3D Medical Image Segmentation

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Overview

This field develops methods that label anatomical structures and disease in 3D CT, MRI, PET, and other scans, supporting diagnosis, treatment planning, and quantitative analysis. U-Net and nnU-Net remain common baselines, alongside Transformer and state-space models; newer work also uses anatomical and topological constraints, foundation models with prompts, and efficient ways to process volumes. To reduce dependence on costly voxel-level labels, researchers use self-supervised pretraining, synthetic data, semi-supervised learning, and interactive correction, evaluating methods on tasks such as BraTS, BTCV, and ACDC. A central challenge is that strong scores on familiar datasets may not hold across hospitals, scanners, or modalities, while thin structures, uncertain boundaries, and limited compute make reliable clinical deployment difficult.

Latest papers

CardsList

212 papers14 papers in the last four weeks, down 53% on the four weeks before. 0.1% of all new papers.

  1. nnInteractive Agent: General-Purpose AI Agents as 3D Image Annotators

    Oct 22, 2026Fabian Isensee, Constantin Ulrich Harsy, Maximilian Rokuss +3Medical AI AgentsTool-Using Agents

    Division of Medical Image Computing (MIC), German Cancer Research Center (DKFZ), Heidelberg, Germany · National Center for Tumor Diseases (NCT) Heidelberg, a partnership between the German Cancer Research Center (DKFZ) and Heidelberg University Hospital (UKHD), Heidelberg, Germany · Helmholtz Imaging, German Cancer Research Center (DKFZ), Heidelberg, Germany +4

  2. LatticeRank: Spacing-Ranked Consistency for Native-Grid 3D Medical Image Segmentation

    Oct 20, 2026Jingjia Yan, Yue Zhuo, Zhonghua XieMedical Image Segmentation3D Medical Image Segmentation

    Huizhou University, Huizhou 516007, Guangdong, China

  3. SlimFormer++: Token Mixing Where It Matters for Efficient 3D Medical Image Segmentation

    Oct 18, 2026Yang Hong, Lei Zhang, Zhihong Liu +23D Medical Image Segmentation

    the University of Exeter, Exeter, U.K. · Guangdong University of Technology

  4. Contrastive uncertainty learning for robust multi-structure segmentation in lower-pelvic MR

    Oct 14, 2026Bilal Sidiqi, Yipei Wang, Wen Yan +3Medical Image Segmentation3D Medical Image Segmentation

    UCL Hawkes Institute, University College London, London, UK · Department of Medical Physics and Biomedical Engineering, University College London, London, UK · Centre for Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London, United Kingdom +2

  5. Benchmarking Self-Supervised 3D Medical Vision Foundation Models and Transferability Estimation

    Oct 13, 2026Jiaqi Tang, Yu Wang, Yang Liu +7Medical Imaging Foundation ModelsMedical Image Benchmarks

    National Institution of Health Data Science, Peking University, Beijing, China. · Institute of Medical Technology, Peking University, Beijing, China. · State Key Laboratory of General Artificial Intelligence, Peking University, Beijing, China. +5

  6. NoduleFlow: Automatic 3D Lung Nodule Detection and Segmentation

    Oct 12, 2026Giulia Romoli, Filippo Ruffini, Francesco Di Feola +3Lung Nodule DetectionMedical Image Segmentation

    Department of Diagnostics and Intervention, Radiation Physics, Biomedical Engineering, Umeå University, Universitetstorget 4, Umeå, Sweden. · Unit of Artificial Intelligence and Computer Systems, Department of Engineering, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, Rome, Italy. · Department of Naval, Electrical, Electronic, and Telecommunications Engineering, University of Genoa, Via Opera Pia 11A, Genoa, Italy.

  7. Hybrid Context Forests and Bilateral Viterbi Matching for 3D Rib Centerline Tracing in CT

    Oct 12, 2026Quan Wang3D Medical Image SegmentationComputed Tomography

  8. A4-MR: Abnormality-aware Anatomical Alignment for MR

    Oct 9, 2026Noel D'souza, Zhijian Yang, Nishank Singla +14Medical Imaging Foundation ModelsRadiology VLMs

    GE Healthcare, Seattle, USA · GE Healthcare, Budapest, Hungary · Amazon, USA

  9. CIRSeg: Coarse-to-Fine Intensity-Robust Liver Segmentation with Source-Free Continual Test-Time Adaptation

    Oct 7, 2026Ruoshi Xu, Mingqi Gao, Shengda Luo +1Medical Image Segmentation3D Medical Image Segmentation

    Chinese Medicine Guangdong Laboratory, Zhuhai, China · School of Computer Science, University of Sheffield, Sheffield, UK · School of Automation, Northwestern Polytechnical University, Xi’an, China

  10. Quantifying Volumetric Risk: Class-Aware Asymmetric Weighted Conformal Prediction for 3D Medical Image Segmentation

    Oct 7, 2026Shadi Alijani, Fereshteh Aghaee Meibodi, Homayoun NajjaranConformal PredictionSegmentation Uncertainty Estimation

    University of Victoria, 800 Finnerty Road, Victoria, BC, Canada

  11. Active-DiNTS: Active Differentiable Network Topology Search

    Oct 3, 2026Gean Trindade Pereira, Thierry Urruty, Muriel Visani +1Neural Architecture Search3D Medical Image Segmentation

    Institute of Mathematics and Computer Sciences (ICMC) University of São Paulo São Carlos, 13560-970, São Paulo, Brazil · XLIM, Université de Poitiers Université de Limoges, CNRS Poitiers, 86000, Vienne, France · Laboratoire Informatique, Image et Interaction (L3i) La Rochelle Université La Rochelle, 17042, Charente-Maritime, France

  12. UniPro: Unified Multi-Mode Medical Image Segmentation from 2D Images to 3D Volumes via Propagation

    Oct 3, 2026Bangwei Guo, Yunhe Gao, Meng Ye +5Medical Image Segmentation3D Medical Image Segmentation

    Rutgers University · Stanford University · The University of Texas at Arlington +1

  13. MAGEFormer: Learning Metric-Consistent Representations for Anisotropic CT Segmentation

    Oct 2, 2026Jiaying Li, Paolo RemagninoMedical Image Segmentation3D Medical Image Segmentation

    Department of Computer Science, Durham University, Durham, UK

  14. Preserving Anatomical Continuity: Three-Stage Pipeline for Colon Segmentation in 3D Abdominal CT Scans

    Oct 2, 2026Deshan Kalupahana, Sonit Singh, Praveen Ravindran +13D Medical Image SegmentationTopology-Preserving Image Segmentation

    School of Computer Science and Engineering, University of New South Wales, Sydney, Australia · Sydney Adventist Hospital, Wahroonga, Australia

  15. Parameter-Efficient 3D Segmentation of Liver and Liver tumors: Depthwise factorization Scales Better Than Dense Convolution with Spatial Dimensionality

    Sep 27, 2026Adham M. Alkhadrawi, Mohammed A. B. MahmoudDepthwise Separable ConvolutionMedical Image Segmentation

    Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA · Faculty of Computer Studies, Arab Open University, Riyadh 11681, Kingdom of Saudi Arabia

  16. KneePreM: Towards 3D Knee MRI Foundation Models via Large-Scale Unlabeled Pretraining and Label-Efficient Fine-Tuning

    Sep 25, 2026Xinxin Wang, Liam Hazan, Jing Li +3Medical Imaging Foundation ModelsSelf-Supervised Pre-Training

    Program of Advanced Musculoskeletal Imaging, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, United States · Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, United States · Department of Computer and Data Science, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States +2

  17. AxonSynth: Domain-Randomized Synthetic Data for Zero-Shot 3D Axon Segmentation in Light-Sheet Microscopy

    Sep 25, 2026Edward Gaibor, Kyriaki-Margarita Bintsi, Chiara Mauri +9Domain RandomizationSynthetic-to-Real Domain Adaptation

    Department of Computer Science, University of Massachusetts Boston, Boston, MA, USA · Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA · Universidad San Sebastián, Chile +4

  18. Learning Spectral Allocation: A Fractional Diffusion Framework for Adaptive Volumetric Segmentation

    Sep 23, 2026Yi-Hui Shen, Tie-Qiang LiSemi-Supervised Medical Image Segmentation3D Medical Image Segmentation

    School of Arts and Sciences, Fujian Medical University, Fuzhou, China · School of Medical Imaging, Fujian Medical University, Fuzhou, China · Department of Medical Radiation Physics and Nuclear Medicine, Karolinska University Hospital, Stockholm, Sweden +2

  19. Less Is More in the Long Tail: Stage-Adaptive Sample Selection for Annotation-Efficient Dense Prediction

    Sep 22, 2026Xiaofei Du, Lei Zhang, Shuyu Yan +2Active LearningData-Efficient Learning

    Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China · Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, China · Frontier Innovation Center, Department of Systems Biology for Medicine, Qidong-Fudan Innovative Institute of Medical Sciences, School of Basic Medical Sciences, Zhongshan Hospital Clinical Center for Biotherapy, Fudan University, Shanghai 200032, China +1

  20. SAMI3D-DW: Interactive Segmentation of Any 3D Medical Images

    Sep 22, 2026Ping Gong, Shiyuan Su, Fandong Zhang +4Interactive Medical Image Segmentation3D Medical Image Segmentation

    Artificial Intelligence Laboratory, Deepwise Healthcare · The University of Hong Kong

  21. Brain Metastases Segmentation for BraTS 2026 Task 1: A Multi-Architecture Comparison

    Sep 21, 2026Mahdi Islam, Musarrat TabassumU-NetMedical Image Segmentation

    Center for Computational & Data Sciences, Independent University, Bangladesh · Department of Electrical and Electronic Engineering, Independent University, Bangladesh · Independent Researcher

  22. Confidence-Aware Teacher-Student Distillation for 3D Medical Segmentation

    Sep 20, 2026Georgios Triantafyllou, Dimitris K. IakovidisSemi-Supervised Medical Image SegmentationMedical Image Segmentation

    Department of Computer Science and Biomedical Informatics, University of Thessaly, 2-4 Papasiopoulou st. 35131, Lamia, Greece

  23. BrainIAC: Interactive 3D Brain Lesion Segmentation across Heterogeneous MRI Modalities with Online Adaptation

    Sep 19, 2026Wentian Xu, Anthony P Addison, Ziyun Liang +3Medical Image Segmentation3D Medical Image Segmentation

    Department of Engineering Science, University of Oxford, UK

  24. Catena: A Comprehensive Software Suite for Large-Scale Connectomics

    Sep 18, 2026Samia Mohinta, Pedro Gómez-Gálvez, Shi Yan Lee +5Electron MicroscopyMicroscopy Image Analysis

    Dept. of Physiology, Development and Neuroscience, University of Cambridge, UK · MRC Laboratory of Molecular Biology, UK · HHMI Janelia, USA +1

  25. Diffusion-Based Tumor Inpainting for Renal Segmentation under Clinical Data Scarcity

    Sep 18, 2026Ekaterina Sedykh, Salme Ussanov, Dmytro Fedorenko +1Synthetic Data AugmentationMedical Image Synthesis

    Institute of Computer Science, University of Tartu, Tartu, Estonia · Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland · Department of Digital Medicine, University of Bern, Bern, Switzerland +4

  26. A Dual-Stream Regulated Reconstruction and Segmentation Network with Hierarchical Artifact-Prior Modeling for Ultra-Low-Field Pediatric Neuroimaging

    Sep 17, 2026Bahram Jafrasteh, Leo Milecki, Qingyu ZhaoMedical Image AnalysisImage Reconstruction

    Department of Radiology, Weill Cornell Medicine, New York, NY, USA

  27. G^2RA-NET: Graph-based Cross-Slice Relation Modeling with Attention Gating for Medical Image Segmentation

    Sep 17, 2026Shengye Wang, Zonglin Wu, Liang Fan +2Graph Neural NetworksMedical Image Segmentation

    College of Computer and Information Science, Southwest University, Chongqing, China · ai.io, London, UK · Chengyi College, Jimei University, Xiamen, China

  28. NeuroTS-Net: Multi-Class Semantic Segmentation of Pediatric Brain Tumors in Multi-Modal MRI

    Sep 15, 2026Darius Peteleaza, Razvan-Gabriel Dumitru, Bogdan Neamtu +3BraTS3D CNNs

    Lucian Blaga University of Sibiu, Sibiu, Romania · University of Arizona, Tucson, AZ, USA · Pediatric Clinical Hospital of Sibiu, Sibiu, Romania +2

  29. IMVS: Interactive Medical Volume Segmentation with Test-Time Adaptation - A New Method for Annotating Radiology Datasets

    Sep 15, 2026Abhilaksh Singh Reen, Kushal Borkar, Ritvik MahapatraInteractive Medical Image SegmentationTest-Time Adaptation

    Independent Researcher, Delhi, India · Independent Researcher, Kolkata, India · California State University, Fresno, CA, USA

  30. De-GAN - Dynamic Parameter Tuned GAN for 3D Medical Image Segmentation: A Step Towards Generalisation

    Sep 15, 2026Zoha Usama, Azadeh AlaviMedical Image Segmentation3D Medical Image Segmentation

    School of Computing Technologies, Royal Melbourne Institute of Technology University (RMIT), Melbourne, Australia