, Malaysia Campus, Malaysia · Department of Electronic & Computer Engineering, Hong Kong University of Science & Technology, Hong Kong, P.R. China · Harbin Institute of Technology, Harbin, P.R. China +1

EndoscopyImage SegmentationDomain GeneralizationPolyp SegmentationMedical Image SegmentationSemantic Segmentation
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May 15, 2026

Segmentation, Detection and Explanation: A Unified Framework for CT Appearance Reasoning

Recent progress in deep learning has significantly advanced CT image analysis, particularly for segmentation tasks. However, these advances are largely confined to image-level pattern recognition, with most methods lacking explicit anatomical or contextual reasoning. Large vision-language models introduce linguistic context into image analysis, yet most approaches typically focus on a single task, which is insufficient for clinical workflow analysis that requires multiple fine-grained types of analysis, such as anatomy detection and segmentation. In this paper, we propose a unified autoregressive framework that integrates language-guided visual reasoning into CT interpretation. Our method introduces task-routing tokens that trigger detection and segmentation heads conditioned on the hidden states of a large vision-language model, enabling coherent generation of visual outputs (e.g., masks and bounding boxes) and textual reasonings. To progressively enhance localisation accuracy and semantic clarity, we further design a "closer-look" mechanism that allows the model to perform progressive coarse-to-fine visits to regions of interest under refined fields of view. To support model training and evaluation, we curated a new multimodal CT dataset containing pixel-wise masks, bounding boxes, spatial prompts, and structured descriptions for visual objects constructed through an AI-assisted annotation process with human verification. Experiments on public benchmarks demonstrate consistent improvements over the SoTA, achieving up to 1.0% Dice on BTCV and 1.7% Dice on MosMed+, while additionally providing appearance reasoning outputs. The code and dataset will be available.

Yuyuan Liu, Can Peng, Yingyu Yang +3

Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford

Image SegmentationMedical VLMsMedical Image SegmentationComputed TomographyMedical Image Localization
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May 15, 2026

Semi-MedRef: Semi-Supervised Medical Referring Image Segmentation with Cross-Modal Alignment

Medical referring image segmentation (MRIS) requires pixel-level masks aligned with textual descriptions of anatomical locations, making annotation costly in low-label regimes. Semi-supervised learning (SSL) can mitigate this burden by leveraging unlabeled data, but its success hinges on maintaining reliable image-text alignment under perturbations. Most existing SSL-based referred segmentation methods use either independent or simplistic multi-modal perturbations (e.g., left-right flips), without fully addressing cross-modal alignment under strong augmentation, while CutMix, highly effective in single-modal SSL, remains underexplored in multi-modal settings due to its tendency to disrupt image-text coherence. We propose Semi-MedRef, a teacher-student SSL framework designed to explicitly maintain consistency between medical images and positional language through three alignment-preserving components: T-PatchMix, a cross-modal CutMix-style augmentation that synchronizes patch mixing with referring expressions via position-constrained and probability-driven rules; PosAug, a position-aware text augmentation that masks or fuzzes anatomical phrases; and ITCL, a position-guided image-text contrastive learning module, which leverages positional pseudo-labels to construct soft anatomical positives and strengthen medically grounded cross-modal alignment. Experiments on QaTa-COV19 and MosMedData+ demonstrate that Semi-MedRef consistently outperforms both fully supervised and semi-supervised baselines across all label regimes.

Yuchen Li, Zhen Zhao, Yi Liu +1

The University of Sydney, Sydney, NSW 2006, Australia · Shanghai Artificial Intelligence Laboratory, Shanghai, China · Changzhou University, Changzhou, China

Interactive Medical Image SegmentationCross-Modal AlignmentReferring Image SegmentationSemi-Supervised Medical Image SegmentationMedical Image SegmentationMultimodal Contrastive Learning
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May 15, 2026

Evaluation of Anatomical Shape Priors in Deep Learning-Based Cardiac Multi-Compartment Segmentation

Whole-heart multi-compartment CT segmentation is clinically important, but standard CNNs do not explicitly enforce anatomical plausibility. Based on statistics derived from the training data, we evaluate whether lightweight explicit shape priors, implemented as shape-aware losses and spatial label distribution heatmap-guided U-Net variants, improve 3D cardiac segmentation on MM-WHS CT and WHS++. Across all experiments, a standard 3D U-Net surprisingly remained a very strong baseline, with handcrafted priors yielding at best marginal and inconsistent changes and often degrading performance. These results suggest that the baseline already captures substantial implicit anatomical regularities and that future gains will likely require more expressive learned priors rather than simple handcrafted anatomical shape constraints.

Michael Hudler, Franz Thaler, Martin Urschler

Institute for Medical Informatics, Statistics and Documentation Medical University of Graz

U-NetMedical Image Segmentation3D Medical Image Segmentation
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May 14, 2026

Beyond Instance-Level Self-Supervision in 3D Multi-Modal Medical Imaging

Self-supervised pre-training methods in medical imaging typically treat each individual as an isolated instance, learning representations through augmentation-based objectives or masked reconstruction. They often do not adequately capitalize on a key characteristic of physiological features: anatomical structures maintain consistent spatial relationships across individuals (instances), such as the thalamus being medial to the basal ganglia, regardless of variations in brain size, shape, or pathology. We propose leveraging this cross-instance topological consistency as a supervisory signal. The challenge arises from the inherent variability in medical imaging, which can differ significantly across instances and modalities. To tackle this, we focus on two alignment regimes. (i) Intra-instance: with pixel-level correspondences available, a cross-modal triplet objective explicitly preserves local neighborhood topology. (ii) Inter-instance: without such supervision, we derive pseudo-correspondences to control partial neighborhood alignment and prevent topology collapse across modalities. We validate our approach across 7 downstream multi-modal tasks, achieving average improvements of 1.1% and 5.94% in segmentation and classification tasks, respectively, and demonstrating significantly better robustness when modalities are missing at test time.

Tan Pan, Shuhao Mei, Yixuan Sun +8

Fudan University, China · Shanghai Academy of AI for Science, China · Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore +2

Representation LearningMultimodal RobustnessSelf-Supervised Pre-TrainingCross-Modal AlignmentMedical Image SegmentationTopological Representation Learning
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May 14, 2026

Med-DisSeg: Dispersion-Driven Representation Learning for Fine-Grained Medical Image Segmentation

Accurate medical image segmentation is fundamental to precision medicine, yet robust delineation remains challenging under heterogeneous appearances, ambiguous boundaries, and large anatomical variability. Similar intensity and texture patterns between targets and surrounding tissues often lead to blurred activations and unreliable separation. We attribute these failures to representation collapse during encoding and insufficient fine grained multi scale decoding. To address these issues, we propose Med DisSeg, a dispersion driven medical image segmentation framework that jointly improves representation learning and anatomical delineation. Med DisSeg combines a lightweight Dispersive Loss with adaptive attention for fine grained structure segmentation. The Dispersive Loss enlarges inter sample margins by treating in batch hidden representations as negative pairs, producing well dispersed and boundary aware embeddings with negligible overhead. Based on these enhanced representations, the encoder strengthens structure sensitive responses, while the decoder performs adaptive multi scale calibration to preserve complementary local texture and global shape information. Extensive experiments on five datasets spanning three imaging modalities demonstrate consistent state of the art performance. Moreover, Med DisSeg achieves competitive results on multi organ CT segmentation, supporting its robustness and cross task applicability.

Zhiquan Chen, Haitao Wang, Guowei Zou +1

School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China · Guangdong Key Laboratory of Big Data Analysis and Processing, Guangzhou, China

Image SegmentationMetric LearningMedical Image SegmentationMedical Image Representation Learning
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May 14, 2026

SpectraFlow: Unifying Structural Pretraining and Frequency Adaptation for Medical Image Segmentation

Medical image segmentation remains challenging in low-data regimes, where scarce annotations often yield poor generalization and ambiguous boundaries with missing fine structures. Recent self-supervised pretraining has improved transferability, but it often exhibits a texture bias. In contrast, accurate segmentation is inherently geometry-aware and depends on both topological consistency and precise boundary preservation. To address this problem, we propose a two-stage framework that couples structure-aware encoder pretraining with boundary-oriented decoding. In Stage-1, we aim to learn structure-aware representations for downstream segmentation in low-data regimes. To this end, we propose Mixed-Domain MeanFlow Pretraining, which aligns images and binary masks in a shared latent space through latent transport regression, where masks act as conditional structural guidance rather than prediction targets, making the pretraining task-agnostic. To further improve training stability under scarce supervision, we incorporate a lightweight Dispersive Loss to prevent representation collapse. In Stage-2, we fine-tune the pretrained encoder with a lightweight decoder that combines Direct Attentional Fusion for adaptive cross-scale gating and Frequency-Directional Dynamic Convolution for high-frequency boundary refinement under appearance variation. Experiments on ISIC-2016, Kvasir-SEG, and GlaS demonstrate consistent gains over state-of-the-art methods, with improved robustness in low-data settings and sharper boundary delineation.

Zhiquan Chen, Haitao Wang, Guowei Zou +1

School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China · Guangdong Key Laboratory of Big Data Analysis and Processing, Guangzhou, China

Flow MatchingImage SegmentationSelf-Supervised Pre-TrainingMedical Image SegmentationBoundary-Aware SegmentationMedical Image Representation Learning+1
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May 14, 2026

Towards Real-Time Autonomous Navigation: Transformer-Based Catheter Tip Tracking in Fluoroscopy

Purpose: Mechanical thrombectomy (MT) improves stroke outcomes, but is limited by a lack of local treatment access. Widespread distribution of reinforcement learning (RL)-based robotic systems can be used to alleviate this challenge through autonomous navigation, but current RL methods require live device tip coordinate tracking to function. This paper aims to develop and evaluate a real-time catheter tip tracking pipeline under fluoroscopy, addressing challenges such as low contrast, noise, and device occlusion. Methods: A multi-threaded pipeline was designed, incorporating frame reading, preprocessing, inference, and post-processing. Deep learning segmentation models, including U-Net, U-Net+Transformer, and SegFormer, were trained and benchmarked using two-class and three-class formulations. Post-processing involved two-step component filtering, one-pixel medial skeletonization, and greedy arc-length path following with contour fall-back. Results: On manually-labeled moderate complexity fluoroscopic video data, the two-class SegFormer achieved a mean absolute error of 4.44 mm, outperforming U-Net (4.60 mm), U-Net+Transformer (6.20 mm) and all three-class models (5.19-7.74 mm). On segmentation benchmarks, the system exceeded state-of-the-art CathAction results with improvements of up to +5% in Dice scores for three-segmentation. Conclusion: The results demonstrate that the proposed multi-threaded tracking framework maintains stable performance under challenging imaging conditions, outperforming prior benchmarks, while providing a reliable and efficient foundation for RL-based autonomous MT navigation.

Harry Robertshaw, Yanghe Hao, Weiyuan Deng +6

Surgical & Interventional Engineering School of Biomedical Engineering & Imaging Sciences2026 Kings College London London · School of Engineering & Materials Science Queen Mary London14 London

Medical Image SegmentationSemantic SegmentationMedical Image Localization
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May 14, 2026

Automatic Landmark-Based Segmentation of Human Subcortical Structures in MRI

Precise segmentation of brain structures in magnetic resonance imaging (MRI) is essential for reliable neuroimaging analysis, yet voxel-wise deep models often yield anatomically inconsistent results that diverge from expert-defined boundaries. In this research, we propose a landmark-guided 3D brain segmentation approach that explicitly mimics the manual segmentation protocol of the Harvard--Oxford Atlas. A Global-to-Local network automatically detects 16 landmarks representing key subcortical reference points. Then, a semantic segmentation model produces a coarse segmentation of 12 anatomical labels, each grouping multiple subcortical regions. Finally, a landmark-driven post-processing step separates these 12 labels into 26 distinct structures by enforcing local anatomical constraints. Experimental results demonstrate consistent improvements in boundary accuracy. Overall, integrating learned landmarks aligns segmentations more closely with manual protocols.

Ahmed Rekik, R. Jarrett Rushmore, Sylvain Bouix +1

1 ´Ecole de technologie sup´erieure (´ETS), Montr´eal, Canada · 2Boston University School of Medicine, Boston, MA, USA · 3Signal and Smart Systems Lab (L3S), National School of Engineering of Tunis, University of Tunis El Manar, Tunisia

Image SegmentationAnatomical Landmark DetectionMedical Image Segmentation3D Medical Image SegmentationBrain MRI
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May 13, 2026

MedCore: Boundary-Preserving Medical Core Pruning for MedSAM

Medical segmentation foundation models such as SAM and MedSAM provide strong prompt-driven segmentation, but their image encoders are still too large for many clinical settings. Compression is also risky in medicine because a model can keep high Dice while losing boundary fidelity. We propose MedCore, a structured pruning framework for MedSAM. The main idea is to preserve two kinds of structures: structures that became important during SAM-to-MedSAM adaptation, and structures that have high boundary leverage. We identify the first type by a dual-intervention score that compares zeroing a group with resetting it to its original SAM weight. We identify the second type by boundary-aware Fisher estimation. We also introduce a boundary leverage principle, which shows that compression-induced boundary displacement is controlled by logit perturbation on the boundary divided by the logit spatial gradient. This principle explains why boundary metrics can degrade even when Dice remains high. On polyp segmentation benchmarks, MedCore reduces parameters by 60.0% and FLOPs by 58.4% while achieving Dice 0.9549, Boundary F1 0.6388, and HD95 5.14 after recovery fine-tuning. It also reaches 86.6% parameter reduction and 90.4G FLOPs with strong boundary quality. Our analysis further shows that MedSAM lies in a head-fragile boundary regime: head-pruning steps have 2.887 times larger 95th-percentile boundary leverage than MLP-pruning steps, and this logit-level effect is consistent with BF1 and HD95 degradation. Our code is available at https://github.com/cenweizhang/MedCore.

Cenwei Zhang, Suncheng Xiang, Lei You

Shanghai Jiao Tong University Shanghai, China · Technical University of Denmark Ballerup, Denmark

Model CompressionImage SegmentationMedical Imaging Foundation ModelsHealthcareMedical Image SegmentationStructured Pruning+1
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May 12, 2026

Optimization in Sparse 2D to Dense 3D Weakly Supervised Learning: Application to Multi-Label Segmentation of Large ex vivo MRI Data

INTRODUCTION | Fully supervised 3D segmentation of high-resolution ex vivo MRI is limited by the prohibitive cost of volumetric annotation, forcing reliance on sparse 2D slices. Weakly supervised Sparse-to-Dense frameworks bridge this gap, but guidelines remain ambiguous regarding human-centric visual enhancements and transferring optimization strategies across dimensions. We analyze divergent regularization needs for multi-class segmentation of high-resolution ex vivo spinal cord MRI. METHODS | We used 9.4T MRI of multiple sclerosis spinal cords (>104,000 slices) with sparse annotations (428 slices). A 2D Teacher trained on sparse slices generated dense pseudo-labels to train a 3D Student. We systematically evaluated the impact of human-centric preprocessing, spatial augmentation, and soft-label regularization on both architectures. RESULTS | We identified a critical divergence in training dynamics. The 2D Teacher required strong spatial augmentation and soft-labeling to overcome data scarcity, improving White Matter Lesion Dice scores by >11 points. However, propagating these techniques to the 3D Student degraded its performance. Furthermore, human-centric preprocessing (e.g., CLAHE) disrupted global statistical cues, dropping Gray Matter Lesion Dice scores by ~25 points. DISCUSSION | Our study highlights a perception divergence (human-centric contrast enhancement harms machine models) and a regularization conflict across dimensions. 3D architectures trained on dense pseudo-labels exhibit fundamentally different optimization landscapes than 2D counterparts and require distinct, conservative regularization. Code and models: https://github.com/ivadomed/model_seg_sc-gm-lesion_human_ms_exvivo_t2star.

Paul Hoareau, Kuan Yi Wang, Brandon Bujak +6

NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada · ´Ecole Centrale de Lyon, Lyon, France · Mila - Quebec AI Institute, Montreal, QC, Canada +9

Weakly Supervised Image SegmentationWeakly Supervised Semantic SegmentationWeakly Supervised LearningMedical Image SegmentationPseudo-Labeling3D Medical Image Segmentation
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May 12, 2026

SEMIR: Semantic Minor-Induced Representation Learning on Graphs for Visual Segmentation

Segmenting small and sparse structures in large-scale images is fundamentally constrained by voxel-level, lattice-bound computation and extreme class imbalance -- dense, full-resolution inference scales poorly and forces most pipelines to rely on fixed regionization or downsampling, coupling computational cost to image resolution and attenuating boundary evidence precisely where minority structures are most informative. We introduce SEMIR (Semantic Minor-Induced Representation Learning), a representation framework that decouples inference from the native grid by learning a task-adapted, topology-preserving latent graph representation with exact decoding. SEMIR transforms the underlying grid graph into a compact, boundary-aligned graph minor through parameterized edge contraction, node deletion, and edge deletion, while preserving an exact lifting map from minor predictions to lattice labels. Minor construction is formalized as a few-shot structure learning problem that replaces hand-tuned preprocessing with a boundary-alignment objective: minor parameters are learned by maximizing agreement between predicted boundary elements and target-specific semantic edges under a boundary Dice criterion, and the induced minor is annotated with scale- and rotation-robust geometric and intensity descriptors and supports efficient region-level inference via message passing on a graph neural network (GNN) with relational edge features. We benchmark SEMIR on three tumor segmentation datasets -- BraTS 2021, KiTS23, and LiTS -- where targets exhibit high structural variability and distributional uncertainty. SEMIR yields consistent improvements in minority-structure Dice at practical runtime. More broadly, SEMIR establishes a framework for learning task-adapted, topology-preserving latent representations with exact decoding for high-resolution structured visual data.

Luke James Miller, Yugyung Lee

Department of Computing, Analytics and Mathematics; University of Missouri-Kansas City, Kansas City, United States.

Graph Structure LearningImage SegmentationGraph CoarseningTopology-Preserving Image SegmentationMedical Image Segmentation3D Medical Image Segmentation+1
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May 12, 2026

Vision Transformer-Conditioned UNet for Domain-Adaptive Semantic Segmentation

Semantic segmentation is essential for analysing anatomical features in biomedical research, yet a performance gap remains for Vision Transformers (ViTs) in the field, particularly for sparse, fine-structured, and low signal-to-noise targets. We attribute this challenge in part to the lightweight pixel decoders commonly used in promptable ViT models, who may lack the local inductive bias needed for high-precision biomedical masks. We bridge this gap by introducing ViTC-UNet, which conditions a UNet on frozen pre-trained ViT representations through learnable tokens and a two-way attention decoder. This combines ViT global visual priors with the local inductive bias and high-resolution decoding capacity of UNets, while avoiding end-to-end ViT fine-tuning even in cross-domain settings. ViTC-UNet outperforms baseline results in semantic segmentation tasks across MRI and CT modalities, demonstrating that structure-conditioned UNet decoding can efficiently adapt large-scale visual priors to high-complexity biomedical segmentation.

Joel Valdivia Ortega, Tingying Peng, Marion Jasnin

Helmholtz AI, Helmoltz Munich, Neuherberg, Germany · Helmholtz Pioneer Campus, Helmholtz Munich, Neuherberg, Germany · School of Computation, Information and Technology, TUM, Garching, Germany +1

Hybrid CNN-Transformer ArchitecturesVision Foundation Model AdaptationMedical Image SegmentationSemantic Segmentation
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May 12, 2026

DiffSegLung: Diffusion Radiomic Distillation for Unsupervised Lung Pathology Segmentation

Unsupervised segmentation of pulmonary pathologies in CT remains an open challenge due to the absence of annotated multi pathology cohorts and the failure of existing diffusion-based methods to exploit the quantitative Hounsfield Unit (HU) signal that physically distinguishes tissue classes. To address this, we propose DiffSegLung,a framework that introduces Diffusion Radiomic Distillation, in which handcrafted radiomic descriptors serve as a physics grounded teacher to shape the bottleneck of a 3D diffusion U-Net via a contrastive objective, transferring pathology discriminative structure into the learned representation without any annotations. At inference, the teacher is discarded and multitimestep bottleneck features are clustered by a Gaussian Mixture Model with HU-guided label assignment, followed by Sobel Diffusion Fusion for boundary refinement. Evaluated on 190 expert annotated axial slices drawn from four heterogeneous CT cohorts, Diff-SegLung improves segmentation across all four pathology classes over unsupervised baselines and improves generation fidelity over prior CT diffusion models.

Rezkellah Noureddine Khiati, Pierre-Yves Brillet, Catalin Fetita

No Institute Given

Image SegmentationSemi-Supervised Medical Image SegmentationDiffusion Models for Medical Image SegmentationMedical Image Segmentation3D Medical Image SegmentationRadiomics
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May 11, 2026

USEMA: a Scalable Efficient Mamba Like Attention for Medical Image Segmentation

Accurate medical image segmentation is an integral part of the medical image analysis pipeline that requires the ability to merge local and global information. While vision transformers are able to capture global interactions using vanilla self-attention, their quadratic computational complexity in the input size remains a struggle for medical image segmentation tasks. Motivated by the dispersion property of vanilla self-attention and recent development of Mamba form of attention, Scalable and Efficient Mamba like Attention (SEMA) utilizes token localization via local window attention to avoid dispersion and maintain focusing, complemented by theoretically consistent arithmetic averaging to capture global aspect of attention. In this work, we present USEMA, a hybrid UNet architecture that merges the local feature extraction ability of convolutional neural networks (CNNs) with SEMA attention. We conduct experiments with USEMA across a variety of modalities and image sizes, demonstrating improved computational efficiency compared to transformer based models using full self-attention, and superior segmentation performance relative to purely convolution and Mamba-based models.

Elisha Dayag, Nhat Thanh Tran, Jack Xin

University of California Irvine, Irvine CA 92697

Image SegmentationHybrid CNN-Transformer ArchitecturesSelf-AttentionU-NetEfficient AttentionMedical Image Segmentation
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