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 31, 2026

ResNet-34 with Lightweight Decoder for Accurate and Efficient Segmentation of Fetal Brain MRI

Accurate segmentation of fetal brain tissues in Magnetic Resonance Imaging (MRI) is critical for early diagnosis of congenital abnormalities and improving prenatal care. However, the task remains difficult because of fetal motion, low tissue contrast, and major anatomical variability throughout gestational ages, particularly in segmenting complex structures such as white matter, gray matter, lateral ventricles, deep gray matter, extra-cerebrospinal fluid, cerebellum, and brainstem. As a solution to these difficulties, this research introduces a novel deep learning model that combines a ResNet-34 encoder with a lightweight decoder leveraging multi-layer perceptron (MLP) modules for adaptive feature refinement. This design specifically enhances the model's ability to preserve anatomical boundaries and mitigate segmentation errors caused by motion artifacts and intensity inhomogeneities. Computational efficiency is achieved by reducing parameter count, employing bilinear upsampling instead of transposed convolutions, and optimizing the decoder for speed without sacrificing accuracy. Trained and validated on the FeTA 2021 dataset using 5-fold cross-validation, the proposed model outperforms baseline architectures such as UNet, UNet++, DeepLabV3, and DeepLabV3+, achieving an average Accuracy of 97.37% with a mean Dice Similarity Coefficient (DSC) of 90.33%, mean Intersection over Union (IoU) of 86.93%, and Precision of 90.83%. Additionally, its fast inference time and reduced computational load make it well-suited for integration into real-time clinical workflows.

Ashiqur Rahman, Muhammad E. H. Chowdhury, Md. Abu Sayed +3

Department of Biomedical Physics and Technology, University of Dhaka, Dhaka, Bangladesh. · Department of Electrical Engineering, College of Engineering, Qatar University, Doha, Qatar. · Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh.

Medical Image SegmentationSemantic SegmentationBrain MRI
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May 31, 2026

AMN: An Adaptive Multi-Scale Fusion Network with Boundary and Uncertainty Modeling for Nuclei Segmentation

Accurate classification of nuclei subtypes in histopathology images is critical for downstream tasks including tumor grading, immune infiltrate quantification, and prognosis prediction. Existing approaches rely on either convolutional or transformer-based encoders in isolation, limiting their ability to simultaneously capture fine-grained local texture and long-range spatial context. We present AMN (Adaptive Multi-Scale Nuclei Network), a dual-encoder segmentation framework that jointly leverages a Swin Transformer and a ResNet-50 feature pyramid, fused via a learned per-channel gating mechanism that dynamically weighs each encoder's contribution at every scale. AMN is trained with a multi-objective loss combining class-weighted focal loss, boundary-aware loss with positive-pixel emphasis, and a novel uncertainty-modulated classification term that suppresses overconfident erroneous predictions. Evaluated on the CoNIC benchmark across seven nuclei classes, AMN achieves a mean Dice of 0.82 and mean F1 of 0.68, with an F1 of 0.67 on the diagnostically challenging lymphocyte class. AMN outperforms eight baseline models spanning pure-CNN, pure-transformer, and recent hybrid architectures: U-Net, ResU-Net, DeepLabV3+, SegNet, ViT-Small, HmsU-Net, ConvFormer-UNet, and BEFUnet. Cross-dataset evaluation on MoNuSeg demonstrates strong generalization without retraining and validating the domain robustness of the learned representations.

Spoorthi M, Suja Palaniswamy

Department of Computer Science & Engineering, Amrita School of Computing, Bengaluru, Amrita Vishwa Vidyapeetham, India

Histopathology Image SegmentationHybrid CNN-Transformer ArchitecturesMulti-Scale Feature FusionMedical Image Segmentation
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May 30, 2026

Single-Channel Tissue Segmentation via Cross-Modal Distillation from Foundation Models

Multiplexed fluorescence microscopy improves tissue segmentation by providing complementary channels including nuclear (DAPI) and membrane (E-cadherin), that together encode richer spatial context than single-channel imaging alone. However, multiplexed models require all channels at inference, limiting deployment where only a subset is available. This work proposes a cross-modal knowledge distillation framework that transfers semantic information from a frozen foundation model teacher processing multiplexed input to a lightweight student operating on the nuclear channel only. The distillation objective combines MSE-based probability matching, boundary-aware supervision, and learnable uncertainty weighting. SAM ViT-H and CellSAM are evaluated as teachers across four U-Net students: Swin-Tiny (27M), ResNet18 (11M), EfficientNet-B0 (5.3M), and MobileNetV3 (1.5M), on TissueNet and BBBC038. On TissueNet, the SAM-distilled Swin-Tiny student achieves Dice 78.36 (plus or minus 1.44), a 13.05-point improvement over the no-KD baseline (65.31 plus or minus 1.35) and 87.9% recovery of teacher oracle performance (89.12 plus or minus 1.21) at a 23x parameter reduction. KD consistently improves all four students by approximately 12 Dice points, confirming architecture-agnostic distillation. SAM ViT-H outperforms CellSAM as teacher across all settings. Cross-dataset evaluation on BBBC038 shows consistent gains without teacher retraining.

Sakib Mohammad, Jarin Ritu, Md Sakhawat Hossain

Department of Engineering Technology Fairmont State University Fairmont, WV, USA · Department of Electrical and Computer Engineering Texas A&M University College Station, TX, USA · Department of Mechanical Engineering Auburn University Auburn, AL, USA

Cross-Modal Knowledge DistillationFluorescence MicroscopyMedical Image SegmentationMicroscopy Image Analysis
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May 30, 2026

Pre-Deployment Robustness Stress Testing for CT Segmentation Systems Using Clinically Motivated Multi-Corruption Augmentation

Deep learning-based CT segmentation systems often achieve high accuracy on clean benchmark images, but their performance may degrade under heterogeneous clinical imaging conditions such as noise, resolution loss, contrast variation, intensity shift, and artifacts. This instability can limit reliable deployment in real-world medical imaging workflows. We propose Robustness via Augmented Multi-corruption Pipeline (RAMP), a robustness-oriented augmentation framework for CT segmentation. RAMP combines anatomically constrained spatial perturbations, CT intensity transformations, and stochastic multi-corruption composition to expose models to clinically plausible image degradation during training. Across two CT segmentation evaluation settings, RAMP achieved the strongest corrupted-image performance and the smallest clean-to-corrupted robustness gap. In the five-organ noisy evaluation benchmark, RAMP improved mean corrupted Dice from 0.610 to 0.753 and reduced the robustness gap from 0.264 to 0.064 compared with the nnU-Net baseline. In Abdomen1K, RAMP improved mean corrupted Dice from 0.633 to 0.789 and reduced the robustness gap from 0.290 to 0.070. Although RAMP did not achieve the highest clean-image Dice, it substantially mitigated worst-case segmentation collapse under severe image degradation. These results suggest that multi-corruption augmentation can serve as a practical pre-deployment strategy for improving the reliability of CT segmentation systems in heterogeneous clinical environments.

CholMin Kanga, Jonghyun Chung, Amanpreet Kaur +2

Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Korea · Google Inc., 1600 Amphitheatre Parkway, Mountain View, 94043, California, United States

Image Corruption RobustnessData AugmentationMedical Image SegmentationComputed Tomography
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May 29, 2026

LegSegNet: A Public Deep Learning System for Lower Extremity CT Tissue Segmentation and Quantification

Lower extremity computed tomography (CT) contains clinically relevant information for body composition analysis, sarcopenia assessment, and musculoskeletal disease monitoring, but extracting these measurements at scale requires accurate tissue segmentation and an automated quantification workflow. Existing public segmentation tools are not designed for comprehensive lower extremity CT analysis, particularly for clinically important inter/intramuscular adipose tissue, and most public methods only provide mask prediction rather than an end-to-end quantification system. To address this problem, we present LegSegNet, a deep learning system for lower extremity CT tissue segmentation and body composition quantification. Given an input CT scan, LegSegNet segments bone, skeletal muscle, subcutaneous adipose tissue, and inter/intramuscular adipose tissue. It then computes quantitative tissue measurements for downstream analysis. We developed the segmentation model using 1,302 manually annotated CT slices and evaluated it on 900 held-out test slices, with all annotations reviewed by radiologists. We benchmark LegSegNet against a broad set of 2D segmentation methods, including CNN-based models, transformer-based models, and finetuned foundation models, and further evaluate its generalization on an external public CT dataset. LegSegNet achieves the best overall segmentation performance, with an average Dice score of 89.31 on the held-out test set. To our knowledge, LegSegNet is the first publicly available end-to-end system for lower extremity CT tissue segmentation and quantification, providing a practical evaluation tool for future computer vision research in medical image analysis. The code and model weights are available at: https://github.com/mazurowski-lab/LegSegNet

Yuwen Chen, Yaqian Chen, Roy Colglazier +4

Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708 · Department of Radiology, Duke University, Durham, NC 27708 · Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27708 +2

Medical Image AnalysisMedical Image SegmentationComputed Tomography
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May 28, 2026

Geodesics with Unified Tangent-constrained Priors and Curvature Regularization

Curvature-penalized geodesic models have proven their effectiveness in image segmentation by computing globally optimal curves. Unfortunately, these models remain susceptible to shortcuts when delineating objects with complex shapes and image intensity distributions, as they lack mechanisms to enforce shape-aware tangent constraints. To address this limitation, we propose a unified geodesic framework that integrates tangent-constrained priors with curvature penalization. The key idea is to formulate tangent admissibility directly within the orientation-lifted space, where path tangents are restricted to spatially varying angular sectors derived from intrinsic shape representatives (ISR) such as skeletons or interior landmarks. This formulation gives rise to a family of tangent-constrained Finslerian metrics, extending the classical curvature-penalized geodesic models while enforcing mandatory tangent constraints. The resulting Hamilton-Jacobi-Bellman (HJB) partial differential equations (PDEs) admit efficient numerical solutions via variants of the fast marching method, preserving the single-pass computational complexity. Experiments on synthetic, natural, and medical images demonstrate that the proposed geodesic framework indeed improves robustness against weak boundaries and topological shortcuts, yielding segmentation results with enhanced shape fidelity compared to existing geodesic models.

Chong Di, Li Liu, Jinglin Zhang +3

Shandong Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China · Yuanshen Rehabilitation Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China · School of Control Science and Engineering, Shandong University, Jinan, Shandong, China +2

Finsler GeometryMedical Image Segmentation
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May 28, 2026

A Novel Global Context-aware Deep Neural Network for Enhanced Brain Tumor Segmentation using Magnetic Resonance Images

Brain cancer's severity necessitates precise brain tumor segmentation, which is crucial for effective brain tumor diagnosis. Manual identification, burdened by high costs, labor, and error risks, highlights the need for automated methods. In this study, we introduce the Global Context-aware Squeeze and Excite Residual UNet (GCSER-UNet), which facilitates a fusion of spatial and channel-wise attention and thus enhances the model's capacity to capture intricate spatial dependencies and contextual information. GCSER-UNet efficiently extracts tumor segments from multimodal MRI slices, delivering exceptional performance. Evaluations on benchmark databases exhibit its superiority, achieving a notable 94 percent dice score on the TCGA LGG dataset, surpassing the state-of-the-art dice score of 91.8 percent. In the BraTS 2020 dataset, the proposed GCSER-UNet ensemble approach yielded dice scores of 95 percent, 92 percent, and 90 percent for the tumor regions - Whole Tumor (W), Tumor Core (T), and Enhancing Tumor (E), respectively. The current state-of-the-art dice scores were 94 percent, 93 percent, and 88 percent. These compelling outcomes highlight the efficacy of GCSER-UNet in precise brain tumor segmentation and thus can aid neurologists in effective brain cancer management and treatment planning.

Sourjya Mukherjee, Ananya Bhattacharjee, R. Murugan

Biomedical Imaging Laboratory, Department of Electronics and Communication Engineering, National Institute of Technology Silchar, Silchar, Assam, India, 788010

U-NetMedical Image SegmentationAttention MechanismsBrain Tumor Segmentation
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May 28, 2026

SwInception -- Local Attention Meets Convolutions

Sparse vision transformers have gained popularity as efficient encoders for medical volumetric segmentation, with Swin emerging as a prominent choice. Swin uses local attention to reduce complexity and yields excellent performance for many tasks but still tends to overfit on small datasets. To mitigate this weakness, we propose a novel architecture that further enhances Swin's inductive bias by introducing Inception blocks in the feed-forward layers. The introduction of these multi-branch convolutions enables more direct reasoning over local, multi-scale features within the transformer block. We have also modified the decoder layers in order to capture finer details using fewer parameters. We demonstrate a performance improvement on eleven different medical datasets through extensive experimentation. We specifically showcase advancements over the previous state-of-the-art backbones on benchmark challenges like the Medical Segmentation Decathlon and Beyond the Cranial Vault. By showing that the existing inductive bias in Swin can be further improved, our work presents a promising avenue for enhancing the capabilities of sparse vision transformers for both medical and natural image segmentation tasks. Code and pre-trained weights can be accessed at https://github.com/Eiphodos/SwInception.

David Hagerman, Roman Naeem, Jakob Lindqvist +3

Chalmers University of technology, 412 96 Gothenburg, Sweden · Zenseact, Lindholmspiren 2, 417 56 Gothenburg, Sweden

Hybrid CNN-Transformer ArchitecturesEfficient ViTsMedical Image Segmentation3D Medical Image Segmentation
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May 28, 2026

Towards the automated segmentation of epicardial and mediastinal fats: A multi-manufacturer approach using intersubject registration and random forest

The amount of fat on the surroundings of the heart is correlated to several health risk factors such as carotid stiffness, coronary artery calcification, atrial fibrillation, atherosclerosis, cancer incidence and others. Furthermore, the cardiac fat varies unrelated to the overall fat of the subject, and, therefore, it reinforces the quantitative analysis of these adipose tissues as being essential. Clinical decision support systems are computer programs capable of evaluating information and providing a corresponding diagnosis or data to complement the physicists' analyses. The aim of this work is to propose a method capable of fully automatically segmenting two types of cardiac adipose tissues that stand apart from each other by the pericardium on CT images obtained by the standard acquisition protocol used for coronary calcium scoring. Much effort was devoted to promote minimal user intervention and ease of reproducibility. The methodology proposed in this work consists of a registration, which will roughly adjust input images to a standard, an extraction of features related to pixels and their surrounding area and a segmentation step based on data mining classification algorithms that define if an incoming pixel is of a certain type. Experimentations showed that the achieved mean accuracy for the epicardial and mediastinal fats was 98.4% with a mean true positive rate of 96.2%. In average, the Dice similarity index was equal to 96.8%.

É. O. Rodrigues, A. Conci, F. F. C. Morais +1

Institute of Computing Universidade Federal Fluminense Niterói, Brazil · Institute of Medicine / Pró-Laudo Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil · Fac. de Ing. en Sist. Electr. e Ind. Universidad Técnica de Ambato Ambato, Ecuador

Medical Image Segmentation
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May 27, 2026

MORI-Seg: Learning Morphological Geometry for Instance Segmentation without Instance Annotations

Instance-level quantification of kidney functional units is essential for morphometric analysis, yet most publicly available pathology datasets provide only semantic segmentation annotations, where adjacent structures of the same class are merged into single regions. This prevents reliable instance-level analysis and limits downstream quantitative studies. Existing heuristic post-processing methods often yield suboptimal instance separation, particularly in crowded and adherent regions, while deep learning-based instance segmentation approaches typically require intensive instance-level annotations that are costly and labor-intensive to obtain. We propose MORI-Seg, a deep learning framework that enables instance segmentation without requiring instance-level annotations. Instead of heuristic splitting or instance supervision, MORI-Seg learns morphology-aware geometric representations directly from semantic masks by jointly modeling object-centric distance fields and boundary-band representations to encode interior structure and contact interfaces. A class-conditioned feature disentanglement module further promotes intra-instance coherence and inter-instance separation. Under semantic-only supervision, MORI-Seg decomposes connected semantic regions into distinct instance masks in an end-to-end manner. Experiments demonstrate improved instance separation accuracy and more reliable morphometric quantification compared with classical post-processing pipelines and representative semantic-to-instance learning approaches. The official implementation is publicly available at https://github.com/ddrrnn123/MORI-Seg.

Leiyue Zhao, Tianyu Shi, Daniel Reisenbuchler +12

Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China · Sichuan University, Chengdu, Sichuan, 610064, China · University of Regensburg, Regensburg, Bavaria, 93053, Germany +6

Image SegmentationWeakly Supervised Image SegmentationInstance SegmentationMedical Image Segmentation
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May 26, 2026

SCKAN: Structural Consensus-based KAN Prototype Learning for Semi-Supervised Pancreas Segmentation

Accurate pancreas segmentation is critical for early cancer diagnosis, where annotation scarcity necessitates Semi-Supervised Learning (SSL). However, due to significant inter-sample morphological variability, existing SSL methods face severe generalizability limitations under sparse supervision, leading to the Supervision Bias problem. To address this, we propose Structural Consensus-based KAN Prototype Learning (SCKAN), which constructs the first cross-sample structural consensus learning with Kolmogorov-Arnold Networks (KANs), to achieve more generalizable and accurate segmentation. Specifically, SCKAN contains two key designs: Structure-constrained Prototype Consistency Learning (SPCL), which prompts unbiased structural representation by enforcing cross-sample consistency via prototype-level contrastive optimization, and Consensus-based Kolmogorov-Arnold Fusion (CKaF), which reduces morphology-specific bias by aggregating stable consensus and filtering sample-wise noise via KAN's adaptive B-spline nonlinearity. Extensive experiments on two public pancreas datasets demonstrate the effectiveness of SCKAN. Code is at https://github.com/rhodaliu17/SCKAN.

Yuqi Liu, Yufei Chen, Wei Fu +2

School of Computer Science and Technology, Tongji University, Shanghai, China · Artificial Intelligence Institute, Shanghai University, Shanghai, China · Department of Computer and Data Science and Department of Biomedical2026 Engineering, Case Western Reserve University, Cleveland, USA

Prototype LearningMedical Image SegmentationSemi-Supervised Learning
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May 26, 2026

Cesarean Scar Defect Segmentation in Transvaginal Ultrasound Images: a Dataset and Benchmark

Cesarean Scar Defect (CSD) is one of the most prevalent complications following cesarean delivery. Transvaginal ultrasonography is widely used for primary CSD screening. Accurate determination of CSD outline and dimensions is crucial for treatment. However, CSDs are frequently overlooked by sonographers due to small size and irregular morphology, suboptimal image quality, and limited clinical awareness in resource-constrained settings. Despite artificial intelligence advances in medical imaging, no public dataset exists for transvaginal ultrasound CSD segmentation. To address this gap, we present a comprehensive CSD dataset comprising 1,111 images and 16 videos, yielding 501 positive samples with confirmed CSD and precise pixel-level manual annotations. Annotations are performed following standardized clinical guidelines through collaboration between experienced sonographers and trained PhD students. This work provides high-quality benchmark resources for advancing medical image segmentation algorithms and promoting clinical innovation. Ultimately, improved CSD diagnosis and subsequent treatment strategies can enhance the quality of life in women of reproductive age, representing significant value for both medical research and clinical practice.

Yuan Tian, Yue Li, Wei Xia +10

Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital affiliated to Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Xuhui District, 200030, Shanghai, China. · School of Computer Science, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo, 315100, Zhejiang, China. · School of Computer Science, University of Nottingham, University Park, Nottingham, NG7 2RD, UK. +4

Ultrasound Image SegmentationUltrasound ImagingMedical Image SegmentationMedical Image Benchmarks
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May 26, 2026

Measuring Prediction Uncertainty in Neural Cellular Automata

Neural cellular automata (NCA) provide a lightweight alternative to encoder-decoder segmentation networks. However, it can be difficult to decide when a prediction should be trusted. Here, we study uncertainty estimation for NCA-based medical image segmentation without modifying the underlying architecture or retraining the model. Our approach is motivated by viewing the NCA as a dynamical system where convergent attractors correspond to confident predictions. Concretely, we propose resilience, a simple measure that leverages the intrinsic iterative structure of NCAs by probing the stability of the final prediction under small perturbations of the automaton state. Predictions that return to the same solution are deemed confident, while those that change substantially are flagged as uncertain. We evaluate uncertainty by its ability to predict segmentation quality using selective prediction metrics (ΔΔDice@90 and AURC) and ranking metrics (AUROC and AUPRC). Across multiple medical segmentation benchmarks, resilience identifies failure cases more reliably than baselines, improving trust and safety in NCA-based models.

Ario Sadafi, Michael Deutges, Nassir Navab +1

Computational Health Center, Helmholtz Munich, Neuherberg, Germany · Helmholtz AI, Helmholtz Munich, Neuherberg, Germany · Computer Aided Medical Procedures, Technical University of Munich, Munich, Germany +4

Neural Cellular AutomataImage SegmentationUncertainty QuantificationMedical Image SegmentationSegmentation Uncertainty Estimation
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May 26, 2026

Attenuation-Resilient Alternating Optimization for Laparoscopic Liver Landmark Detection

Liver surface landmark detection is a fundamental prerequisite for anatomical guidance in laparoscopic liver surgery. However, it remains unreliable in practice due to two pervasive challenges: illumination attenuation in underexposed regions and the structural mismatch between pixel-wise localization and continuous curvilinear geometry. To address these limitations, we propose A2ONet, an attenuation-resilient alternating optimization network for robust liver landmark detection. To mitigate illumination attenuation, A2ONet embraces an illumination field compensation (IFC) block that adaptively enhances dark regions while preserving structural consistency. Meanwhile, we introduce a lightweight frequency-orientation selective filter (FOSF) to suppress repetitive texture interference and preserve salient curvilinear cues. Building upon these resilient representations, we design an alternating seg-curve optimization (ASCO) decoder that iteratively couples dense segmentation with explicit curve modeling, enabling mutual guidance to optimize both structural continuity and endpoint localization. Extensive evaluations on L3D-2K, L3D, and P2ILF demonstrate consistent improvements over competitive methods, establishing a more reliable foundation for intraoperative anatomy guidance. Our code will be available at https://github.com/hyperiondk115/A2ONet.

Lanqing Liu, Ruize Cui, Jialun Pei +4

The Hong Kong Polytechnic University, Hong Kong, China · The Chinese University of Hong Kong, Hong Kong, China

Anatomical Landmark DetectionMedical Image SegmentationLaparoscopic SurgeryMedical Image Localization
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May 25, 2026

Detail Consistent Stage-Wise Distillation for Efficient 3D MRI Segmentation

Deploying high-performing 3D medical image segmenters (e.g., nnU-Net) is often limited by memory footprint and inference latency. Compression is therefore necessary, but compact 3D encoders tend to lose fine structural cues (small lesions and sharp boundaries) as downsampling repeats across multi-resolution stages. We propose Detail Consistent Distillation (DCD), a stage-wise distillation framework that preserves structural detail across scales by aligning teacher-student features in a wavelet-decomposed representation. At each encoder stage, DCD distills directional detail components in the wavelet domain while leaving the coarse approximation comparatively unconstrained, avoiding over-regularization of global semantics. DCD is used only during training and introduces no inference-time overhead. Experiments on the BraTS 2024 and ISLES 2022 benchmarks demonstrate that our approach achieves superior performance in MRI segmentation using 3D multi-modal data. Code and implementation details for DCD are publicly available at https://github.com/ClinicaAlpha/DCD-3D-MedSeg.

Mengchen Fan, Baocheng Geng, Xi Xiao +5

University of Alabama at Birmingham, Birmingham, AL, USA · Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany · UTHealth Houston, Houston, TX, USA

Image SegmentationMedical Image Segmentation3D Medical Image SegmentationKnowledge Distillation
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May 25, 2026

VesselSim: learning 3D blood vessel segmentation without expert annotations

Blood vessel segmentation is a core task in medical image analysis for the care of vascular diseases and surgical planning, yet the challenges of providing expert vascular annotations pose a major obstacle for the progress of related deep learning techniques. To address this, we propose VesselSim, a two-stage framework for universal 3D blood vessel segmentation that eliminates the need for real annotated data during training. First, we introduce a stochastic, geometry-driven vascular simulation framework that models recursive branching, curvature-controlled growth, and collision-aware topology, followed by domain-randomized intensity synthesis to generate 16,500 anatomically plausible 3D angiographic volumes. Second, a 3D U-Net is trained solely on this synthetic data. To bridge the domain gap from synthetic to real images at inference time, we introduce a test-time adaptation strategy via a self-supervised mask reconstruction decoder, enabling adaptation to unseen clinical scans without prior domain knowledge. We evaluate VesselSim in a zero-shot setting on multiple real-world datasets spanning MR and CT across several anatomical regions, including the brain and kidneys. Despite being trained exclusively on synthetic data, VesselSim achieves performance competitive with state-of-the-art vascular segmentation foundation models. These findings suggest that learning vessel geometry from synthetic tubular structures is effective for robust cross-domain generalization, substantially reducing the reliance on acquired medical imaging data and more importantly, expert annotations.

Erin Rainville, Melissa Ananian, Tristan Mirolla +2

Department of Electrical and Computer Engineering, Concordia University, Montreal, Canada · Department of Computer Science and Software Engineering, Concordia University, Montreal, Canada

Synthetic-to-Real Domain AdaptationSynthetic Data AugmentationImage SegmentationMedical Image Segmentation3D Medical Image Segmentation
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May 25, 2026

MARVEL: Universal Murray's Law-informed Vessel Tree Segmentation and Topology Estimation

Vascular circulation follows fundamental biophysical principles that optimize mass transport and metabolic energy expenditure, which can be effectively modeled by Murray's law. However, contemporary deep learning methods for vascular segmentation often neglect these biophysical constraints. This leads to physiologically implausible branching and misclassification vascular trees, rendering. These automated segmentation results are unreliable unreliable for downstream clinical tasks such as blood flow simulation or disease quantification. In this paper, we introduce MARVEL (Universal MurrAy's law-infoRmed Vessel sEgmentation and topoLogy estimation), a backbone-agnostic framework that integrates biophysical priors into vascular tree extraction. MARVEL combines per-pixel supervision with explicit radius predictions to enforce local bifurcation constraints derived from an empirical width-exponent mapping. We implement these constraints as differentiable regularizers during training to guide models toward physiologically consistent reconstructions. We evaluate MARVEL on eight public datasets across multiple vascular modalities and segmentation backbones. Results demonstrate MARVEL's superior performance in segmentation accuracy, topological consistency, and physiological plausibility. By converting segmented masks into graph-based hemodynamic simulations, we demonstrate that MARVEL preserves the subtle pathological narrowing and topological connectivity required to distinguish hypertensive from normotensive eyes. Results show that MARVEL significantly improves the classification of hypertension via arteriovenous pressure differences in the eye (p < 0.001), outperforming baseline models in both topological consistency and clinical predictive value.

Yi Zhou, Thiara Sana Ahmed, Jacqueline Chua +7

Singapore Eye Research Institute, Singapore National Eye Centre, Singapore · Ophthalmology & Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore · Centre for Innovation & Precision Eye Health, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore +12

Retinal Vessel SegmentationMedical Image AnalysisMedical Image SegmentationPhysics-Informed ML
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May 22, 2026

ImPartial: Multi-channel Whole-Cell Segmentation using Partial Annotations

Accurate cell segmentation in pathology images typically requires dense pixel-wise annotations, which are costly and time-consuming to obtain. This challenge is especially important for emerging biological imaging modalities and multiplexed datasets with variable channel configurations, where expert-labeled data are scarce. In this work, we introduce ImPartial, a deep learning framework designed to achieve state-of-the-art segmentation performance in low-annotation regimes using sparse scribbles and limited supervision. ImPartial augments the segmentation objective via self-supervised multi-channel quantized imputation. This approach leverages the observation that perfect pixel-wise reconstruction or denoising of the image is not needed for accurate segmentation, and thus, introduces a self-supervised classification objective that better aligns with the overall segmentation goal. We demonstrate that ImPartial achieves performance at par with fully supervised models while requiring substantially fewer annotations. Extensive experiments on benchmark multiplexed cellular imaging and single-plex clinical brightfield immunohistochemistry datasets show consistent improvements over strong baselines with only partial annotations. All benchmark datasets and code are available via our Github: https://github.com/nadeemlab/ImPartial.

Gunjan Shrivastava, Saad Nadeem

Memorial Sloan Kettering Cancer Center, New York NY 10065, USA

Image SegmentationWeakly Supervised Image SegmentationHistopathology Image SegmentationSelf-Supervised LearningWeakly Supervised LearningMedical Image Segmentation+1
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May 22, 2026

Exploiting Longitudinal Context in Clinician-Verified Interactive Lesion Tracking

Tracking tumor lesions across serial CT scans is essential for oncological response assessment. Existing automated methods face a fundamental trade-off: end-to-end trackers achieve high automation but offer no opportunity to correct silent tracking failures, while decoupled registration-segmentation pipelines permit user verification yet discard the lesion's prior appearance, limiting accuracy in ambiguous cases. In this work, we propose a Verified Tracking paradigm: a clinician verifies a registration-proposed prompt, which the model leverages alongside the baseline lesion appearance to resolve segmentation ambiguities. We present a unified framework combining early spatial prompt fusion with latent temporal difference weighting for longitudinally-informed segmentation. To address data scarcity, we leverage large-scale synthetic pretraining, proving essential for exploiting longitudinal context, improving performance by up to 4.5 Dice points over training from scratch. Our approach secured first place in the MICCAI autoPET IV challenge. We further curate and release PanTrack, a new longitudinal pancreatic cancer benchmark, to assess out-of-distribution generalization. Experiments show that our model outperforms prior work in both fully automatic and the proposed verified tracking setting offering a clinically safe middle ground between automation and control. Code, model and dataset will be released at https://github.com/MIC-DKFZ/LongiSeg

Yannick Kirchhoff, Maximilian Rokuss, Daniel Philipp Mertens +5

German Cancer Research Center (DKFZ) Heidelberg, Division of Medical Image Computing, Germany · Faculty of Mathematics and Computer Science, Heidelberg University, Germany · HIDSS4Health – Helmholtz Information and Data Science School for Health, Karlsruhe/Heidelberg, Germany +3

Interactive Medical Image SegmentationMedical ImagingLongitudinal Medical Image AnalysisMedical Image SegmentationOncologyMedical Image Benchmarks
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May 21, 2026

SegGuidedNet: Sub-Region-Aware Attention Supervision for Interpretable Brain Tumor Segmentation

Accurate segmentation of brain tumour sub-regions from multi-parametric MRI is critical for treatment planning yet remains challenging due to morphological variability, class imbalance, and overlapping appearances of tumour regions across imaging sequences. We propose SegGuidedNet, a three-dimensional residual encoder--decoder network introducing a novel SegAttentionGate module that explicitly supervises the decoder to produce spatially discriminative attention maps for each tumour sub-region necrotic core, peritumoral oedema, and enhancing tumour via a lightweight auxiliary loss, adding less than 0.2% parameter overhead. This sub-region supervision maintains decoder discriminability between visually ambiguous classes while providing free-of-cost spatial interpretability at inference without any post-hoc explanation method. Evaluated independently on BraTS2021 and BraTS2023 GLI across 251 held-out subjects each, SegGuidedNet achieves mean Dice of 0.905 (ET= 0.873, TC=0.906, WT=0.935) and 0.897 (ET=0.859, TC=0.902, WT=0.931) respectively, surpassing ensemble-based nnU-Net and HNF-Netv2 as a single model and approaching Swin UNETR a 10-model ensemble within 2--4 Dice points at a fraction of the inference cost. The consistency of results across two benchmark editions further confirms the generalisability of the proposed approach, offering competitive accuracy with built-in interpretability in a lightweight, clinically practical framework.

Hasaan Maqsood, Saif Ur Rehman Khan, Sebastian Vollmer +2

National University of Sciences and Technology (NUST), Islamabad, Pakistan. · Department of Computer Science, Rhineland-Palatinate Technical University of Kaiserslautern-Landau, Kaiserslautern, 67663, Germany. · German Research Center for Artificial Intelligence, Kaiserslautern, 67663, Germany. +2

Image SegmentationBraTSMedical Image Segmentation3D Medical Image SegmentationExplainable Medical Image AnalysisBrain MRI+1
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May 21, 2026

VEELA: A Clinically-Constrained Benchmark for Liver Vessel Segmentation in Computed Tomography Angiography

Accurate segmentation of hepatic and portal vessels in contrast-enhanced computed tomography angiography (CTA) remains challenging due to complex vascular topology, peripheral visibility limitations, and acquisition-induced ambiguities. While existing public datasets offer valuable benchmarks, few include clinically realistic annotation constraints. We introduce VEELA (Vessel Extraction and Extrication for Liver Analysis), a rigorously curated liver vessel dataset derived from 40 CTA scans inherited from the CHAOS grand-challenge cohort. All vessels were manually delineated slice-by-slice under multi-expert consensus, using a strict visibility-driven annotation policy and avoiding anatomically inferred interpolation. This design explicitly captures anatomical variability and imaging-related uncertainty. As a continuation of the CHAOS challenge, VEELA enables reproducible cross-benchmark evaluation while extending the scope to fine-grained hepatic and portal vessel segmentation. We further establish a standardized benchmarking framework and analyze complementary evaluation metrics, including topology-aware (clDice), overlap-based (IoU), boundary-sensitive (NSD), and geometry-aware (area, length) measures. Our results demonstrate that different metrics capture distinct aspects of vascular integrity, underscoring the necessity of multi-perspective evaluation for clinically meaningful vessel segmentation. VEELA is publicly released to facilitate reproducible research and support the development of robust vascular segmentation methods. Researchers can access the evaluation metrics, dataset, and submission platform at https://www.synapse.org/Synapse:syn65471967.

Ziya Ata Yazıcı, N. Sinem Gezer, İlkay Öksüz +19

Huawei Türkiye R&D Center, Istanbul, 34768, Türkiye · Department of Radiology, Dokuz Eylul University, Izmir, 35100, Türkiye · Department of Computer Engineering, Istanbul Technical University, Istanbul, 34469, Türkiye +8

Medical Image SegmentationComputed TomographyMedical Image Benchmarks
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May 21, 2026

Robustness of breast lesion segmentation under MRI undersampling improves with k-space-aware deep learning

Purpose: To assess whether breast lesion segmentation can be learned directly from acquired MRI k-space, and whether doing so improves robustness when data are accelerated or noisy. Materials and Methods: This retrospective study used public breast dynamic contrast-enhanced MRI (DCE-MRI) datasets with acquired and synthetic k-space, together with a within-dataset synthetic control. We compared four 3D U-Net variants: a hybrid k-space-to-image model, a native k-space model, and magnitude and complex image-space baselines. Models were evaluated under increasing undersampling and added complex Gaussian k-space noise. The primary outcome was patient-level Dice similarity coefficient under cross-validation, with the hybrid model prespecified as the main comparison against the magnitude image-space baseline. Results: At full sampling, the hybrid and image-space models performed similarly. As acceleration increased, the hybrid model retained substantially more segmentation accuracy and significantly outperformed the magnitude image-space baseline across moderate to high undersampling levels. The same pattern was observed when noise was added directly to k-space: the hybrid model degraded more slowly, whereas the image-space baseline failed under heavier noise. This advantage was reproduced in the within-dataset synthetic control. Feature analysis suggested that the k-space stage and image-space stage played complementary roles, with frequency-domain filtering concentrated before image-domain lesion localization. Conclusion: K-space-aware deep learning improves the robustness of breast lesion segmentation under MRI undersampling and k-space noise, while matching image-space methods at full sampling.

Lukas T. Rotkopf, Marco Schlimbach, Julius C. Holzschuh +3

Institute for AI in Medicine (IKIM), University Hospital Essen, Essen, Germany · Department of Physics, Technical University Dortmund, Dortmund, Germany · 3Division of Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany +4

Magnetic Resonance ImagingMedical Image Segmentation3D Medical Image Segmentation
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May 21, 2026

ConvNeXt-FD: A Fractal-Based Deep Model for Robust Biomedical Image Segmentation

Biomedical image segmentation is a critical task in medical diagnosis and treatment planning, enabling precise delineation of anatomical structures and pathological regions. Despite significant advancements, challenges persist due to the inherent variability, noise, and complex morphology present in diverse medical imaging modalities. This paper introduces ConvNeXt-FD, a novel deep learning architecture for robust biomedical image segmentation, built upon a U-Net-like encoder-decoder framework leveraging the powerful ConvNeXt backbone. Our approach integrates a hybrid loss function combining the Dice coefficient with a boundary-aware regularization term inspired by a differentiable formulation of Fractal Dimension, designed to enhance the model's sensitivity to object boundaries and shape fidelity. We rigorously evaluate ConvNeXt-FD across six distinct biomedical datasets: BUSI (Breast Ultrasound Images), DDTI (Thyroid Ultrasound Images), FluoCells (Fluorescent Cell Images), IDRiD (Diabetic Retinopathy Images for Optic Disc Segmentation), ISIC2018 (Skin Lesion Images), and MoNuSeg (Nuclei Segmentation). Experimental results demonstrate that ConvNeXt-FD, particularly when initialized with ImageNet pre-trained weights, achieves competitive and often superior performance compared to existing state-of-the-art methods across various metrics, including Dice, Jaccard, Accuracy, Sensitivity, Specificity, and False Positive Rate. The integration of ConvNeXt as a strong encoder, coupled with the boundary-aware regularization, proves effective in capturing both high-level semantic features and fine-grained boundary details, leading to more accurate and reliable segmentations in challenging biomedical contexts.

Joao Batista Florindo, Amanda Pontes de Oliveira Ornelas

Institute of Mathematics, Statistics and Scientific Computing, Department of Applied Mathematics, University of Campinas, Rua Sergio Buarque de Holanda, 651, Campinas, 13083-859, Sao Paulo, Brazil

Medical Image SegmentationConvolutional Neural Networks
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May 20, 2026

An Open Multi-Center Whole-Body FDG PET/CT Foundation Model for Tumor Segmentation

The synergistic interpretation of anatomical information from computed tomography (CT) and metabolic information from positron emission tomography (PET) is important to oncologic imaging. However, existing deep learning methods for PET/CT remain largely task-specific, are often trained on single-center cohorts, or adopt dual-branch fusion schemes that delay cross-modal interaction and underutilize early spatial correspondence between PET and CT. To address these limitations, we present an open-source, multi-center, whole-body FDG PET/CT foundation model utilizing 4,997 harmonized scans from four public datasets. Our framework employs hierarchical UNet-shaped backbones with early channel-wise concatenation, enabling anatomical and metabolic features to interact from the first embedding layer onward. We further introduce a masked autoencoding objective based on zero-mean imputation, combined with a weighted global reconstruction loss. This design avoids non-physical intensity discontinuities at masked-region boundaries that arise from learnable mask tokens. On downstream AutoPET lesion segmentation, the proposed models demonstrate strong label efficiency: with only 10% of the labeled training data, they achieve performance comparable to models trained from scratch on the full dataset. Under extreme 5-shot linear probing, joint PET/CT pretraining also achieves higher Dice scores than separated-modality pretraining. This multi-center foundation model demonstrates label efficiency and cross-modality representation learning for PET/CT tumor segmentation. It provides a robust, open-source basis for advancing automated oncologic imaging, significantly reducing the need for large-scale manual annotations in clinical practice.

Xiaofeng Liu, Qianru Zhang, Thibault Marin +4

Department of Radiology and Biomedical Imaging, Yale Biomedical Imaging Institute, Yale University, New Haven, CT, USA

Cross-Modality Medical Image SegmentationMedical Imaging Foundation ModelsMultimodal PretrainingPET/CT ImagingMedical Image SegmentationPET/CT Tumor Segmentation+1
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May 20, 2026

VRXU-net: A Deep Learning Approach for Brain Ischemic Stroke Lesion Detection and Segmentation in T1W MRI

When the blood supply to the brain is obstructed by a clot, oxygen delivery to brain tissues becomes insufficient, leading to cellular necrosis. In healthcare settings, accurately identifying and delineating ischemic lesion boundaries is essential for treatment and surgical planning. However, ischemic stroke lesions vary widely in shape, size, and location, and in grayscale MRI modalities such as T1W they may resemble surrounding brain structures. This makes lesion detection and segmentation a challenging task for clinicians. This study introduces a novel VRU-Net architecture, derived from visual features, residual connections, and a U-shaped network, for detecting and segmenting ischemic stroke lesions in 3D magnetic resonance imaging scans. The proposed method first uses a modified VGG model to identify ischemic stroke in separate 2D slices. Then, a U-shaped segmentation model with residual blocks segments the lesion in each slice. This procedure is applied independently to the axial, sagittal, and coronal planes, and the final output is generated by aggregating the three segmentation results. To improve both performance and processing speed, a high-performance classifier is applied before the segmentation model in a sequential framework. This strategy reduces unnecessary segmentation of non-lesion slices and improves overall accuracy. In addition, decomposing 3D images into 2D slices reduces model complexity while allowing information from three anatomical planes to support more accurate lesion localization. The proposed model is trained on the Anatomical Tracings of Lesions After Stroke dataset and outperforms state-of-the-art models in terms of accuracy and Dice coefficient. Moreover, the segmentation output provides feedback that helps the classification model reduce false-positive predictions.

Sayed Amir Mousavi Mobarakeh

Medical Image AnalysisU-NetMedical Image Segmentation3D Medical Image Segmentation
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May 20, 2026

Local-sensitive connectivity filter (ls-cf): A post-processing unsupervised improvement of the frangi, hessian and vesselness filters for multimodal vessel segmentation

A retinal vessel analysis is a procedure that can be used as an assessment of risks to the eye. This work proposes an unsupervised multimodal approach that improves the response of the Frangi filter, enabling automatic vessel segmentation. We propose a filter that computes pixel-level vessel continuity while introducing a local tolerance heuristic to fill in vessel discontinuities produced by the Frangi response. This proposal, called the local-sensitive connectivity filter (LS-CF), is compared against a naive connectivity filter to the baseline thresholded Frangi filter response and to the naive connectivity filter response in combination with the morphological closing and to the current approaches in the literature. The proposal was able to achieve competitive results in a variety of multimodal datasets. It was robust enough to outperform all the state-of-the-art approaches in the literature for the OSIRIX angiographic dataset in terms of accuracy and 4 out of 5 works in the case of the IOSTAR dataset while also outperforming several works in the case of the DRIVE and STARE datasets and 6 out of 10 in the CHASE-DB dataset. For the CHASE-DB, it also outperformed all the state-of-the-art unsupervised methods.

Erick O Rodrigues, Lucas O Rodrigues, João HP Machado +5

Department of Academic Informatics (DAINF), Universidade Tecnologica Federal do Parana (UTFPR), Pato Branco 85503-390, PR, Brazil · Graduate Program of Sciences Applied to Health Products, Universidade Federal Fluminense (UFF), Niteroi 24241000, RJ, Brazil · Institute of Technological Sciences (ICT), Universidade Federal de Itajuba (UNIFEI), Ttabira 35903-087, MG, Brazil +1

Retinal Vessel SegmentationMedical Image SegmentationUnsupervised Image Segmentation
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May 20, 2026

SpineContextResUNet: A Computationally Efficient Residual UNet for Spine CT Segmentation

Automated segmentation of the vertebral column in Computed Tomography (CT) scans is a prerequisite for pathological assessment and surgical planning. However, state-of-the-art methods, particularly those based on Transformers or large-scale ensembles, demand substantial GPU resources, creating a barrier for clinical adoption in resource-constrained environments or on edge devices. To address this, we introduce SpineContextResUNet, a computationally efficient 3D Residual U-Net designed for rapid spinal localization. Our architecture integrates a lightweight Context Block that employs parallel multi-dilated convolutions to capture long-range anatomical dependencies without the high latency of Recurrent Neural Networks (RNNs) or the memory overhead of Self-Attention mechanisms. Extensive validation on two public benchmarks, VerSe2020 and CTSpine1K, demonstrates that our model achieves a Dice score of 88.17% and 88.13% respectively. To evaluate performance under strict hardware constraints, we compared our model against a bottlenecked SwinUNETR scaled to match our ~1.7M hardware footprint. While the constrained Transformer suffers severe performance degradation due to a lack of spatial inductive biases in a limited-data regime, our CNN-based approach successfully maintains high accuracy. Crucially, heavy baselines like TotalSegmentator fail due to memory exhaustion on commodity hardware (Intel Core i5, 8GB RAM), our model performs robust inference, making it a viable solution for point-of-care diagnostics and deployment on edge platforms like the Nvidia Jetson Orin Nano.

K S Nithurshen, Saurabh J. Shigwan

Shiv Nadar University, Delhi NCR, India

Efficient Neural Network InferenceU-NetMedical Image Segmentation3D Medical Image SegmentationComputed Tomography
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May 20, 2026

Gaze into the Details: Locality-Sensitive Enhancement for OCTA Retinal Vessel Segmentation

Existing deep learning frameworks for Optical Coherence Tomography Angiography (OCTA) vessel segmentation are largely derived from the U-Net architecture, which serves as the foundation for most current designs. However, most of these methods focus only on holistic representation, struggling to address the problem of low local contrast unique to OCTA, which leads to vessel discontinuities and loss of detail. To address these problems, we propose LSENet, which builds upon the U-Net architecture by introducing three core innovative modules: To address vessel discontinuities, we introduce the Patch Information Enhance module (PIE), which replaces standard skip connections to execute patch-wise attention. To mitigate detail loss, the Multiscale Feature Fusion module (MFF) is proposed to feed the PIE module rich, multi-scale information by extracting visually interpretable features from both the original input and preceding layers. Finally, the Connectivity Refinement Decoder (CRD) is designed to refine features from all levels and utilize a large kernel in the final convolutional layer to reduce fragmentation. Experiments on three public datasets (OCTA-500, ROSE-1, and ROSSA) demonstrate that our proposed LSENet achieves state-of-the-art performance while requiring fewer parameters.

Tuopusen Huang, Ding Ma, Xiangqian Wu

Faculty of Computing Harbin Institute of Technology Harbin, China

Medical ImagingRetinal Vessel SegmentationU-NetOptical Coherence TomographyMulti-Scale Feature FusionMedical Image Segmentation
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May 19, 2026

Uncertainty-Guided Conservative Propagation for Structured Inference in Vessel Segmentation

Accurate vessel segmentation is essential for medical image analysis, yet remains challenging due to complex vascular patterns and imaging ambiguity. Most deep models rely on single-pass prediction, limiting their ability to refine uncertain or disconnected regions during inference. To address this limitation, we propose Uncertainty-Guided Conservative Propagation (UGCP), a general plug-in module for vessel segmentation. Instead of directly using a one-shot output as the final prediction, UGCP performs a small number of logit-space update steps to refine the segmentation through local predictions interaction. Predictive uncertainty guides reliable regions to support ambiguous regions, while structure-aware modulation and source-based stabilization reduce unreliable propagation and excessive drift. The module is differentiable and can be trained end-to-end with different segmentation networks. We evaluate UGCP on four public vessel segmentation datasets covering 2D and 3D tasks, including retinal vessel, coronary artery, and cerebral vessel segmentation. Experiments with convolutional neural network-based and Transformer-based backbones show consistent improvements in Dice similarity coefficient, centerline Dice, and 95th percentile Hausdorff distance. Further analysis demonstrates that UGCP reduces vessel disconnections and improves structural consistency with limited additional computation. The code will be made available at https://github.com/chenzhao2023/UGC_PR.

Huan Huang, Michele Esposito, Chen Zhao

Department of Computer Science, Kennesaw State University, Marietta, 30060, GA, USA · Department of Cardiology, Medical University of South Carolina, Charleston, SC, USA

Image SegmentationMedical Image Segmentation3D Medical Image Segmentation
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May 19, 2026

Understanding Model Behavior in Monocular Polyp Sizing

Accurate polyp size stratification guides surveillance decisions, with lesions larger than 5 mm typically requiring closer follow-up. However, monocular colonoscopy lacks a reliable metric reference. We present a diagnostic audit of binary polyp size classification (<=5 mm vs. >5 mm) across multiple public multi-center datasets, model families, and patient-stratified cross-validation. Across architectures and input modalities, including RGB appearance, relative depth, and photometry, model performance is moderately consistent, suggesting reliance on cues correlated with examination behavior rather than true metric scales. By providing ground-truth scale at varying granularities, we quantify the potential improvement from perfect scale information and show that current depth estimation and global calibration offer limited gains. We further demonstrate that segmentation errors under distribution shift eliminate most of this potential, with oracle scale under predicted masks recovering only baseline performance. These results highlight metric scale and mask robustness as two independent bottlenecks and provide reusable evaluation tools such as oracle scale ladders, shortcut partitions, and mask substitution for auditing future polyp sizing pipelines. Our code is publicly accessible at https://github.com/anaxqx/polyp-sizing-audit.

Xinqi Xiong, Andrea Dunn Beltran, Junmyeong Choi +3

University of North Carolina at Chapel Hill · University of California, San Diego

EndoscopyMedical Image ClassificationMedical Image SegmentationMedical Image Benchmarks
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