For the immanent challenge of insufficiently annotated samples in the medical field, semi-supervised medical image segmentation (SSMIS) offers a promising solution. Despite achieving impressive results in delineating primary target areas, most current methodologies struggle to precisely capture the subtle details of boundaries. This deficiency often leads to significant diagnostic inaccuracies. To tackle this issue, we introduce C3S3, a novel semi-supervised segmentation model that synergistically integrates complementary competition and contrastive selection. This design significantly sharpens boundary delineation and enhances overall precision. Specifically, we develop an Outcome-Driven Contrastive Learning module dedicated to refining boundary localization. Additionally, we incorporate a Dynamic Complementary Competition module that leverages two high-performing sub-networks to generate pseudo-labels, thereby further improving segmentation quality. The proposed C3S3 undergoes rigorous validation on two publicly accessible datasets, encompassing the practices of both MRI and CT scans. The results demonstrate that our method achieves superior performance compared to previous cutting-edge competitors. Especially, on the 95HD and ASD metrics, our approach achieves a notable improvement of at least 6%, highlighting the significant advancements. The code is available at https://github.com/Y-TARL/C3S3.
In the era of information explosion, efficiently leveraging large-scale unlabeled data while minimizing the reliance on high-quality pixel-level annotations remains a critical challenge in the field of medical imaging. Semi-supervised learning (SSL) enhances the utilization of unlabeled data by facilitating knowledge transfer, significantly improving the performance of fully supervised models and emerging as a highly promising research direction in medical image analysis. Inspired by the ability of Vision Foundation Models (e.g., SAM-2) to provide rich prior knowledge, we propose SSS (Semi-Supervised SAM-2), a novel approach that leverages SAM-2's robust feature extraction capabilities to uncover latent knowledge in unlabeled medical images, thus effectively enhancing feature support for fully supervised medical image segmentation. Specifically, building upon the single-stream "weak-to-strong" consistency regularization framework, this paper introduces a Discriminative Feature Enhancement (DFE) mechanism to further explore the feature discrepancies introduced by various data augmentation strategies across multiple views. By leveraging feature similarity and dissimilarity across multi-scale augmentation techniques, the method reconstructs and models the features, thereby effectively optimizing the salient regions. Furthermore, a prompt generator is developed that integrates Physical Constraints with a Sliding Window (PCSW) mechanism to generate input prompts for unlabeled data, fulfilling SAM-2's requirement for additional prompts. Extensive experiments demonstrate the superiority of the proposed method for semi-supervised medical image segmentation on two multi-label datasets, i.e., ACDC and BHSD. Notably, SSS achieves an average Dice score of 53.15 on BHSD, surpassing the previous state-of-the-art method by +3.65 Dice. Code will be available at https://github.com/AIGeeksGroup/SSS.
Confronting the critical challenge of insufficiently annotated samples in medical domain, semi-supervised medical image segmentation (SSMIS) emerges as a promising solution. Specifically, most methodologies following the Mean Teacher (MT) or Dual Students (DS) architecture have achieved commendable results. However, to date, these approaches face a performance bottleneck due to two inherent limitations, \textit{e.g.}, the over-coupling problem within MT structure owing to the employment of exponential moving average (EMA) mechanism, as well as the severe cognitive bias between two students of DS structure, both of which potentially lead to reduced efficacy, or even model collapse eventually. To mitigate these issues, a Decoupled Competitive Framework (DCF) is elaborated in this work, which utilizes a straightforward competition mechanism for the update of EMA, effectively decoupling students and teachers in a dynamical manner. In addition, the seamless exchange of invaluable and precise insights is facilitated among students, guaranteeing a better learning paradigm. The DCF introduced undergoes rigorous validation on three publicly accessible datasets, which encompass both 2D and 3D datasets. The results demonstrate the superiority of our method over previous cutting-edge competitors. Code will be available at https://github.com/JiaheChen2002/DCF.
Both limited annotation and domain shift are prevalent challenges in medical image segmentation. Traditional semi-supervised segmentation and unsupervised domain adaptation methods address one of these issues separately. However, the coexistence of limited annotation and domain shift is quite common, which motivates us to introduce a novel and challenging scenario: Mixed Domain Semi-supervised medical image Segmentation (MiDSS), where limited labeled data from a single domain and a large amount of unlabeled data from multiple domains. To tackle this issue, we propose the UST-RUN framework, which fully leverages intermediate domain information to facilitate knowledge transfer. We employ Unified Copy-paste (UCP) to construct intermediate domains, and propose a Symmetric GuiDance training strategy (SymGD) to supervise unlabeled data by merging pseudo-labels from intermediate samples. Subsequently, we introduce a Training Process aware Random Amplitude MixUp (TP-RAM) to progressively incorporate style-transition components into intermediate samples. To generate more diverse intermediate samples, we further select reliable samples with high-quality pseudo-labels, which are then mixed with other unlabeled data. Additionally, we generate sophisticated intermediate samples with high-quality pseudo-labels for unreliable samples, ensuring effective knowledge transfer for them. Extensive experiments on four public datasets demonstrate the superiority of UST-RUN. Notably, UST-RUN achieves a 12.94% improvement in Dice score on the Prostate dataset. Our code is available at https://github.com/MQinghe/UST-RUN
Semi-supervised medical image segmentation (SSMIS) leverages unlabeled data to reduce reliance on manually annotated images. However, current SOTA approaches predominantly focus on foreground-oriented modeling (i.e., segmenting only the foreground region) and have largely overlooked the potential benefits of explicitly modeling the background region. Our study theoretically and empirically demonstrates that highly certain predictions in background modeling enhance the confidence of corresponding foreground modeling. Building on this insight, we propose the Cross-view Bidirectional Modeling (CVBM) framework, which introduces a novel perspective by incorporating background modeling to improve foreground modeling performance. Within CVBM, background modeling serves as an auxiliary perspective, providing complementary supervisory signals to enhance the confidence of the foreground model. Additionally, CVBM introduces an innovative bidirectional consistency mechanism, which ensures mutual alignment between foreground predictions and background-guided predictions. Extensive experiments demonstrate that our approach achieves SOTA performance on the LA, Pancreas, ACDC, and HRF datasets. Notably, on the Pancreas dataset, CVBM outperforms fully supervised methods (i.e., DSC: 84.57% vs. 83.89%) while utilizing only 20% of the labeled data. Our code is publicly available at https://github.com/caoluyang0830/CVBM.git.
Large pretrained visual foundation models exhibit impressive general capabilities. However, the extensive prior knowledge inherent in these models can sometimes be a double-edged sword when adapting them to downstream tasks in specific domains. In the context of semi-supervised medical image segmentation with domain shift, foundation models like MedSAM tend to make overconfident predictions, some of which are incorrect. The error accumulation hinders the effective utilization of unlabeled data and limits further improvements. In this paper, we introduce a Synergistic training framework for Foundation and Conventional models (SynFoC) to address the issue. We observe that a conventional model trained from scratch has the ability to correct the high-confidence mispredictions of the foundation model, while the foundation model can supervise it with high-quality pseudo-labels in the early training stages. Furthermore, to enhance the collaborative training effectiveness of both models and promote reliable convergence towards optimization, the consensus-divergence consistency regularization is proposed. We demonstrate the superiority of our method across four public multi-domain datasets. In particular, our method improves the Dice score by 10.31\% on the Prostate dataset. Our code is available at https://github.com/MQinghe/SynFoC .
Medical image segmentation aims to identify anatomical structures at the voxel-level. Segmentation accuracy relies on distinguishing voxel differences. Compared to advancements achieved in studies of the inter-class variance, the intra-class variance receives less attention. Moreover, traditional linear classifiers, limited by a single learnable weight per class, struggle to capture this finer distinction. To address the above challenges, we propose a Multi-Prototype-based Embedding Refinement method for semi-supervised medical image segmentation. Specifically, we design a multi-prototype-based classification strategy, rethinking the segmentation from the perspective of structural relationships between voxel embeddings. The intra-class variations are explored by clustering voxels along the distribution of multiple prototypes in each class. Next, we introduce a consistency constraint to alleviate the limitation of linear classifiers. This constraint integrates different classification granularities from a linear classifier and the proposed prototype-based classifier. In the thorough evaluation on two popular benchmarks, our method achieves superior performance compared with state-of-the-art methods. Code is available at https://github.com/Briley-byl123/MPER.
Medical ultrasound imaging is ubiquitous, but manual analysis struggles to keep pace. Automated segmentation can help but requires large labeled datasets, which are scarce. Semi-supervised learning leveraging both unlabeled and limited labeled data is a promising approach. State-of-the-art methods use consistency regularization or pseudo-labeling but grow increasingly complex. Without sufficient labels, these models often latch onto artifacts or allow anatomically implausible segmentations. In this paper, we present a simple yet effective pseudo-labeling method with an adversarially learned shape prior to regularize segmentations. Specifically, we devise an encoder-twin-decoder network where the shape prior acts as an implicit shape model, penalizing anatomically implausible but not ground-truth-deviating predictions. Without bells and whistles, our simple approach achieves state-of-the-art performance on two benchmarks under different partition protocols. We provide a strong baseline for future semi-supervised medical image segmentation. Code is available at https://github.com/WUTCM-Lab/Shape-Prior-Semi-Seg.
Deep learning-based medical image segmentation typically requires large amount of labeled data for training, making it less applicable in clinical settings due to high annotation cost. Semi-supervised learning (SSL) has emerged as an appealing strategy due to its less dependence on acquiring abundant annotations from experts compared to fully supervised methods. Beyond existing model-centric advancements of SSL by designing novel regularization strategies, we anticipate a paradigmatic shift due to the emergence of promptable segmentation foundation models with universal segmentation capabilities using positional prompts represented by Segment Anything Model (SAM). In this paper, we present SemiSAM+, a foundation model-driven SSL framework to efficiently learn from limited labeled data for medical image segmentation. SemiSAM+ consists of one or multiple promptable foundation models as generalist models, and a trainable task-specific segmentation model as specialist model. For a given new segmentation task, the training is based on the specialist-generalist collaborative learning procedure, where the trainable specialist model delivers positional prompts to interact with the frozen generalist models to acquire pseudo-labels, and then the generalist model output provides the specialist model with informative and efficient supervision which benefits the automatic segmentation and prompt generation in turn. Extensive experiments on two public datasets and one in-house clinical dataset demonstrate that SemiSAM+ achieves significant performance improvement, especially under extremely limited annotation scenarios, and shows strong efficiency as a plug-and-play strategy that can be easily adapted to different specialist and generalist models.
Although semi-supervised learning has made significant advances in the field of medical image segmentation, fully annotating a volumetric sample slice by slice remains a costly and time-consuming task. Even worse, most of the existing approaches pay much attention to image-level information and ignore semantic features, resulting in the inability to perceive weak boundaries. To address these issues, we propose a novel Semantic-Guided Triplet Co-training (SGTC) framework, which achieves high-end medical image segmentation by only annotating three orthogonal slices of a few volumetric samples, significantly alleviating the burden of radiologists. Our method consist of two main components. Specifically, to enable semantic-aware, fine-granular segmentation and enhance the quality of pseudo-labels, a novel semantic-guided auxiliary learning mechanism is proposed based on the pretrained CLIP. In addition, focusing on a more challenging but clinically realistic scenario, a new triple-view disparity training strategy is proposed, which uses sparse annotations (i.e., only three labeled slices of a few volumes) to perform co-training between three sub-networks, significantly improving the robustness. Extensive experiments on three public medical datasets demonstrate that our method outperforms most state-of-the-art semi-supervised counterparts under sparse annotation settings. The source code is available at https://github.com/xmeimeimei/SGTC.
The limited availability of labeled data has driven advancements in semi-supervised learning for medical image segmentation. Modern large-scale models tailored for general segmentation, such as the Segment Anything Model (SAM), have revealed robust generalization capabilities. However, applying these models directly to medical image segmentation still exposes performance degradation. In this paper, we propose a learnable prompting SAM-induced Knowledge distillation framework (KnowSAM) for semi-supervised medical image segmentation. Firstly, we propose a Multi-view Co-training (MC) strategy that employs two distinct sub-networks to employ a co-teaching paradigm, resulting in more robust outcomes. Secondly, we present a Learnable Prompt Strategy (LPS) to dynamically produce dense prompts and integrate an adapter to fine-tune SAM specifically for medical image segmentation tasks. Moreover, we propose SAM-induced Knowledge Distillation (SKD) to transfer useful knowledge from SAM to two sub-networks, enabling them to learn from SAM's predictions and alleviate the effects of incorrect pseudo-labels during training. Notably, the predictions generated by our subnets are used to produce mask prompts for SAM, facilitating effective inter-module information exchange. Extensive experimental results on various medical segmentation tasks demonstrate that our model outperforms the state-of-the-art semi-supervised segmentation approaches. Crucially, our SAM distillation framework can be seamlessly integrated into other semi-supervised segmentation methods to enhance performance. The code will be released upon acceptance of this manuscript at: https://github.com/taozh2017/KnowSAM
Semi-supervised medical image segmentation (SSMIS) uses consistency learning to regularize model training, which alleviates the burden of pixel-wise manual annotations. However, it often suffers from error supervision from low-quality pseudo labels. Vision-Language Model (VLM) has great potential to enhance pseudo labels by introducing text prompt guided multimodal supervision information. It nevertheless faces the cross-modal problem: the obtained messages tend to correspond to multiple targets. To address aforementioned problems, we propose a Dual Semantic Similarity-Supervised VLM (DuSSS) for SSMIS. Specifically, 1) a Dual Contrastive Learning (DCL) is designed to improve cross-modal semantic consistency by capturing intrinsic representations within each modality and semantic correlations across modalities. 2) To encourage the learning of multiple semantic correspondences, a Semantic Similarity-Supervision strategy (SSS) is proposed and injected into each contrastive learning process in DCL, supervising semantic similarity via the distribution-based uncertainty levels. Furthermore, a novel VLM-based SSMIS network is designed to compensate for the quality deficiencies of pseudo-labels. It utilizes the pretrained VLM to generate text prompt guided supervision information, refining the pseudo label for better consistency regularization. Experimental results demonstrate that our DuSSS achieves outstanding performance with Dice of 82.52%, 74.61% and 78.03% on three public datasets (QaTa-COV19, BM-Seg and MoNuSeg).
This study introduces SAMatch, a SAM-guided Match-based framework for semi-supervised medical image segmentation, aimed at improving pseudo label quality in data-scarce scenarios. While Match-based frameworks are effective, they struggle with low-quality pseudo labels due to the absence of ground truth. SAM, pre-trained on a large dataset, generalizes well across diverse tasks and assists in generating high-confidence prompts, which are then used to refine pseudo labels via fine-tuned SAM. SAMatch is trained end-to-end, allowing for dynamic interaction between the models. Experiments on the ACDC cardiac MRI, BUSI breast ultrasound, and MRLiver datasets show SAMatch achieving state-of-the-art results, with Dice scores of 89.36%, 77.76%, and 80.04%, respectively, using minimal labeled data. SAMatch effectively addresses challenges in semi-supervised segmentation, offering a powerful tool for segmentation in data-limited environments. Code and data are available at https://github.com/apple1986/SAMatch.
The annotation of patient organs is a crucial part of various diagnostic and treatment procedures, such as radiotherapy planning. Manual annotation is extremely time-consuming, while its automation using modern image analysis techniques has not yet reached levels sufficient for clinical adoption. This paper investigates the idea of semi-supervised medical image segmentation using human gaze as interactive input for segmentation correction. In particular, we fine-tuned the Segment Anything Model in Medical Images (MedSAM), a public solution that uses various prompt types as additional input for semi-automated segmentation correction. We used human gaze data from reading abdominal images as a prompt for fine-tuning MedSAM. The model was validated on a public WORD database, which consists of 120 CT scans of 16 abdominal organs. The results of the gaze-assisted MedSAM were shown to be superior to the results of the state-of-the-art segmentation models. In particular, the average Dice coefficient for 16 abdominal organs was 85.8%, 86.7%, 81.7%, and 90.5% for nnUNetV2, ResUNet, original MedSAM, and our gaze-assisted MedSAM model, respectively.
Annotating 3D medical images demands expert knowledge and is time-consuming. As a result, semi-supervised learning (SSL) approaches have gained significant interest in 3D medical image segmentation. The significant size differences among various organs in the human body lead to imbalanced class distribution, which is a major challenge in the real-world application of these SSL approaches. To address this issue, we develop a novel Shape Transformation driven by Active Contour (STAC), that enlarges smaller organs to alleviate imbalanced class distribution across different organs. Inspired by curve evolution theory in active contour methods, STAC employs a signed distance function (SDF) as the level set function, to implicitly represent the shape of organs, and deforms voxels in the direction of the steepest descent of SDF (i.e., the normal vector). To ensure that the voxels far from expansion organs remain unchanged, we design an SDF-based weight function to control the degree of deformation for each voxel. We then use STAC as a data-augmentation process during the training stage. Experimental results on two benchmark datasets demonstrate that the proposed method significantly outperforms some state-of-the-art methods. Source code is publicly available at https://github.com/GuGuLL123/STAC.
Semi-supervised learning (SSL) techniques address the high labeling costs in 3D medical image segmentation, with the teacher-student model being a common approach. However, using an exponential moving average (EMA) in single-teacher models may cause coupling issues, where the weights of the student and teacher models become similar, limiting the teacher's ability to provide additional knowledge for the student. Dual-teacher models were introduced to address this problem but often neglected the importance of maintaining teacher model diversity, leading to coupling issues among teachers. To address the coupling issue, we incorporate a double-copy-paste (DCP) technique to enhance the diversity among the teachers. Additionally, we introduce the Staged Selective Ensemble (SSE) module, which selects different ensemble methods based on the characteristics of the samples and enables more accurate segmentation of label boundaries, thereby improving the quality of pseudo-labels. Experimental results demonstrate the effectiveness of our proposed method in 3D medical image segmentation tasks. Here is the code link: https://github.com/Fazhan-cs/DCP.
Achieving precise medical image segmentation is vital for effective treatment planning and accurate disease diagnosis. Traditional fully-supervised deep learning methods, though highly precise, are heavily reliant on large volumes of labeled data, which are often difficult to obtain due to the expertise required for medical annotations. This has led to the rise of semi-supervised learning approaches that utilize both labeled and unlabeled data to mitigate the label scarcity issue. In this paper, we introduce the Manifold-Aware Local Feature Modeling Network (MANet), which enhances the U-Net architecture by incorporating manifold supervision signals. This approach focuses on improving boundary accuracy, which is crucial for reliable medical diagnosis. To further extend the versatility of our method, we propose two variants: MA-Sobel and MA-Canny. The MA-Sobel variant employs the Sobel operator, which is effective for both 2D and 3D data, while the MA-Canny variant utilizes the Canny operator, specifically designed for 2D images, to refine boundary detection. These variants allow our method to adapt to various medical image modalities and dimensionalities, ensuring broader applicability. Our extensive experiments on datasets such as ACDC, LA, and Pancreas-NIH demonstrate that MANet consistently surpasses state-of-the-art methods in performance metrics like Dice and Jaccard scores. The proposed method also shows improved generalization across various semi-supervised segmentation networks, highlighting its robustness and effectiveness. Visual analysis of segmentation results confirms that MANet offers clearer and more accurate class boundaries, underscoring the value of manifold information in medical image segmentation.
Semi-supervised medical image segmentation (SSMIS) has been demonstrated the potential to mitigate the issue of limited medical labeled data. However, confirmation and cognitive biases may affect the prevalent teacher-student based SSMIS methods due to erroneous pseudo-labels. To tackle this challenge, we improve the mean teacher approach and propose the Students Discrepancy-Informed Correction Learning (SDCL) framework that includes two students and one non-trainable teacher, which utilizes the segmentation difference between the two students to guide the self-correcting learning. The essence of SDCL is to identify the areas of segmentation discrepancy as the potential bias areas, and then encourage the model to review the correct cognition and rectify their own biases in these areas. To facilitate the bias correction learning with continuous review and rectification, two correction loss functions are employed to minimize the correct segmentation voxel distance and maximize the erroneous segmentation voxel entropy. We conducted experiments on three public medical image datasets: two 3D datasets (CT and MRI) and one 2D dataset (MRI). The results show that our SDCL surpasses the current State-of-the-Art (SOTA) methods by 2.57\%, 3.04\%, and 2.34\% in the Dice score on the Pancreas, LA, and ACDC datasets, respectively. In addition, the accuracy of our method is very close to the fully supervised method on the ACDC dataset, and even exceeds the fully supervised method on the Pancreas and LA dataset. (Code available at \url{https://github.com/pascalcpp/SDCL}).
Semi-supervised medical image segmentation has shown promise in training models with limited labeled data and abundant unlabeled data. However, state-of-the-art methods ignore a potentially valuable source of unsupervised semantic information -- spatial registration transforms between image volumes. To address this, we propose CCT-R, a contrastive cross-teaching framework incorporating registration information. To leverage the semantic information available in registrations between volume pairs, CCT-R incorporates two proposed modules: Registration Supervision Loss (RSL) and Registration-Enhanced Positive Sampling (REPS). The RSL leverages segmentation knowledge derived from transforms between labeled and unlabeled volume pairs, providing an additional source of pseudo-labels. REPS enhances contrastive learning by identifying anatomically-corresponding positives across volumes using registration transforms. Experimental results on two challenging medical segmentation benchmarks demonstrate the effectiveness and superiority of CCT-R across various semi-supervised settings, with as few as one labeled case. Our code is available at https://github.com/kathyliu579/ContrastiveCross-teachingWithRegistration.
Medical image segmentation, a critical application of semantic segmentation in healthcare, has seen significant advancements through specialized computer vision techniques. While deep learning-based medical image segmentation is essential for assisting in medical diagnosis, the lack of diverse training data causes the long-tail problem. Moreover, most previous hybrid CNN-ViT architectures have limited ability to combine various attentions in different layers of the Convolutional Neural Network. To address these issues, we propose a Lagrange Duality Consistency (LDC) Loss, integrated with Boundary-Aware Contrastive Loss, as the overall training objective for semi-supervised learning to mitigate the long-tail problem. Additionally, we introduce CMAformer, a novel network that synergizes the strengths of ResUNet and Transformer. The cross-attention block in CMAformer effectively integrates spatial attention and channel attention for multi-scale feature fusion. Overall, our results indicate that CMAformer, combined with the feature fusion framework and the new consistency loss, demonstrates strong complementarity in semi-supervised learning ensembles. We achieve state-of-the-art results on multiple public medical image datasets. Example code are available at: \url{https://github.com/lzeeorno/Lagrange-Duality-and-CMAformer}.