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

• 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 us 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. In addition, several backbones networks (both 2D and 3D) are also supported in this repo, such as UNet, VNet, AttentionUNet, ENet, etc.

• This project was originally developed for our previous works URPC (MICCAI2021 early accept). 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:

    @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{luo2021semi,
    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
2021-12	X. Luo and S. Zhang	Semi-Supervised Medical Image Segmentation via Cross Teaching between CNN and Transformer	Code	Arxiv
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	Z. Xu and R. Tong	All-Around Real Label Supervision: Cyclic Prototype Consistency Learning for Semi-supervised Medical Image Segmentation	None	Arxiv
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	Arxiv
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	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	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

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: [email protected] or QQ Group (Chinese):906808850.