Awesome

Semi-supervised-learning-for-medical-image-segmentation.

[New] We have transferred to a new topic about active learning and source-free domain adaptation for medical image analysis, which may be closer to the real clinical requirement. The new benchmark is here.
We are reformatting the codebase to support the 5-fold cross-validation and randomly select labeled cases, the reformatted methods in this Branch.
Recently, semi-supervised image segmentation has become a hot topic in medical image computing, unfortunately, there are only a few open-source codes and datasets, since the privacy policy and others. For easy evaluation and fair comparison, we are trying to build a semi-supervised medical image segmentation benchmark to boost the semi-supervised learning research in the medical image computing community. If you are interested, you can push your implementations or ideas to this repo or contact me at any time.
This repo has re-implemented these semi-supervised methods (with some modifications for semi-supervised medical image segmentation, more details please refer to these original works): (1) Mean Teacher; (2) Entropy Minimization; (3) Deep Adversarial Networks; (4) Uncertainty Aware Mean Teacher; (5) Interpolation Consistency Training; (6) Uncertainty Rectified Pyramid Consistency; (7) Cross Pseudo Supervision; (8) Cross Consistency Training; (9) Deep Co-Training; (10) Cross Teaching between CNN and Transformer; (11) FixMatch; (12) Regularized Dropout. In addition, several backbones networks (both 2D and 3D) are also supported in this repo, such as UNet, nnUNet, VNet, AttentionUNet, ENet, Swin-UNet, etc.

This project was originally developed for our previous works. Now and future, we are still working on extending it to be more user-friendly and support more approaches to further boost and ease this topic research. If you use this codebase in your research, please cite the following works:

  @article{media2022urpc,
  title={Semi-Supervised Medical Image Segmentation via Uncertainty Rectified Pyramid Consistency},
  author={Luo, Xiangde and Wang, Guotai and Liao, Wenjun and Chen, Jieneng and Song, Tao and Chen, Yinan and Zhang, Shichuan, Dimitris N. Metaxas, and Zhang, Shaoting},
  journal={Medical Image Analysis},
  volume={80},
  pages={102517},
  year={2022},
  publisher={Elsevier}}
  
  @inproceedings{luo2021ctbct,
  title={Semi-supervised medical image segmentation via cross teaching between cnn and transformer},
  author={Luo, Xiangde and Hu, Minhao and Song, Tao and Wang, Guotai and Zhang, Shaoting},
  booktitle={International Conference on Medical Imaging with Deep Learning},
  pages={820--833},
  year={2022},
  organization={PMLR}}

  @InProceedings{luo2021urpc,
  author={Luo, Xiangde and Liao, Wenjun and Chen, Jieneng and Song, Tao and Chen, Yinan and Zhang, Shichuan and Chen, Nianyong and Wang, Guotai and Zhang, Shaoting},
  title={Efficient Semi-supervised Gross Target Volume of Nasopharyngeal Carcinoma Segmentation via Uncertainty Rectified Pyramid Consistency},
  booktitle={Medical Image Computing and Computer Assisted Intervention -- MICCAI 2021},
  year={2021},
  pages={318--329}}
   
  @InProceedings{luo2021dtc,
  title={Semi-supervised Medical Image Segmentation through Dual-task Consistency},
  author={Luo, Xiangde and Chen, Jieneng and Song, Tao and  Wang, Guotai},
  journal={AAAI Conference on Artificial Intelligence},
  year={2021},
  pages={8801-8809}}
  
  @misc{ssl4mis2020,
  title={{SSL4MIS}},
  author={Luo, Xiangde},
  howpublished={\url{https://github.com/HiLab-git/SSL4MIS}},
  year={2020}}

Literature reviews of semi-supervised learning approach for medical image segmentation (SSL4MIS).

Date	The First and Last Authors	Title	Code	Reference
2023-07	H. Wang and X. Li	DHC: Dual-debiased Heterogeneous Co-training Framework for Class-imbalanced Semi-supervised Medical Image Segmentation	Code	MICCAI2023
2023-07	Q. Wei and Y. Zhou	Consistency-guided Meta-Learning for Bootstrapping Semi-Supervised Medical Image Segmentation	Code	MICCAI2023
2023-07	H. Peiris and M. Harandi	Uncertainty-guided dual-views for semi-supervised volumetric medical image segmentation	Code	Nature Machine Intelligence
2023-07	S. Gao and S. Zhang	Correlation-Aware Mutual Learning for Semi-supervised Medical Image Segmentation	Code	MICCAI2023
2023-07	Z. Xu and R. Tong	Ambiguity-selective consistency regularization for mean-teacher semi-supervised medical image segmentation	Code	MedIA2023
2023-06	P. Liu and G. Zheng	C3PS: Context-aware Conditional Cross Pseudo Supervision for Semi-supervised Medical Image Segmentation	None	Arxiv
2023-05	Z. Zhang and Z. Jiao	Cross-supervised Dual Classifiers for Semi-supervised Medical Image Segmentation	None	Arxiv
2023-05	Z. Zhang and Z. Jiao	Self-aware and Cross-sample Prototypical Learning for Semi-supervised Medical Image Segmentation	None	MICCAI2023
2023-05	H. Cai and Y. Gao	Orthogonal Annotation Benefits Barely-supervised Medical Image Segmentation	Code	CVPR2023
2023-05	H. Basak and Z. yin	Pseudo-Label Guided Contrastive Learning for Semi-Supervised Medical Image Segmentation	Code	CVPR2023
2023-05	Y. Wang and X. Gao	MCF: Mutual Correction Framework for Semi-Supervised Medical Image Segmentation	Code	CVPR2023
2023-05	L. Zhong and G. Wang	Semi-supervised Pathological Image Segmentation via Cross Distillation of Multiple Attentions	Code	MICCAI2023
2023-05	J. Du and T. Wang	Coarse-Refined Consistency Learning using Pixel-level Features for Semi-supervised Medical Image Segmentation	None	JBHI2023
2023-05	L. Qiu and H. Ren	Federated Semi-Supervised Learning for Medical Image Segmentation via Pseudo-Label Denoising	None	JBHI2023
2023-05	R. Aralikatti and J. Rajan	A Dual-Stage Semi-Supervised Pre-Training Approach for Medical Image Segmentation	Code	TAI2023
2023-05	Y. Zhao and J. Lu	Semi-Supervised Medical Image Segmentation With Voxel Stability and Reliability Constraints	Code	JBHI2023
2023-05	M. Xu and J. Jacob	Expectation Maximization Pseudo Labelling for Segmentation with Limited Annotations	Code	Arxiv
2023-05	Y. Bai and Y. Wang	Bidirectional Copy-Paste for Semi-Supervised Medical Image Segmentation	Code	CVPR2023
2023-04	H. Wu and K. Cheng	Compete to Win: Enhancing Pseudo Labels for Barely-supervised Medical Image Segmentation	Code	Arixv
2023-04	A. Lou and J. Noble	Min-Max Similarity: A Contrastive Semi-Supervised Deep Learning Network for Surgical Tools Segmentation	Code	TMI2023
2023-04	C.You and J. Duncan	ACTION++: Improving Semi-supervised Medical Image Segmentation with Adaptive Anatomical Contrast	None	Arxiv
2023-03	Y. Zhu and R. Zhang	Inherent Consistent Learning for Accurate Semi-supervised Medical Image Segmentation	Code	MIDL2023
2023-03	C. Xu and S. Zhao	Dual Uncertainty-guided Mixing Consistency for Semi-Supervised 3D Medical Image Segmentation	Code	TBD2023
2023-03	K. Chaitanya and E. Konukoglu	Local contrastive loss with pseudo-label based self-training for semi-supervised medical image segmentation	Code	MedIA2023
2023-03	J. Zhu and E. Meijering	Hybrid Dual Mean-Teacher Network With Double-Uncertainty Guidance for Semi-Supervised Segmentation of MRI Scans	Code	Arxiv
2023-02	P. Wang and C. Desrosiers	CAT: Constrained Adversarial Training for Anatomically-plausible Semi-supervised Segmentation	Code	TMI2023
2023-02	C. You and J. Duncan	Rethinking Semi-Supervised Medical Image Segmentation: A Variance-Reduction Perspective	None	Arxiv
2023-02	L. Zeng and W. Wang	SS-TBN: A Semi-Supervised Tri-Branch Network for COVID-19 Screening and Lesion Segmentation	None	TPAMI2023
2023-01	X. Zhao and L. Zhang	RCPS: Rectified Contrastive Pseudo Supervision for Semi-Supervised Medical Image Segmentation	Code	Arxiv
2023-01	Z. Shen and O. Zaiane	Co-training with High-Confidence Pseudo Labels for Semi-supervised Medical Image Segmentation	Code	Arxiv
2023-01	D. Chen and Y. Wang	MagicNet: Semi-Supervised Multi-Organ Segmentation via Magic-Cube Partition and Recovery	None	CVPR2023
2022-12	P. Qiao and J. Chen	Semi-supervised CT Lesion Segmentation Using Uncertainty-based Data Pairing and SwapMix	None	TMI2022
2022-12	Z. Wang and Z. Ni	Adversarial Vision Transformer for Medical Image Semantic Segmentation with Limited Annotations	Code	BMVC2022
2022-12	T. Lei and A. Nandi	Semi-supervised medical image segmentation using adversarial consistency learning and dynamic convolution network	Code	TMI2022
2022-11	L. Wang and P. Heng	Dual Multi-scale Mean Teacher Network for Semi-supervised Infection Segmentation in Chest CT Volume for COVID-19	Code	TCYB2022
2022-10	H. Ni and X. Huang	Semi-supervised Body Parsing and Pose Estimation for Enhancing Infant General Movement Assessment	None	MedIA2023
2022-10	F. Fyu and P. Yuen	Pseudo-Label Guided Image Synthesis for Semi-Supervised COVID-19 Pneumonia Infection Segmentation	Code	TMI2022
2022-10	J. Shi and C. Li	Semi-Supervised Pixel Contrastive Learning Framework for Tissue Segmentation in Histopathological Image	None	JBHI2022
2022-10	C. Xu and S. Li	BMAnet: Boundary Mining with Adversarial Learning for Semi-supervised 2D Myocardial Infarction Segmentation	None	JBHI2022
2022-10	D. Xiang and B. Tian	Semi-supervised Dual Stream Segmentation Network for Fundus Lesion Segmentation	None	TMI2022
2022-10	F. Wu and X. Zhuang	Minimizing Estimated Risks on Unlabeled Data: A New Formulation for Semi-Supervised Medical Image Segmentation	Code	TPAMI2022
2022-10	S. Zhang and Z. Xu	Multi-modal contrastive mutual learning and pseudo-label re-learning for semi-supervised medical image segmentation	None	MedIA2022
2022-10	J. Chen and J. Han	Semi-supervised Unpaired Medical Image Segmentation Through Task-affinity Consistency	Code	TMI2022
2022-09	H. Huang and Y. Zou	Complementary consistency semi-supervised learning for 3D left atrial image segmentation	Code	Arxiv
2022-09	R. Gu and S. Zhang	Contrastive Semi-supervised Learning for Domain Adaptive Segmentation Across Similar Anatomical Structures	Code	TMI2022
2022-09	Q. Jin and R. Su	Semi-supervised Histological Image Segmentation via Hierarchical Consistency Enforcement	None	MICCAI2022
2022-09	J. Xiang and Y. Yang	FUSSNet: Fusing Two Sources of Uncertainty for Semi-supervised Medical Image Segmentation	Code	MICCAI2022
2022-09	V. Nath and D. Xu	Warm Start Active Learning with Proxy Labels and Selection via Semi-supervised Fine-Tuning	None	MICCAI2022
2022-09	J. Liu and Y. Zhou	Semi-supervised Medical Image Segmentation Using Cross-Model Pseudo-Supervision with Shape Awareness and Local Context Constraints	Code	MICCAI2022
2022-09	Y. Meng and Y. Zheng	Shape-Aware Weakly/Semi-Supervised Optic Disc and Cup Segmentation with Regional/Marginal Consistency	Code	MICCAI2022
2022-09	X. Zhao and G. Li	Semi-supervised Spatial Temporal Attention Network for Video Polyp Segmentation	Code	MICCAI2022
2022-09	J. Wu and D. Ding	Semi-supervised Learning for Nerve Segmentation in Corneal Confocal Microscope Photography	None	MICCAI2022
2022-09	H. Basak and R. Sarkar	Addressing Class Imbalance in Semi-supervised Image Segmentation: A Study on Cardiac MRI	None	MICCAI2022
2022-08	Q. Wang and J. Chen	A regularization-driven Mean Teacher model based on semi-supervised learning for medical image segmentation	Code	PMB2022
2022-08	Y. Meng and Y. Zheng	Dual Consistency Enabled Weakly and Semi-Supervised Optic Disc and Cup Segmentation with Dual Adaptive Graph Convolutional Networks	Code	TMI2022
2022-08	T. Lei and B. Lu	Semi-Supervised 3D Medical Image Segmentation Using Shape-Guided Dual Consistency Learning	None	ICME2022
2022-08	J. Chen and C. Sham	Uncertainty teacher with dense focal loss for semi-supervised medical image segmentation	None	CBM2022
2022-08	L. Xie and Y. Feng	Semi-supervised region-connectivity-based cerebrovascular segmentation for time-of-flight magnetic resonance angiography image	Code	CBM2022
2022-08	G. Wang and S. Zhang	PyMIC: A deep learning toolkit for annotation-efficient medical image segmentation	Code	Arxiv
2022-08	J. Zammit and P. Hu	Semi-supervised COVID-19 CT image segmentation using deep generative models	Code	BMC Bioinformatics
2022-08	Z. Wang and B. Huang	When CNN Meet with ViT: Towards Semi-Supervised Learning for Multi-Class Medical Image Semantic Segmentation	Code	Arxiv2022
2022-08	Z. Wang and I. Voiculescu	Triple-View Feature Learning for Medical Image Segmentation	Code	Arxiv2022
2022-08	Z. Zhang and Z. Jiao	Dynamic Prototypical Feature Representation Learning Framework for Semi-supervised Skin Lesion Segmentation	None	NeuCom2022
2022-08	M. Xu and J. Jacob	Bayesian Pseudo Labels: Expectation Maximization for Robust and Efficient Semi-Supervised Segmentation	Code	MICCAI2022
2022-07	X. Li and S. Gao	TCCNet: Temporally Consistent Context-Free Network for Semi-supervised Video Polyp Segmentation	Code	IJCAI2022
2022-07	T. Wang and H. Kong	Uncertainty-Guided Pixel Contrastive Learning for Semi-Supervised Medical Image Segmentation	None	IJCAI2022
2022-07	R. Jiao and J. Zhang	Learning with Limited Annotations: A Survey on Deep Semi-Supervised Learning for Medical Image Segmentation	None	Arxiv2022
2022-07	Z. Yang and S. Tang	VoxSeP: semi-positive voxels assist self-supervised 3D medical segmentation	None	MMSystems2022
2022-07	Z. Xu and T. Lukasiewicz	PCA: Semi-supervised Segmentation with Patch Confidence Adversarial Training	None	Arxiv2022
2022-07	N. Shen and J. Li	SCANet: A Unified Semi-supervised Learning Framework for Vessel Segmentation	Code	TMI2022
2022-07	Z. Zhao and C. Guan	MMGL: Multi-Scale Multi-View Global-Local Contrastive learning for Semi-supervised Cardiac Image Segmentation	None	ICIP2022
2022-07	Z. Zhao and C. Guan	ACT-Net: Asymmetric Co-Teacher Network for Semi-supervised Memory-efficient Medical Image Segmentation	None	ArXiv2022
2022-07	K. Wang and L. Zhou	An Efficient Semi-Supervised Framework with Multi-Task and Curricu-lum Learning for Medical Image Segmentation	Code	IJNS2022
2022-07	B. Fazekas and H. Bogunovi´c	SD-LayerNet: Semi-supervised retinal layer segmentation in OCT using disentangled representation with anatomical priors	Code	MICCAI2022
2022-06	C. Chen and R. Xiao	Generative Consistency for Semi-Supervised Cerebrovascular Segmentation from TOF-MRA	Code	TMI2022
2022-06	X. Luo and S. Zhang	Semi-Supervised Medical Image Segmentation via Uncertainty Rectified Pyramid Consistency	Code	MedIA2022
2022-06	Y. Liu and S. Li	A Contrastive Consistency Semi-supervised Left Atrium Segmentation Model	Code	CMIG2022
2022-06	J. Wang and T. Lukasiewicz	Rethinking Bayesian Deep Learning Methods for Semi-Supervised Volumetric Medical Image Segmentation	Code	CVPR2022
2022-06	H. Wu and J. Qin	Cross-patch Dense Contrastive Learning for Semi-supervised Segmentation of Cellular Nuclei in Histopathologic Images	Code	CVPR2022
2022-06	Y. Xiao and G. Yang	Semi-Supervised Segmentation of Mitochondria from Electron Microscopy Images Using Spatial Continuity	Code	ISBI2022
2022-06	X. Liu and J. Woo	ACT: Semi-supervised Domain-adaptive Medical Image Segmentation with Asymmetric Co-Training	None	MICCAI2022
2022-06	C. You and J. Duncan	Bootstrapping Semi-supervised Medical Image Segmentation with Anatomical-aware Contrastive Distillation	None	Arxiv
2022-06	Z. Zhang and Z. Jiao	Mutual- and Self- Prototype Alignment for Semisupervised Medical Image Segmentation	None	Arxiv
2022-06	X. Chen and Y. Yu	MASS: Modality-collaborative semi-supervised segmentation by exploiting cross-modal consistency from unpaired CT and MRI images	Code	MedIA
2022-05	Y. Lu and M. Meng	Multiple Consistency Supervision based Semi-supervised OCT Segmentation using Very Limited Annotations	None	ICRA2022
2022-05	W. Huang and F. Wu	Semi-Supervised Neuron Segmentation via Reinforced Consistency Learning	Code	TMI2022
2022-05	C. Lee and M. Chung	Voxel-wise Adversarial Semi-supervised Learning for Medical Image Segmentation	None	Arxiv
2022-05	Y. Lin and X. Li	Calibrating Label Distribution for Class-Imbalanced Barely-Supervised Knee Segmentation	Code	MICCAI2022
2022-05	K. Zheng and J. Wei	Double Noise Mean Teacher Self-Ensembling Model for Semi-Supervised Tumor Segmentation	None	ICASSP2022
2022-04	Y. Xiao and G. Yang	Semi-Supervised Segmentation of Mitochondria from Electron Microscopy Images Using Spatial Continuity	Code	ISBI2022
2022-04	H. He and V. Grau	Semi-Supervised Coronary Vessels Segmentation from Invasive Coronary Angiography with Connectivity-Preserving Loss Function	None	ISBI2022
2022-04	B. Thompson and J. Voisey	Pseudo-Label Refinement Using Superpixels for Semi-Supervised Brain Tumour Segmentation	None	ISBI2022
2022-04	Z li and X. Fan	Coupling Deep Deformable Registration with Contextual Refinement for Semi-Supervised Medical Image Segmentation	None	ISBI2022
2022-04	A. Xu and X. Xia	Ca-Mt: A Self-Ensembling Model for Semi-Supervised Cardiac Segmentation with Elliptical Descriptor Based Contour-Aware	None	ISBI2022
2022-04	X. Wang and S. Chen	SSA-Net: Spatial Self-Attention Network for COVID-19 Pneumonia Infection Segmentation with Semi-supervised Few-shot Learning	None	MedIA2022
2022-04	Z. Zhang and X. Tian	Discriminative Error Prediction Network for Semi-supervised Colon Gland Segmentation	None	MedIA2022
2022-04	Z. Xiao and W. Zhang	Efficient Combination of CNN and Transformer for Dual-Teacher Uncertainty-Aware Guided Semi-Supervised Medical Image Segmentation	None	SSRN
2022-04	K. Han and Z. Liu	An Effective Semi-supervised Approach for Liver CT Image Segmentation	None	JBHI2022
2022-04	J. Yang and Q. Chen	Self-Supervised Sequence Recovery for SemiSupervised Retinal Layer Segmentation	None	JBHI2022
2022-04	T. Cheng and C. Cheng	Feature-enhanced Adversarial Semi-supervised Semantic Segmentation Network for Pulmonary Embolism Annotation	None	Arxiv
2022-04	K. Wang and Y. Wang	Semi-supervised Medical Image Segmentation via a Tripled-uncertainty Guided Mean Teacher Model with Contrastive Learning	None	MedIA2022
2022-04	M. Liu and Q. He	CCAT-NET: A Novel Transformer Based Semi-supervised Framework for Covid-19 Lung Lesion Segmentation	None	ISBI2022
2022-03	Y. Liu and G. Carneiro	Translation Consistent Semi-supervised Segmentation for 3D Medical Images	Code	Arxiv
2022-03	Z. Xu and R. Tong	All-Around Real Label Supervision: Cyclic Prototype Consistency Learning for Semi-supervised Medical Image Segmentation	None	JBHI2022
2022-03	M. Huang and Q. Feng	Semi-Supervised Hybrid Spine Network for Segmentation of Spine MR Images	Code	Arxiv
2022-03	S. Adiga V and H. Lombaert	Leveraging Labeling Representations in Uncertainty-based Semi-supervised Segmentation	None	Arxiv
2022-03	M. Tran and T. Peng	S5CL: Unifying Fully-Supervised, Self-Supervised, and Semi-Supervised Learning Through Hierarchical Contrastive Learning	Code	Arxiv
2022-03	M. Waerebeke and J. Dole	On the pitfalls of entropy-based uncertainty for multi-class semi-supervised segmentation	None	Arxiv
2022-03	W. Cui and R. M. Leahy	Semi-supervised Learning using Robust Loss	None	Arxiv
2022-02	Z. Fang and Y. Yin	Annotation-Efficient COVID-19 Pneumonia Lesion Segmentation using Error-Aware Unified Semi-supervised and Active Learning	None	TAI2022
2022-03	Y. Wu and J. Cai	Exploring Smoothness and Class-Separation for Semi-supervised Medical Image Segmentation	None	Arxiv
2022-02	Y. Hua and L. Zhang	Uncertainty-Guided Voxel-Level Supervised Contrastive Learning for Semi-Supervised Medical Image Segmentation	None	IJNS2022
2022-02	Y. Shu and W. Li	Cross-Mix Monitoring for Medical Image Segmentation with Limited Supervision	None	TMM2022
2022-02	H. Huang and H. Hu	MTL-ABS3Net: Atlas-Based Semi-Supervised Organ Segmentation Network with Multi-Task Learning for Medical Images	None	JHBI2022
2022-02	H. Wu and J. Qin	Semi-supervised Segmentation of Echocardiography Videos via Noise-resilient Spatiotemporal Semantic Calibration and Fusion	None	MedIA2022
2022-02	Z. Liu and C. Zhao	Semi-supervised Medical Image Segmentation via Geometry-aware Consistency Training	None	Arxiv
2022-02	X. Zhao and G. Li	Cross-level Contrastive Learning and Consistency Constraint for Semi-supervised Medical Image Segmentation	Code	ISBI2022
2022-02	H. Basak and A. Chatterjee	An Embarrassingly Simple Consistency Regularization Method for Semi-Supervised Medical Image Segmentation	Code	ISBI2022
2022-01	Q. Chen and D. Ming	Semi-supervised 3D Medical Image Segmentation Based on Dual-task Consistent joint Leanrning and Task-Level Regularization	None	TCBB2022
2022-01	H. Yao and X. Li	Enhancing Pseudo Label Quality for Semi-Supervised Domain-Generalized Medical Image Segmentation	None	AAAI2022
2021-12	S. Li and X. Yang	Semi-supervised Cardiac MRI Segmentation Based on Generative Adversarial Network and Variational Auto-Encoder	None	BIBM2021
2021-12	N. Zhang and Y. Zhang	Semi-supervised Medical Image Segmentation with Distribution Calibration and Non-local Semantic Constraint	None	BIBM2021
2021-12	S. Liu and G. Cao	Shape-aware Multi-task Learning for Semi-supervised 3D Medical Image Segmentation	None	BIBM2021
2021-12	X. Xu and P. Yan	Shadow-consistent Semi-supervised Learning for Prostate Ultrasound Segmentation	Code	TMI2021
2021-12	L. Hu and Y. Wang	Semi-supervised NPC segmentation with uncertainty and attention guided consistency	None	KBS2021
2021-12	J. Peng and M. Pedersoli	Self-Paced Contrastive Learning for Semi-supervised Medical Image Segmentation with Meta-labels	Code	NeurIPS2021
2021-12	Y. Xie and Y. Xia	Intra- and Inter-pair Consistency for Semi-supervised Gland Segmentation	None	TIP2021
2021-12	M. Xu and J. Jacob	Learning Morphological Feature Perturbations for Semi-Supervised Segmentation	Code	MIDL2022
2021-12	X. Luo and S. Zhang	Semi-Supervised Medical Image Segmentation via Cross Teaching between CNN and Transformer	Code	MIDL2022
2021-12	Y. Zhang and J. Zhang	Uncertainty-Guided Mutual Consistency Learning for Semi-Supervised Medical Image Segmentation	None	Arxiv
2021-12	J. Wang and Q. Zhou	Separated Contrastive Learning for Organ-at-Risk and Gross-Tumor-Volume Segmentation with Limited Annotat	Code	AAAI2022
2021-12	J. Chen and Y. Lu	MT-TransUNet: Mediating Multi-Task Tokens in Transformers for Skin Lesion Segmentation and Classification	Code	Arxiv
2021-12	C. Seibold and R. Stiefelhagen	Reference-guided Pseudo-Label Generation for Medical Semantic Segmentation	None	AAAI2022
2021-11	X. Zheng and C. Sham	Uncertainty-Aware Deep Co-training for Semi-supervised Medical Image Segmentation	None	Arxiv
2021-11	J. Peng and M. Pedersoli	Diversified Multi-prototype Representation for Semi-supervised Segmentation	Code	Arxiv
2021-10	J. Hou and J. Deng	Semi-Supervised Semantic Segmentation of Vessel Images using Leaking Perturbations	None	WACV2021
2021-10	M. Xu and J. Jacob	MisMatch: Learning to Change Predictive Confidences with Attention for Consistency-Based, Semi-Supervised Medical Image Segmentation	None	Arxiv
2021-10	H. Wu and J. Qin	Collaborative and Adversarial Learning of Focused and Dispersive Representations for Semi-supervised Polyp Segmentation	None	ICCV2021
2021-10	Y. Shi and Y. Gao	Inconsistency-aware Uncertainty Estimation for Semi-supervised Medical Image Segmentation	Code	TMI2021
2021-09	G. Wang and S. Zhang	Semi-Supervised Segmentation of Radiation-Induced Pulmonary Fibrosis from Lung CT Scans with Multi-Scale Guided Dense Attention	Code	TMI2021
2021-09	K. Wang and Y. Wang	Tripled-Uncertainty Guided Mean Teacher Model for Semi-supervised Medical Image Segmentation	Code	MICCAI2021
2021-09	H. Huang and R. Tong	3D Graph-S2Net: Shape-Aware Self-ensembling Network for Semi-supervised Segmentation with Bilateral Graph Convolution	None	MICCAI2021
2021-09	L. Zhu and B. Ooi	Semi-Supervised Unpaired Multi-Modal Learning for Label-Efficient Medical Image Segmentation	Code	MICCAI2021
2021-09	R. Zhang and G. Li	Self-supervised Correction Learning for Semi-supervised Biomedical Image Segmentation	Code	MICCAI2021
2021-09	D. Kiyasseh and A. Chen	Segmentation of Left Atrial MR Images via Self-supervised Semi-supervised Meta-learning	None	MICCAI2021
2021-09	Y. Wu and J. Cai	Enforcing Mutual Consistency of Hard Regions for Semi-supervised Medical Image Segmentation	None	Arxiv
2021-09	X. Zeng and Y. Wang	Reciprocal Learning for Semi-supervised Segmentation	Code	MICCAI2021
2021-09	G. Zhang and S. Jiang	Automatic segmentation of organs at risk and tumors in CT images of lung cancer from partially labelled datasets with a semi-supervised conditional nnU-Net	None	CMPB2021
2021-09	J. Chen and G. Yang	Adaptive Hierarchical Dual Consistency for Semi-Supervised Left Atrium Segmentation on Cross-Domain Data	Code	TMI2021
2021-09	X. Hu and Y. Shi	Semi-supervised Contrastive Learning for Label-efficient Medical Image Segmentation	Code	MICCAI2021
2021-09	G. Chen and J. Shi	MTANS: Multi-Scale Mean Teacher Combined Adversarial Network with Shape-Aware Embedding for Semi-Supervised Brain Lesion Segmentation	Code	NeuroImage2021
2021-08	H. Peiris and M. Harandi	Duo-SegNet: Adversarial Dual-Views for Semi-Supervised Medical Image Segmentation	Code	MICCAI2021
2021-08	J. Sun and Y. Kong	Semi-Supervised Medical Image Semantic Segmentation with Multi-scale Graph Cut Loss	None	ICIP2021
2021-08	X. Shen and J. Lu	PoissonSeg: Semi-Supervised Few-Shot Medical Image Segmentation via Poisson Learning	None	ArXiv
2021-08	C. You and J. Duncan	SimCVD: Simple Contrastive Voxel-Wise Representation Distillation for Semi-Supervised Medical Image Segmentation	None	Arxiv
2021-08	C. Li and P. Heng	Self-Ensembling Co-Training Framework for Semi-supervised COVID-19 CT Segmentation	None	JBHI2021
2021-08	H. Yang and P. H. N. With	Medical Instrument Segmentation in 3D US by Hybrid Constrained Semi-Supervised Learning	None	JBHI2021
2021-07	Q. Xu and X. Wang	Semi-supervised Medical Image Segmentation with Confidence Calibration	None	IJCNN
2021-07	W. Ding and H. Hawash	RCTE: A Reliable and Consistent Temporal-ensembling Framework for Semi-supervised Segmentation of COVID-19 Lesions	None	Information Fusion2021
2021-06	X. Liu and S. A. Tsaftaris	Semi-supervised Meta-learning with Disentanglement for Domain-generalised Medical Image Segmentation	Code	MICCAI2021
2021-06	P. Pandey and Mausam	Contrastive Semi-Supervised Learning for 2D Medical Image Segmentation	None	MICCAI2021
2021-06	C. Li and Y. Yu	Hierarchical Deep Network with Uncertainty-aware Semi-supervised Learning for Vessel Segmentation	None	Arxiv
2021-05	J. Xiang and S. Zhang	Self-Ensembling Contrastive Learning for Semi-Supervised Medical Image Segmentation	None	Arxiv
2021-05	S. Li and C. Guan	Hierarchical Consistency Regularized Mean Teacher for Semi-supervised 3D Left Atrium Segmentation	None	Arxiv
2021-05	C. You and J. Duncan	Momentum Contrastive Voxel-wise Representation Learning for Semi-supervised Volumetric Medical Image Segmentation	None	MICCAI2022
2021-05	Z. Xie and J. Yang	Semi-Supervised Skin Lesion Segmentation with Learning Model Confidence	None	ICASSP2021
2021-04	S. Reiß and R. Stiefelhagen	Every Annotation Counts: Multi-label Deep Supervision for Medical Image Segmentation	None	CVPR2021
2021-04	S. Chatterjee and A. Nurnberger	DS6, Deformation-aware Semi-supervised Learning: Application to Small Vessel Segmentation with Noisy Training Data	Code	MIDL
2021-04	A. Meyer and M. Rak	Uncertainty-Aware Temporal Self-Learning (UATS): Semi-Supervised Learning for Segmentation of Prostate Zones and Beyond	Code	Arxiv
2021-04	Y. Li and P. Heng	Dual-Consistency Semi-Supervised Learning with Uncertainty Quantification for COVID-19 Lesion Segmentation from CT Images	None	MICCAI2021
2021-03	Y. Zhang and C. Zhang	Dual-Task Mutual Learning for Semi-Supervised Medical Image Segmentation	Code	PRCV2021
2021-03	J. Peng and C. Desrosiers	Boosting Semi-supervised Image Segmentation with Global and Local Mutual Information Regularization	Code	MELBA
2021-03	Y. Wu and L. Zhang	Semi-supervised Left Atrium Segmentation with Mutual Consistency Training	None	MICCAI2021
2021-02	J. Peng and Y. Wang	Medical Image Segmentation with Limited Supervision: A Review of Deep Network Models	None	Arxiv
2021-02	J. Dolz and I. B. Ayed	Teach me to segment with mixed supervision: Confident students become masters	Code	IPMI2021
2021-02	C. Cabrera and K. McGuinness	Semi-supervised Segmentation of Cardiac MRI using Image Registration	None	Under review for MIDL2021
2021-02	Y. Wang and A. Yuille	Learning Inductive Attention Guidance for Partially Supervised Pancreatic Ductal Adenocarcinoma Prediction	None	TMI2021
2021-02	R. Alizadehsaniand U R. Acharya	Uncertainty-Aware Semi-supervised Method using Large Unlabelled and Limited Labeled COVID-19 Data	None	Arxiv
2021-02	D. Yang and D. Xu	Federated Semi-Supervised Learning for COVID Region Segmentation in Chest CT using Multi-National Data from China, Italy, Japan	None	MedIA2021
2020-01	E. Takaya and S. Kurihara	Sequential Semi-supervised Segmentation for Serial Electron Microscopy Image with Small Number of Labels	Code	Journal of Neuroscience Methods
2021-01	Y. Zhang and Z. He	Semi-supervised Cardiac Image Segmentation via Label Propagation and Style Transfer	None	Arxiv
2020-12	H. Wang and D. Chen	Unlabeled Data Guided Semi-supervised Histopathology Image Segmentation	None	Arxiv
2020-12	X. Luo and S. Zhang	Efficient Semi-supervised Gross Target Volume of Nasopharyngeal Carcinoma Segmentation via Uncertainty Rectified Pyramid Consistency	Code	MICCAI2021
2020-12	M. Abdel‐Basset and M. Ryan	FSS-2019-nCov: A Deep Learning Architecture for Semi-supervised Few-Shot Segmentation of COVID-19 Infection	None	Knowledge-Based Systems2020
2020-11	A. Chartsias and S. A. Tsaftaris	Disentangle, Align and Fuse for Multimodal and Semi-Supervised Image Segmentation	Code	TMI2021
2020-11	N. Horlava and N. Scherf	A comparative study of semi- and self-supervised semantic segmentation of biomedical microscopy data	None	Arxiv
2020-11	P. Wang and C. Desrosiers	Self-paced and self-consistent co-training for semi-supervised image segmentation	None	MedIA2021
2020-10	Y. Sun and L. Wang	Semi-supervised Transfer Learning for Infant Cerebellum Tissue Segmentation	None	MLMI2020
2020-10	L. Chen and D. Merhof	Semi-supervised Instance Segmentation with a Learned Shape Prior	Code	LABELS2020
2020-10	S. Shailja and B.S. Manjunath	Semi supervised segmentation and graph-based tracking of 3D nuclei in time-lapse microscopy	Code	Arxiv
2020-10	L. Sun and Y. Yu	A Teacher-Student Framework for Semi-supervised Medical Image Segmentation From Mixed Supervision	None	Arxiv
2020-10	J. Ma and X. Yang	Active Contour Regularized Semi-supervised Learning for COVID-19 CT Infection Segmentation with Limited Annotations	Code	Physics in Medicine & Biology2020
2020-10	W. Hang and J. Qin	Local and Global Structure-Aware Entropy Regularized Mean Teacher Model for 3D Left Atrium Segmentation	Code	MICCAI2020
2020-10	K. Tan and J. Duncan	A Semi-supervised Joint Network for Simultaneous Left Ventricular Motion Tracking and Segmentation in 4D Echocardiography	None	MICCAI2020
2020-10	Y. Wang and Z. He	Double-Uncertainty Weighted Method for Semi-supervised Learning	None	MICCAI2020
2020-10	K. Fang and W. Li	DMNet: Difference Minimization Network for Semi-supervised Segmentation in Medical Images	None	MICCAI2020
2020-10	X. Cao and L. Cheng	Uncertainty Aware Temporal-Ensembling Model for Semi-supervised ABUS Mass Segmentation	None	TMI2020
2020-09	Z. Zhang and W. Zhang	Semi-supervised Semantic Segmentation of Organs at Risk on 3D Pelvic CT Images	None	Arxiv
2020-09	J. Wang and G. Xie	Semi-supervised Active Learning for Instance Segmentation via Scoring Predictions	None	BMVC2020
2020-09	X. Luo and S. Zhang	Semi-supervised Medical Image Segmentation through Dual-task Consistency	Code	AAAI2021
2020-08	X. Huo and Q. Tian	ATSO: Asynchronous Teacher-Student Optimization for Semi-Supervised Medical Image Segmentation	None	Arxiv
2020-08	Y. Xie and Y. Xia	Pairwise Relation Learning for Semi-supervised Gland Segmentation	None	MICCAI2020
2020-07	K. Chaitanya and E. Konukoglu	Semi-supervised Task-driven Data Augmentation for Medical Image Segmentation	Code	Arxiv
2020-07	H. Ni and X. Huang	SiamParseNet: Joint Body Parsing and Label Propagation in Infant Movement Videos	Code	MICCAI2020
2020-07	S. Li and X. He	Shape-aware Semi-supervised 3D Semantic Segmentation for Medical Images	Code	MICCAI2020
2020-07	Y. Li and Y. Zheng	Self-Loop Uncertainty: A Novel Pseudo-Label for Semi-Supervised Medical Image Segmentation	None	MICCAI2020
2020-07	Z. Zhao and P. Heng	Learning Motion Flows for Semi-supervised Instrument Segmentation from Robotic Surgical Video	Code	MICCAI2020
2020-07	Y. Zhou and P. Heng	Deep Semi-supervised Knowledge Distillation for Overlapping Cervical Cell Instance Segmentation	Code	MICCAI2020
2020-07	A. Tehrani and H. Rivaz	Semi-Supervised Training of Optical Flow Convolutional Neural Networks in Ultrasound Elastography	None	MICCAI2020
2020-07	Y. He and S. Li	Dense biased networks with deep priori anatomy and hard region adaptation: Semi-supervised learning for fine renal artery segmentation	None	MedIA2020
2020-07	J. Peng and C. Desrosiers	Mutual information deep regularization for semi-supervised segmentation	Code	MIDL2020
2020-07	Y. Xia and H. Roth	Uncertainty-aware multi-view co-training for semi-supervised medical image segmentation and domain adaptation	None	WACV2020,MedIA2020
2020-07	X. Li and P. Heng	Transformation-Consistent Self-Ensembling Model for Semisupervised Medical Image Segmentation	Code	TNNLS2020
2020-06	F. Garcıa and S. Ourselin	Simulation of Brain Resection for Cavity Segmentation Using Self-Supervised and Semi-Supervised Learning	None	MICCAI2020
2020-06	H. Yang and P. With	Deep Q-Network-Driven Catheter Segmentation in 3D US by Hybrid Constrained Semi-Supervised Learning and Dual-UNet	None	MICCAI2020
2020-05	G. Fotedar and X. Ding	Extreme Consistency: Overcoming Annotation Scarcity and Domain Shifts	None	MICCAI2020
2020-04	C. Liu and C. Ye	Semi-Supervised Brain Lesion Segmentation Using Training Images with and Without Lesions	None	ISBI2020
2020-04	R. Li and D. Auer	A Generic Ensemble Based Deep Convolutional Neural Network for Semi-Supervised Medical Image Segmentation	Code	ISBI2020
2020-04	K. Ta and J. Duncan	A Semi-Supervised Joint Learning Approach to Left Ventricular Segmentation and Motion Tracking in Echocardiography	None	ISBI2020
2020-04	Q. Chang and D. Metaxas	Soft-Label Guided Semi-Supervised Learning for Bi-Ventricle Segmentation in Cardiac Cine MRI	None	ISBI2020
2020-04	D. Fan and L. Shao	Inf-Net: Automatic COVID-19 Lung Infection Segmentation from CT Images	Code	TMI2020
2019-10	L. Yu and P. Heng	Uncertainty-aware self-ensembling model for semi-supervised 3D left atrium segmentation	Code	MICCAI2019
2019-10	G. Bortsova and M. Bruijne	Semi-Supervised Medical Image Segmentation via Learning Consistency under Transformations	None	MICCAI2019
2019-10	Y. He and S. Li	DPA-DenseBiasNet: Semi-supervised 3D Fine Renal Artery Segmentation with Dense Biased Network and Deep Priori Anatomy	None	MICCAI2019
2019-10	H. Zheng and X. Han	Semi-supervised Segmentation of Liver Using Adversarial Learning with Deep Atlas Prior	None	MICCAI2019
2019-10	P. Ganayea and H. Cattin	Removing Segmentation Inconsistencies with Semi-Supervised Non-Adjacency Constraint	Code	MedIA2019
2019-10	Y. Zhao and C. Liu	Multi-view Semi-supervised 3D Whole Brain Segmentation with a Self-ensemble Network	None	MICCAI2019
2019-10	H. Kervade and I. Ayed	Curriculum semi-supervised segmentation	None	MICCAI2019
2019-10	S. Chen and M. Bruijne	Multi-task Attention-based Semi-supervised Learning for Medical Image Segmentation	None	MICCAI2019
2019-10	Z. Xu and M. Niethammer	DeepAtlas: Joint Semi-Supervised Learning of Image Registration and Segmentation	None	MICCAI2019
2019-10	S. Sedai and R. Garnavi	Uncertainty Guided Semi-supervised Segmentation of Retinal Layers in OCT Images	None	MICCAI2019
2019-10	G. Pombo and P. Nachev	Bayesian Volumetric Autoregressive Generative Models for Better Semisupervised Learning	Code	MICCAI2019
2019-06	W. Cui and C. Ye	Semi-Supervised Brain Lesion Segmentation with an Adapted Mean Teacher Model	None	IPMI2019
2019-06	K. Chaitanya and E. Konukoglu	Semi-supervised and Task-Driven Data Augmentation	Code	IPMI2019
2019-04	M. Jafari and P. Abolmaesumi	Semi-Supervised Learning For Cardiac Left Ventricle Segmentation Using Conditional Deep Generative Models as Prior	None	ISBI2019
2019-03	Z. Zhao and Z. Zeng	Semi-Supervised Self-Taught Deep Learning for Finger Bones Segmentation	None	BHI
2019-03	J. Peng and C. Desrosiers	Deep co-training for semi-supervised image segmentation	Code	PR2020
2019-01	Y. Zhou and A. Yuille	Semi-Supervised 3D Abdominal Multi-Organ Segmentation via Deep Multi-Planar Co-Training	None	WACV2019
2018-10	P. Ganaye and H. Cattin	Semi-supervised Learning for Segmentation Under Semantic Constraint	Code	MICCAI2018
2018-10	A. Chartsias and S. Tsaftari	Factorised spatial representation learning: application in semi-supervised myocardial segmentation	None	MICCAI2018
2018-09	X. Li and P. Heng	Semi-supervised Skin Lesion Segmentation via Transformation Consistent Self-ensembling Model	Code	BMVC2018
2018-04	Z. Feng and D. Shen	Semi-supervised learning for pelvic MR image segmentation based on multi-task residual fully convolutional networks	None	ISBI2018
2017-09	L. Gu and S. Aiso	Semi-supervised Learning for Biomedical Image Segmentation via Forest Oriented Super Pixels(Voxels)	None	MICCAI2017
2017-09	S. Sedai and R. Garnavi	Semi-supervised Segmentation of Optic Cup in Retinal Fundus Images Using Variational Autoencoder	None	MICCAI2017
2017-09	W. Bai and D. Rueckert	Semi-supervised Learning for Network-Based Cardiac MR Image Segmentation	None	MICCAI2017
2016-09	D. Mahapatra	Semi-supervised learning and graph cuts for consensus based medical image segmentation	None	PR2016

Code for semi-supervised medical image segmentation.

Some implementations of semi-supervised learning methods can be found in this Link.

Conclusion

This repository provides daily-update literature reviews, algorithms' implementation, and some examples of using PyTorch for semi-supervised medical image segmentation. The project is under development. Currently, it supports 2D and 3D semi-supervised image segmentation and includes five widely-used algorithms' implementations.
In the next two or three months, we will provide more algorithms' implementations, examples, and pre-trained models.

Questions and Suggestions

If you have any questions or suggestions about this project, please contact me through email: luoxd1996@gmail.com or QQ Group (Chinese):906808850.