Domain Adaptation (DA) is crucial for robust deployment of medical image segmentation models when applied to new clinical centers with significant domain shifts. Source-Free Domain Adaptation (SFDA) is appealing as it can deal with privacy concerns and access constraints on source-domain data during adaptation to target-domain data. However, SFDA faces challenges such as insufficient supervision in the target domain with unlabeled images. In this work, we propose a Segment Anything Model (SAM)-guided Reliable Pseudo-Labels method for SFDA (SRPL-SFDA) with three key components: 1) Test-Time Tri-branch Intensity Enhancement (T3IE) that not only improves quality of raw pseudo-labels in the target domain, but also leads to SAM-compatible inputs with three channels to better leverage SAM's zero-shot inference ability for refining the pseudo-labels; 2) A reliable pseudo-label selection module that rejects low-quality pseudo-labels based on Consistency of Multiple SAM Outputs (CMSO) under input perturbations with T3IE; and 3) A reliability-aware training procedure in the unlabeled target domain where reliable pseudo-labels are used for supervision and unreliable parts are regularized by entropy minimization. Experiments conducted on two multi-domain medical image segmentation datasets for fetal brain and the prostate respectively demonstrate that: 1) SRPL-SFDA effectively enhances pseudo-label quality in the unlabeled target domain, and improves SFDA performance by leveraging the reliability-aware training; 2) SRPL-SFDA outperformed state-of-the-art SFDA methods, and its performance is close to that of supervised training in the target domain. The code of this work is available online: https://github.com/HiLab-git/SRPL-SFDA.
Recent advances in medical imaging have established deep learning-based segmentation as the predominant approach, though it typically requires large amounts of manually annotated data. However, obtaining annotations for intracranial hemorrhage (ICH) remains particularly challenging due to the tedious and costly labeling process. Semi-supervised learning (SSL) has emerged as a promising solution to address the scarcity of labeled data, especially in volumetric medical image segmentation. Unlike conventional SSL methods that primarily focus on high-confidence pseudo-labels or consistency regularization, we propose SWDL-Net, a novel SSL framework that exploits the complementary advantages of Laplacian pyramid and deep convolutional upsampling. The Laplacian pyramid excels at edge sharpening, while deep convolutions enhance detail precision through flexible feature mapping. Our framework achieves superior segmentation of lesion details and boundaries through a difference learning mechanism that effectively integrates these complementary approaches. Extensive experiments on a 271-case ICH dataset and public benchmarks demonstrate that SWDL-Net outperforms current state-of-the-art methods in scenarios with only 2% labeled data. Additional evaluations on the publicly available Brain Hemorrhage Segmentation Dataset (BHSD) with 5% labeled data further confirm the superiority of our approach. Code and data have been released at https://github.com/SIAT-CT-LAB/SWDL.
The rapid growth of dataset scales has been a key driver in advancing deep learning research. However, as dataset scale increases, the training process becomes increasingly inefficient due to the presence of low-value samples, including excessive redundant samples, overly challenging samples, and inefficient easy samples that contribute little to model improvement.To address this challenge, we propose Scale Efficient Training (SeTa) for large datasets, a dynamic sample pruning approach that losslessly reduces training time. To remove low-value samples, SeTa first performs random pruning to eliminate redundant samples, then clusters the remaining samples according to their learning difficulty measured by loss. Building upon this clustering, a sliding window strategy is employed to progressively remove both overly challenging and inefficient easy clusters following an easy-to-hard curriculum.We conduct extensive experiments on large-scale synthetic datasets, including ToCa, SS1M, and ST+MJ, each containing over 3 million samples.SeTa reduces training costs by up to 50\% while maintaining or improving performance, with minimal degradation even at 70\% cost reduction. Furthermore, experiments on various scale real datasets across various backbones (CNNs, Transformers, and Mambas) and diverse tasks (instruction tuning, multi-view stereo, geo-localization, composed image retrieval, referring image segmentation) demonstrate the powerful effectiveness and universality of our approach. Code is available at https://github.com/mrazhou/SeTa.
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.
Large-scale delineation of individual trees from remote sensing imagery is crucial to the advancement of ecological research, particularly as climate change and other environmental factors rapidly transform forest landscapes across the world. Current RGB tree segmentation methods rely on training specialized machine learning models with labeled tree datasets. While these learning-based approaches can outperform manual data collection when accurate, the existing models still depend on training data that's hard to scale. In this paper, we investigate the efficacy of using a state-of-the-art image segmentation model, Segment Anything Model 2 (SAM2), in a zero-shot manner for individual tree detection and segmentation. We evaluate a pretrained SAM2 model on two tasks in this domain: (1) zero-shot segmentation and (2) zero-shot transfer by using predictions from an existing tree detection model as prompts. Our results suggest that SAM2 not only has impressive generalization capabilities, but also can form a natural synergy with specialized methods trained on in-domain labeled data. We find that applying large pretrained models to problems in remote sensing is a promising avenue for future progress. We make our code available at: https://github.com/open-forest-observatory/tree-detection-framework.
Foundation models like the Segment Anything Model (SAM) have significantly advanced promptable image segmentation in computer vision. However, extending these capabilities to videos presents substantial challenges, particularly in ensuring precise and temporally consistent mask propagation in dynamic scenes. SAM 2 attempts to address this by training a model on massive image and video data from scratch to learn complex spatiotemporal associations, resulting in huge training costs that hinder research and practical deployment. In this paper, we introduce SAM-I2V, an effective image-to-video upgradation method for cultivating a promptable video segmentation (PVS) model. Our approach strategically upgrades the pre-trained SAM to support PVS, significantly reducing training complexity and resource requirements. To achieve this, we introduce three key innovations: (i) an image-to-video feature extraction upgrader built upon SAM's static image encoder to enable spatiotemporal video perception, (ii) a memory filtering strategy that selects the most relevant past frames for more effective utilization of historical information, and (iii) a memory-as-prompt mechanism leveraging object memory to ensure temporally consistent mask propagation in dynamic scenes. Comprehensive experiments demonstrate that our method achieves over 90% of SAM 2's performance while using only 0.2% of its training cost. Our work presents a resource-efficient pathway to PVS, lowering barriers for further research in PVS model design and enabling broader applications and advancements in the field. Code and model are available at: https://github.com/showlab/SAM-I2V.
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
Pathology image segmentation across multiple centers encounters significant challenges due to diverse sources of heterogeneity including imaging modalities, organs, and scanning equipment, whose variability brings representation bias and impedes the development of generalizable segmentation models. In this paper, we propose PathFL, a novel multi-alignment Federated Learning framework for pathology image segmentation that addresses these challenges through three-level alignment strategies of image, feature, and model aggregation. Firstly, at the image level, a collaborative style enhancement module aligns and diversifies local data by facilitating style information exchange across clients. Secondly, at the feature level, an adaptive feature alignment module ensures implicit alignment in the representation space by infusing local features with global insights, promoting consistency across heterogeneous client features learning. Finally, at the model aggregation level, a stratified similarity aggregation strategy hierarchically aligns and aggregates models on the server, using layer-specific similarity to account for client discrepancies and enhance global generalization. Comprehensive evaluations on four sets of heterogeneous pathology image datasets, encompassing cross-source, cross-modality, cross-organ, and cross-scanner variations, validate the effectiveness of our PathFL in achieving better performance and robustness against data heterogeneity.
Medical image segmentation models often struggle to generalize across different domains due to various reasons. Domain Generalization (DG) methods overcome this either through representation learning or data augmentation (DAug). While representation learning methods seek domain-invariant features, they often rely on ad-hoc techniques and lack formal guarantees. DAug methods, which enrich model representations through synthetic samples, have shown comparable or superior performance to representation learning approaches. We propose LangDAug, a novel $\textbf{Lang}$evin $\textbf{D}$ata $\textbf{Aug}$mentation for multi-source domain generalization in 2D medical image segmentation. LangDAug leverages Energy-Based Models (EBMs) trained via contrastive divergence to traverse between source domains, generating intermediate samples through Langevin dynamics. Theoretical analysis shows that LangDAug induces a regularization effect, and for GLMs, it upper-bounds the Rademacher complexity by the intrinsic dimensionality of the data manifold. Through extensive experiments on Fundus segmentation and 2D MRI prostate segmentation benchmarks, we show that LangDAug outperforms state-of-the-art domain generalization methods and effectively complements existing domain-randomization approaches. The codebase for our method is available at https://github.com/backpropagator/LangDAug.
Segmentation is one of the most important tasks in the medical imaging pipeline as it influences a number of image-based decisions. To be effective, fully supervised segmentation approaches require large amounts of manually annotated training data. However, the pixel-level annotation process is expensive, time-consuming, and error-prone, hindering progress and making it challenging to perform effective segmentations. Therefore, models must learn efficiently from limited labeled data. Self-supervised learning (SSL), particularly contrastive learning via pre-training on unlabeled data and fine-tuning on limited annotations, can facilitate such limited labeled image segmentation. To this end, we propose a novel self-supervised contrastive learning framework for medical image segmentation, leveraging inherent relationships of different images, dubbed PolyCL. Without requiring any pixel-level annotations or unreasonable data augmentations, our PolyCL learns and transfers context-aware discriminant features useful for segmentation from an innovative surrogate, in a task-related manner. Additionally, we integrate the Segment Anything Model (SAM) into our framework in two novel ways: as a post-processing refinement module that improves the accuracy of predicted masks using bounding box prompts derived from coarse outputs, and as a propagation mechanism via SAM 2 that generates volumetric segmentations from a single annotated 2D slice. Experimental evaluations on three public computed tomography (CT) datasets demonstrate that PolyCL outperforms fully-supervised and self-supervised baselines in both low-data and cross-domain scenarios. Our code is available at https://github.com/tbwa233/PolyCL.
Most publicly available medical segmentation datasets are only partially labeled, with annotations provided for a subset of anatomical structures. When multiple datasets are combined for training, this incomplete annotation poses challenges, as it limits the model's ability to learn shared anatomical representations among datasets. Furthermore, vision-only frameworks often fail to capture complex anatomical relationships and task-specific distinctions, leading to reduced segmentation accuracy and poor generalizability to unseen datasets. In this study, we proposed a novel CLIP-DINO Prompt-Driven Segmentation Network (CDPDNet), which combined a self-supervised vision transformer with CLIP-based text embedding and introduced task-specific text prompts to tackle these challenges. Specifically, the framework was constructed upon a convolutional neural network (CNN) and incorporated DINOv2 to extract both fine-grained and global visual features, which were then fused using a multi-head cross-attention module to overcome the limited long-range modeling capability of CNNs. In addition, CLIP-derived text embeddings were projected into the visual space to help model complex relationships among organs and tumors. To further address the partial label challenge and enhance inter-task discriminative capability, a Text-based Task Prompt Generation (TTPG) module that generated task-specific prompts was designed to guide the segmentation. Extensive experiments on multiple medical imaging datasets demonstrated that CDPDNet consistently outperformed existing state-of-the-art segmentation methods. Code and pretrained model are available at: https://github.com/wujiong-hub/CDPDNet.git.
Both CNN-based and Transformer-based methods have achieved remarkable success in medical image segmentation tasks. However, CNN-based methods struggle to effectively capture global contextual information due to the inherent limitations of convolution operations. Meanwhile, Transformer-based methods suffer from insufficient local feature modeling and face challenges related to the high computational complexity caused by the self-attention mechanism. To address these limitations, we propose a novel hybrid CNN-Transformer architecture, named MSLAU-Net, which integrates the strengths of both paradigms. The proposed MSLAU-Net incorporates two key ideas. First, it introduces Multi-Scale Linear Attention, designed to efficiently extract multi-scale features from medical images while modeling long-range dependencies with low computational complexity. Second, it adopts a top-down feature aggregation mechanism, which performs multi-level feature aggregation and restores spatial resolution using a lightweight structure. Extensive experiments conducted on benchmark datasets covering three imaging modalities demonstrate that the proposed MSLAU-Net outperforms other state-of-the-art methods on nearly all evaluation metrics, validating the superiority, effectiveness, and robustness of our approach. Our code is available at https://github.com/Monsoon49/MSLAU-Net.
Reasoning Video Object Segmentation is a challenging task, which generates a mask sequence from an input video and an implicit, complex text query. Existing works probe into the problem by finetuning Multimodal Large Language Models (MLLM) for segmentation-based output, while still falling short in difficult cases on videos given temporally-sensitive queries, primarily due to the failure to integrate temporal and spatial information. In this paper, we propose ThinkVideo, a novel framework which leverages the zero-shot Chain-of-Thought (CoT) capability of MLLM to address these challenges. Specifically, ThinkVideo utilizes the CoT prompts to extract object selectivities associated with particular keyframes, then bridging the reasoning image segmentation model and SAM2 video processor to output mask sequences. The ThinkVideo framework is training-free and compatible with closed-source MLLMs, which can be applied to Reasoning Video Instance Segmentation. We further extend the framework for online video streams, where the CoT is used to update the object of interest when a better target starts to emerge and becomes visible. We conduct extensive experiments on video object segmentation with explicit and implicit queries. The results show that ThinkVideo significantly outperforms previous works in both cases, qualitatively and quantitatively.
3D medical image segmentation is vital for clinical diagnosis and treatment but is challenged by high-dimensional data and complex spatial dependencies. Traditional single-modality networks, such as CNNs and Transformers, are often limited by computational inefficiency and constrained contextual modeling in 3D settings. We introduce a novel multimodal framework that leverages Mamba and Kolmogorov-Arnold Networks (KAN) as an efficient backbone for long-sequence modeling. Our approach features three key innovations: First, an EGSC (Enhanced Gated Spatial Convolution) module captures spatial information when unfolding 3D images into 1D sequences. Second, we extend Group-Rational KAN (GR-KAN), a Kolmogorov-Arnold Networks variant with rational basis functions, into 3D-Group-Rational KAN (3D-GR-KAN) for 3D medical imaging - its first application in this domain - enabling superior feature representation tailored to volumetric data. Third, a dual-branch text-driven strategy leverages CLIP's text embeddings: one branch swaps one-hot labels for semantic vectors to preserve inter-organ semantic relationships, while the other aligns images with detailed organ descriptions to enhance semantic alignment. Experiments on the Medical Segmentation Decathlon (MSD) and KiTS23 datasets show our method achieving state-of-the-art performance, surpassing existing approaches in accuracy and efficiency. This work highlights the power of combining advanced sequence modeling, extended network architectures, and vision-language synergy to push forward 3D medical image segmentation, delivering a scalable solution for clinical use. The source code is openly available at https://github.com/yhy-whu/TK-Mamba.
Medical image segmentation, particularly in multi-domain scenarios, requires precise preservation of anatomical structures across diverse representations. While deep learning has advanced this field, existing models often struggle with accurate boundary representation, variability in organ morphology, and information loss during downsampling, limiting their accuracy and robustness. To address these challenges, we propose the Context Enhancement Network (CENet), a novel segmentation framework featuring two key innovations. First, the Dual Selective Enhancement Block (DSEB) integrated into skip connections enhances boundary details and improves the detection of smaller organs in a context-aware manner. Second, the Context Feature Attention Module (CFAM) in the decoder employs a multi-scale design to maintain spatial integrity, reduce feature redundancy, and mitigate overly enhanced representations. Extensive evaluations on both radiology and dermoscopic datasets demonstrate that CENet outperforms state-of-the-art (SOTA) methods in multi-organ segmentation and boundary detail preservation, offering a robust and accurate solution for complex medical image analysis tasks. The code is publicly available at https://github.com/xmindflow/cenet.
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.
Medical image segmentation plays an important role in various clinical applications, but existing models often struggle with the computational inefficiencies and challenges posed by complex medical data. State Space Sequence Models (SSMs) have demonstrated promise in modeling long-range dependencies with linear computational complexity, yet their application in medical image segmentation remains hindered by incompatibilities with image tokens and autoregressive assumptions. Moreover, it is difficult to achieve a balance in capturing both local fine-grained information and global semantic dependencies. To address these challenges, we introduce SAMA-UNet, a novel architecture for medical image segmentation. A key innovation is the Self-Adaptive Mamba-like Aggregated Attention (SAMA) block, which integrates contextual self-attention with dynamic weight modulation to prioritise the most relevant features based on local and global contexts. This approach reduces computational complexity and improves the representation of complex image features across multiple scales. We also suggest the Causal-Resonance Multi-Scale Module (CR-MSM), which enhances the flow of information between the encoder and decoder by using causal resonance learning. This mechanism allows the model to automatically adjust feature resolution and causal dependencies across scales, leading to better semantic alignment between the low-level and high-level features in U-shaped architectures. Experiments on MRI, CT, and endoscopy images show that SAMA-UNet performs better in segmentation accuracy than current methods using CNN, Transformer, and Mamba. The implementation is publicly available at GitHub.
This paper addresses the task of cross-modal medical image segmentation by exploring unsupervised domain adaptation (UDA) approaches. We propose a model-agnostic UDA framework, LowBridge, which builds on a simple observation that cross-modal images share some similar low-level features (e.g., edges) as they are depicting the same structures. Specifically, we first train a generative model to recover the source images from their edge features, followed by training a segmentation model on the generated source images, separately. At test time, edge features from the target images are input to the pretrained generative model to generate source-style target domain images, which are then segmented using the pretrained segmentation network. Despite its simplicity, extensive experiments on various publicly available datasets demonstrate that \proposed achieves state-of-the-art performance, outperforming eleven existing UDA approaches under different settings. Notably, further ablation studies show that \proposed is agnostic to different types of generative and segmentation models, suggesting its potential to be seamlessly plugged with the most advanced models to achieve even more outstanding results in the future. The code is available at https://github.com/JoshuaLPF/LowBridge.
Medical image segmentation relies heavily on convolutional neural networks (CNNs) and Transformer-based models. However, CNNs are constrained by limited receptive fields, while Transformers suffer from scalability challenges due to their quadratic computational complexity. To address these limitations, recent advances have explored alternative architectures. The state-space model Mamba offers near-linear complexity while capturing long-range dependencies, and the Kolmogorov-Arnold Network (KAN) enhances nonlinear expressiveness by replacing fixed activation functions with learnable ones. Building on these strengths, we propose MedVKAN, an efficient feature extraction model integrating Mamba and KAN. Specifically, we introduce the EFC-KAN module, which enhances KAN with convolutional operations to improve local pixel interaction. We further design the VKAN module, integrating Mamba with EFC-KAN as a replacement for Transformer modules, significantly improving feature extraction. Extensive experiments on five public medical image segmentation datasets show that MedVKAN achieves state-of-the-art performance on four datasets and ranks second on the remaining one. These results validate the potential of Mamba and KAN for medical image segmentation while introducing an innovative and computationally efficient feature extraction framework. The code is available at: https://github.com/beginner-cjh/MedVKAN.