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

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

  1. TCATSeg: A Tooth Center-Wise Attention Network for 3D Dental Model Semantic Segmentation

    Mar 17, 2026Qiang He, Wentian Qu, Jiajia Dai +93D Semantic Segmentation3D Point Cloud Segmentation

    Institute of Software, Chinese Academy of Sciences · University of Chinese Academy of Sciences · Department of Computer Science and Technology, Tsinghua University +2

  2. Refining 3D Medical Segmentation with Verbal Instruction

    Mar 15, 2026Kangxian Xie, Jiancheng Yang, Nandor Pinter +33D Medical Image SegmentationInteractive Medical Image Segmentation

    University at Buffalo, Buffalo NY 14260, USA · ELLIS Institute Finland, Espoo 02150, Finland · Aalto University, Espoo 02150, Finland +1

  3. ITKIT: Feasible CT Image Analysis based on SimpleITK and MMEngine

    Mar 15, 2026Yiqin Zhang, Meiling ChenMedical Image Analysis3D Medical Image Segmentation

  4. Leveraging a Statistical Shape Model for Efficient Generation of Annotated Training Data: A Case Study on Liver Landmarks Segmentation

    Mar 14, 2026Denis Krnjaca, Lorena Krames, Werner NahmMedical Image AnalysisSynthetic Data Generation

    Karlsruhe Institute of Technology, Karlsruhe, Germany

  5. Developing Foundation Models for Universal Segmentation from 3D Whole-Body Positron Emission Tomography

    Mar 12, 2026Yichi Zhang, Le Xue, Wenbo Zhang +16Medical Imaging Foundation Models3D Medical Image Segmentation

    Artificial Intelligence Innovation and Incubation Institute, Fudan University, Shanghai, China. · Shanghai Academy of Artificial Intelligence for Science, Shanghai, China. · Department of Nuclear Medicine and PET Center, Huashan Hospital, Fudan University, Shanghai, China. +6

  6. Prompting with the human-touch: evaluating model-sensitivity of foundation models for musculoskeletal CT segmentation

    Mar 11, 2026Caroline Magg, Maaike A. ter Wee, Johannes G. G. Dobbe +4Medical Image SegmentationMedical Imaging Foundation Models

    Quantitative Healthcare Analysis (QurAI) Group, University of Amsterdam, Science Park 900, Amsterdam, 1098 XH, The Netherlands · Department Biomedical Engineering and Physics, Amsterdam UMC, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands · Department Orthopaedics, Amsterdam UMC, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands

  7. A Guideline-Aware AI Agent for Zero-Shot Target Volume Auto-Delineation

    Mar 10, 2026Yoon Jo Kim, Wonyoung Cho, Jongmin Lee +7Text-Guided Image SegmentationMedical Image Segmentation

    Oncosoft Inc., Seoul, South Korea · Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea

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

    Mar 7, 2026Kavyansh Tyagi, Vishwas Rathi, Puneet GoyalMedical Image Segmentation3D Medical Image Segmentation

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

  9. Self-Auditing Parameter-Efficient Fine-Tuning for Few-Shot 3D Medical Image Segmentation

    Mar 6, 2026Son Thai Ly, Hien V. NguyenParameter-Efficient Fine-TuningFew-Shot Medical Image Segmentation

    University of Houston

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

    Mar 5, 2026SangHyuk Kim, Daniel Haehn, Sumientra RampersadMissing-Modality Medical Image SegmentationMedical Image Analysis

    University of Massachusetts Boston

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

    Mar 4, 2026Chao Wu, Mahesh Bhosale, Kangxian Xie +3Diffusion Models for Medical Image SegmentationMedical Image Segmentation

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

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

    Mar 3, 2026Chun-Wun Cheng, Yanqi Cheng, Peiyuan Jing +4U-NetMedical Image Segmentation

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

  13. Aligning Fetal Anatomy with Kinematic Tree Log-Euclidean PolyRigid Transforms

    Mar 2, 2026Yingcheng Liu, Athena Taymourtash, Yang Liu +5Fetal MRIDeformable Image Registration

    Computer Science and Artificial Intelligence Lab, MIT, Cambridge, USA · California Institute of Technology, Pasadena, USA · Boston Children’s Hospital and Harvard Medical School, Boston, USA +1

  14. The Texture-Shape Dilemma: Boundary-Safe Synthetic Generation for 3D Medical Transformers

    Mar 1, 2026Jiaqi Tang, Weixuan Xu, Shu Zhang +2Synthetic Data AugmentationMedical Image Synthesis

    Peking University · Central South University · Deepwise Ltd.

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

    Mar 1, 2026Jiaqi Tang, Mengyan Zheng, Shu Zhang +2Medical Image SegmentationSynthetic Data Pretraining

    Peking University · Beihang University · Deepwise Ltd.

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

    Feb 27, 2026Annayah Usman, Behraj Khan, Tahir Qasim SyedMedical Image Segmentation3D Medical Image Segmentation

    Institute of Business Administration Karachi

  17. BiM-GeoAttn-Net: Linear-Time Depth Modeling with Geometry-Aware Attention for 3D Aortic Dissection CTA Segmentation

    Feb 27, 2026Yuan Zhang, Lei Liu, Jialin Zhang +3Medical Image Segmentation3D Medical Image Segmentation

    College of Computer Science Sichuan Normal University Chengdu, Sichuan 610068, China · Zhejiang University & Ant Group Hangzhou, Zhejiang, China · State Key Laboratory of Public Big Data Guizhou University Guiyang, Guizhou 550025, China

  18. VesselBridge3D: A Foundation Model Adaptation Framework for Label-Efficient 3D Vessel Segmentation

    Feb 27, 2026Kirato Yoshihara, Yohei Sugawara, Yuta Tokuoka +13D Medical Image SegmentationFew-Shot Medical Image Segmentation

    The University of Osaka · Preferred Networks, Inc.

  19. Interactive Medical-SAM2 GUI: A Napari-based semi-automatic annotation tool for medical images

    Feb 26, 2026Woojae Hong, Jong Ha Hwang, Jiyong Chung +3Interactive Medical Image SegmentationHuman-in-the-Loop Annotation

    Department of Biomechatronic Engineering, Sungkyunkwan University, Suwon, Gyeonggi, Republic of Korea · Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea

  20. VasGuideNet: Vascular Topology-Guided Couinaud Liver Segmentation with Structural Contrastive Loss

    Feb 25, 2026Chaojie Shen, Jingjun Gu, Zihao Zhao +4Medical Image Segmentation3D Medical Image Segmentation

    Pujian Medical Technology Co., Ltd., Hangzhou, China · Keyi College of Zhejiang Sci-tech University, ShaoXing, China · College of Computer Science and Technology, Zhejiang University, Hangzhou, China

  21. Federated Learning for Cross-Modality Medical Image Segmentation via Augmentation-Driven Generalization

    Feb 24, 2026Sachin Dudda Nagaraju, Ashkan Moradi, Bendik Skarre Abrahamsen +1Cross-Modality Medical Image SegmentationData Augmentation

    Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway. · Central Staff, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.

  22. Token-UNet: A New Case for Transformers Integration in Efficient and Interpretable 3D UNets for Brain Imaging Segmentation

    Feb 23, 2026Louis Fabrice Tshimanga, Andrea Zanola, Federico Del Pup +13D Medical Image SegmentationHybrid CNN-Transformer Architectures

  23. OrthoAI: A Neurosymbolic Framework for Evidence-Grounded Biomechanical Reasoning in Clear Aligner Orthodontics

    Feb 23, 2026Edouard Lansiaux, Margaux Leman, Mehdi Ammi3D Point Cloud Segmentation3D Medical Image Segmentation

    STaR-AI, Emergency Department, Lille University Hospital, 59000, Lille, France · Artificial Intelligence and Data Semantics Laboratory, Paris 8 University, 93200, Saint-Denis, France

  24. Redefining the Down-Sampling Scheme of U-Net for Precision Biomedical Image Segmentation

    Feb 23, 2026Mingjie Li, Yizheng Chen, Md Tauhidul Islam +1U-NetMedical Image Segmentation

    Department of Radiation Oncology Stanford University, CA, USA

  25. RefineFormer3D: Efficient 3D Medical Image Segmentation via Adaptive Multi-Scale Transformer with Cross Attention Fusion

    Feb 18, 2026Kavyansh Tyagi, Vishwas Rathi, Puneet Goyal3D Medical Image Segmentation3D ViTs

    National Institute of Technology Kurukshetra Department of Electronics and Communication Engineering · National Institute of Technology Kurukshetra Department of Computer Engineering · Indian Institute of Technology Ropar Department of Computer Science and Engineering

  26. Bayesian Optimization for Design Parameters of 3D Image Data Analysis

    Feb 17, 2026David Exler, Joaquin Eduardo Urrutia Gómez, Martin Krüger +53D Medical Image SegmentationAutomated Machine Learning

    Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. · Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. · CeMOS Research and Transfer Center, Technische Hochschule Mannheim, Paul-Wittsack-Straße 10, 68163 Mannheim, Germany.

  27. MedVL-SAM2: A unified 3D medical vision-language model for multimodal reasoning and prompt-driven segmentation

    Jan 14, 2026Yang Xing, Jiong Wu, Savas Ozdemir +4Interactive Medical Image SegmentationUnified Multimodal Models

    Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA · Department of Radiology, University of Florida, Jacksonville, FL, USA · Research Computing, University of Florida, Gainesville, FL, USA +2

  28. ReFRM3D: A Radiomics-enhanced Fused Residual Multiparametric 3D Network with Multi-Scale Feature Fusion for Glioma Characterization

    Dec 27, 2025Md. Abdur Rahman, Md Noman Hossain, Arefin Ittesafun Abian +4BraTSMedical Image Segmentation

    Applied Artificial Intelligence and Intelligent Systems (AAIINS) Laboratory, Dhaka 1217, Bangladesh · Department of Computer Science and Engineering, United International University, Dhaka, 1212, Bangladesh · Department of Data Science and Artificial Intelligence, Monash University, Clayton, VIC, 3153, Australia +1

  29. Confidence-Calibrating Regularization for Robust Brain MRI Segmentation Under Domain Shift

    Sep 27, 2025Behraj Khan, Tahir Qasim Syed, Syed Ahmad Chan BukhariImage SegmentationPromptable Image Segmentation

    St. John’s University New York, USA · Institute of Business Administration Karachi Pakistan

  30. Johnson-Lindenstrauss Lemma Guided Network for Efficient 3D Medical Segmentation

    Sep 26, 2025Jinpeng Lu, Linghan Cai, Yinda Chen +4Cross-Modality Medical Image SegmentationImage Segmentation

    University of Science and Technology of China · Dresden University of Technology · Harbin Institute of Technology, Shenzhen