Medical image segmentation faces persistent challenges due to severe class imbalance and the frequency-specific distribution of anatomical structures. Most conventional CNN-based methods operate in the spatial domain and struggle to capture minority class signals, often affected by frequency aliasing and limited spectral selectivity. Transformer-based models, while powerful in modeling global dependencies, tend to overlook critical local details necessary for fine-grained segmentation. To overcome these limitations, we propose FreqU-FNet, a novel U-shaped segmentation architecture operating in the frequency domain. Our framework incorporates a Frequency Encoder that leverages Low-Pass Frequency Convolution and Daubechies wavelet-based downsampling to extract multi-scale spectral features. To reconstruct fine spatial details, we introduce a Spatial Learnable Decoder (SLD) equipped with an adaptive multi-branch upsampling strategy. Furthermore, we design a frequency-aware loss (FAL) function to enhance minority class learning. Extensive experiments on multiple medical segmentation benchmarks demonstrate that FreqU-FNet consistently outperforms both CNN and Transformer baselines, particularly in handling under-represented classes, by effectively exploiting discriminative frequency bands.
Foundation models (FMs) such as CLIP and SAM have recently shown great promise in image segmentation tasks, yet their adaptation to 3D medical imaging-particularly for pathology detection and segmentation-remains underexplored. A critical challenge arises from the domain gap between natural images and medical volumes: existing FMs, pre-trained on 2D data, struggle to capture 3D anatomical context, limiting their utility in clinical applications like tumor segmentation. To address this, we propose an adaptation framework called TAGS: Tumor Adaptive Guidance for SAM, which unlocks 2D FMs for 3D medical tasks through multi-prompt fusion. By preserving most of the pre-trained weights, our approach enhances SAM's spatial feature extraction using CLIP's semantic insights and anatomy-specific prompts. Extensive experiments on three open-source tumor segmentation datasets prove that our model surpasses the state-of-the-art medical image segmentation models (+46.88% over nnUNet), interactive segmentation frameworks, and other established medical FMs, including SAM-Med2D, SAM-Med3D, SegVol, Universal, 3D-Adapter, and SAM-B (at least +13% over them). This highlights the robustness and adaptability of our proposed framework across diverse medical segmentation tasks.
Image segmentation remains a challenging task in computer vision, demanding robust mask generation and precise classification. Recent mask-based approaches yield high-quality masks by capturing global context. However, accurately classifying these masks, especially in the presence of ambiguous boundaries and imbalanced class distributions, remains an open challenge. In this work, we introduce ViT-P, a novel two-stage segmentation framework that decouples mask generation from classification. The first stage employs a proposal generator to produce class-agnostic mask proposals, while the second stage utilizes a point-based classification model built on the Vision Transformer (ViT) to refine predictions by focusing on mask central points. ViT-P serves as a pre-training-free adapter, allowing the integration of various pre-trained vision transformers without modifying their architecture, ensuring adaptability to dense prediction tasks. Furthermore, we demonstrate that coarse and bounding box annotations can effectively enhance classification without requiring additional training on fine annotation datasets, reducing annotation costs while maintaining strong performance. Extensive experiments across COCO, ADE20K, and Cityscapes datasets validate the effectiveness of ViT-P, achieving state-of-the-art results with 54.0 PQ on ADE20K panoptic segmentation, 87.4 mIoU on Cityscapes semantic segmentation, and 63.6 mIoU on ADE20K semantic segmentation. The code and pretrained models are available at: https://github.com/sajjad-sh33/ViT-P}{https://github.com/sajjad-sh33/ViT-P.
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.
Open vocabulary image segmentation tackles the challenge of recognizing dynamically adjustable, predefined novel categories at inference time by leveraging vision-language alignment. However, existing paradigms typically perform class-agnostic region segmentation followed by category matching, which deviates from the human visual system's process of recognizing objects based on semantic concepts, leading to poor alignment between region segmentation and target concepts. To bridge this gap, we propose a novel Cognition-Inspired Framework for open vocabulary image segmentation that emulates the human visual recognition process: first forming a conceptual understanding of an object, then perceiving its spatial extent. The framework consists of three core components: (1) A Generative Vision-Language Model (G-VLM) that mimics human cognition by generating object concepts to provide semantic guidance for region segmentation. (2) A Concept-Aware Visual Enhancer Module that fuses textual concept features with global visual representations, enabling adaptive visual perception based on target concepts. (3) A Cognition-Inspired Decoder that integrates local instance features with G-VLM-provided semantic cues, allowing selective classification over a subset of relevant categories. Extensive experiments demonstrate that our framework achieves significant improvements, reaching $27.2$ PQ, $17.0$ mAP, and $35.3$ mIoU on A-150. It further attains $56.2$, $28.2$, $15.4$, $59.2$, $18.7$, and $95.8$ mIoU on Cityscapes, Mapillary Vistas, A-847, PC-59, PC-459, and PAS-20, respectively. In addition, our framework supports vocabulary-free segmentation, offering enhanced flexibility in recognizing unseen categories. Code will be public.
We present LlamaSeg, a visual autoregressive framework that unifies multiple image segmentation tasks via natural language instructions. We reformulate image segmentation as a visual generation problem, representing masks as "visual" tokens and employing a LLaMA-style Transformer to predict them directly from image inputs. By adhering to the next-token prediction paradigm, our approach naturally integrates segmentation tasks into autoregressive architectures. To support large-scale training, we introduce a data annotation pipeline and construct the SA-OVRS dataset, which contains 2M segmentation masks annotated with over 5,800 open-vocabulary labels or diverse textual descriptions, covering a wide spectrum of real-world scenarios. This enables our model to localize objects in images based on text prompts and to generate fine-grained masks. To more accurately evaluate the quality of masks produced by visual generative models, we further propose a composite metric that combines Intersection over Union (IoU) with Average Hausdorff Distance (AHD), offering a more precise assessment of contour fidelity. Experimental results demonstrate that our method surpasses existing generative models across multiple datasets and yields more detailed segmentation masks.
Image segmentation is a fundamental task in computer vision, aimed at partitioning an image into semantically meaningful regions. Referring image segmentation extends this task by using natural language expressions to localize specific objects, requiring effective integration of visual and linguistic information. In this work, we propose SegVLM, a vision-language model that incorporates architectural improvements to enhance segmentation accuracy and cross-modal alignment. The model integrates squeeze-and-excitation (SE) blocks for dynamic feature recalibration, deformable convolutions for geometric adaptability, and residual connections for deep feature learning. We also introduce a novel referring-aware fusion (RAF) loss that balances region-level alignment, boundary precision, and class imbalance. Extensive experiments and ablation studies demonstrate that each component contributes to consistent performance improvements. SegVLM also shows strong generalization across diverse datasets and referring expression scenarios.
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 (MIS) includes diverse tasks, from bone to organ segmentation, each with its own challenges in finding the best segmentation model. The state-of-the-art AutoML-related MIS-framework nnU-Net automates many aspects of model configuration but remains constrained by fixed hyperparameters and heuristic design choices. As a full-AutoML framework for MIS, we propose Auto-nnU-Net, a novel nnU-Net variant enabling hyperparameter optimization (HPO), neural architecture search (NAS), and hierarchical NAS (HNAS). Additionally, we propose Regularized PriorBand to balance model accuracy with the computational resources required for training, addressing the resource constraints often faced in real-world medical settings that limit the feasibility of extensive training procedures. We evaluate our approach across diverse MIS datasets from the well-established Medical Segmentation Decathlon, analyzing the impact of AutoML techniques on segmentation performance, computational efficiency, and model design choices. The results demonstrate that our AutoML approach substantially improves the segmentation performance of nnU-Net on 6 out of 10 datasets and is on par on the other datasets while maintaining practical resource requirements. Our code is available at https://github.com/LUH-AI/AutonnUNet.
Perturbation with diverse unlabeled data has proven beneficial for semi-supervised medical image segmentation (SSMIS). While many works have successfully used various perturbation techniques, a deeper understanding of learning perturbations is needed. Excessive or inappropriate perturbation can have negative effects, so we aim to address two challenges: how to use perturbation mechanisms to guide the learning of unlabeled data through labeled data, and how to ensure accurate predictions in boundary regions. Inspired by human progressive and periodic learning, we propose a progressive and periodic perturbation mechanism (P3M) and a boundary-focused loss. P3M enables dynamic adjustment of perturbations, allowing the model to gradually learn them. Our boundary-focused loss encourages the model to concentrate on boundary regions, enhancing sensitivity to intricate details and ensuring accurate predictions. Experimental results demonstrate that our method achieves state-of-the-art performance on two 2D and 3D datasets. Moreover, P3M is extendable to other methods, and the proposed loss serves as a universal tool for improving existing methods, highlighting the scalability and applicability of our approach.
Recently, prototype learning has emerged in semi-supervised medical image segmentation and achieved remarkable performance. However, the scarcity of labeled data limits the expressiveness of prototypes in previous methods, potentially hindering the complete representation of prototypes for class embedding. To overcome this issue, we propose an efficient prototype consistency learning via joint uncertainty quantification and data augmentation (EPCL-JUDA) to enhance the semantic expression of prototypes based on the framework of Mean-Teacher. The concatenation of original and augmented labeled data is fed into student network to generate expressive prototypes. Then, a joint uncertainty quantification method is devised to optimize pseudo-labels and generate reliable prototypes for original and augmented unlabeled data separately. High-quality global prototypes for each class are formed by fusing labeled and unlabeled prototypes, which are utilized to generate prototype-to-features to conduct consistency learning. Notably, a prototype network is proposed to reduce high memory requirements brought by the introduction of augmented data. Extensive experiments on Left Atrium, Pancreas-NIH, Type B Aortic Dissection datasets demonstrate EPCL-JUDA's superiority over previous state-of-the-art approaches, confirming the effectiveness of our framework. The code will be released soon.
In recent years, deep learning-based Monocular Depth Estimation (MDE) models have been widely applied in fields such as autonomous driving and robotics. However, their vulnerability to backdoor attacks remains unexplored. To fill the gap in this area, we conduct a comprehensive investigation of backdoor attacks against MDE models. Typically, existing backdoor attack methods can not be applied to MDE models. This is because the label used in MDE is in the form of a depth map. To address this, we propose BadDepth, the first backdoor attack targeting MDE models. BadDepth overcomes this limitation by selectively manipulating the target object's depth using an image segmentation model and restoring the surrounding areas via depth completion, thereby generating poisoned datasets for object-level backdoor attacks. To improve robustness in physical world scenarios, we further introduce digital-to-physical augmentation to adapt to the domain gap between the physical world and the digital domain. Extensive experiments on multiple models validate the effectiveness of BadDepth in both the digital domain and the physical world, without being affected by environmental factors.
Semi-supervised learning (SSL) has achieved significant progress in medical image segmentation (SSMIS) through effective utilization of limited labeled data. While current SSL methods for medical images predominantly rely on consistency regularization and pseudo-labeling, they often overlook transferable semantic relationships across different clinical domains and imaging modalities. To address this, we propose TransMedSeg, a novel transferable semantic framework for semi-supervised medical image segmentation. Our approach introduces a Transferable Semantic Augmentation (TSA) module, which implicitly enhances feature representations by aligning domain-invariant semantics through cross-domain distribution matching and intra-domain structural preservation. Specifically, TransMedSeg constructs a unified feature space where teacher network features are adaptively augmented towards student network semantics via a lightweight memory module, enabling implicit semantic transformation without explicit data generation. Interestingly, this augmentation is implicitly realized through an expected transferable cross-entropy loss computed over the augmented teacher distribution. An upper bound of the expected loss is theoretically derived and minimized during training, incurring negligible computational overhead. Extensive experiments on medical image datasets demonstrate that TransMedSeg outperforms existing semi-supervised methods, establishing a new direction for transferable representation learning in medical image analysis.
Accurate segmentation of anatomical structures in volumetric medical images is crucial for clinical applications, including disease monitoring and cancer treatment planning. Contemporary interactive segmentation models, such as Segment Anything Model 2 (SAM-2) and its medical variant (MedSAM-2), rely on manually provided prompts like bounding boxes and mouse clicks. In this study, we introduce eye gaze as a novel informational modality for interactive segmentation, marking the application of eye-tracking for 3D medical image segmentation. We evaluate the performance of using gaze-based prompts with SAM-2 and MedSAM-2 using both synthetic and real gaze data. Compared to bounding boxes, gaze-based prompts offer a time-efficient interaction approach with slightly lower segmentation quality. Our findings highlight the potential of using gaze as a complementary input modality for interactive 3D medical image segmentation.