High-resolution segmentation is critical for precise disease diagnosis by extracting micro-imaging information from medical images. Existing transformer-based encoder-decoder frameworks have demonstrated remarkable versatility and zero-shot performance in medical segmentation. While beneficial, they usually require huge memory costs when handling large-size segmentation mask predictions, which are expensive to apply to real-world scenarios. To address this limitation, we propose a memory-efficient framework for high-resolution medical image segmentation, called HRMedSeg. Specifically, we first devise a lightweight gated vision transformer (LGViT) as our image encoder to model long-range dependencies with linear complexity. Then, we design an efficient cross-multiscale decoder (ECM-Decoder) to generate high-resolution segmentation masks. Moreover, we utilize feature distillation during pretraining to unleash the potential of our proposed model. Extensive experiments reveal that HRMedSeg outperforms state-of-the-arts in diverse high-resolution medical image segmentation tasks. In particular, HRMedSeg uses only 0.59GB GPU memory per batch during fine-tuning, demonstrating low training costs. Besides, when HRMedSeg meets the Segment Anything Model (SAM), our HRMedSegSAM takes 0.61% parameters of SAM-H. The code is available at https://github.com/xq141839/HRMedSeg.
Identifying biomarkers in medical images is vital for a wide range of biotech applications. However, recent Transformer and CNN based methods often struggle with variations in morphology and staining, which limits their feature extraction capabilities. In medical image segmentation, where data samples are often limited, state-of-the-art (SOTA) methods improve accuracy by using pre-trained encoders, while end-to-end approaches typically fall short due to difficulties in transferring multiscale features effectively between encoders and decoders. To handle these challenges, we introduce a nested UNet architecture that captures both local and global context through Multiscale Feature Fusion and Attention Mechanisms. This design improves feature integration from encoders, highlights key channels and regions, and restores spatial details to enhance segmentation performance. Our method surpasses SOTA approaches, as evidenced by experiments across four datasets and detailed ablation studies. Code: https://github.com/saadwazir/ReN-UNet
Robots operating in unstructured environments often require accurate and consistent object-level representations. This typically requires segmenting individual objects from the robot's surroundings. While recent large models such as Segment Anything (SAM) offer strong performance in 2D image segmentation. These advances do not translate directly to performance in the physical 3D world, where they often over-segment objects and fail to produce consistent mask correspondences across views. In this paper, we present GraphSeg, a framework for generating consistent 3D object segmentations from a sparse set of 2D images of the environment without any depth information. GraphSeg adds edges to graphs and constructs dual correspondence graphs: one from 2D pixel-level similarities and one from inferred 3D structure. We formulate segmentation as a problem of edge addition, then subsequent graph contraction, which merges multiple 2D masks into unified object-level segmentations. We can then leverage \emph{3D foundation models} to produce segmented 3D representations. GraphSeg achieves robust segmentation with significantly fewer images and greater accuracy than prior methods. We demonstrate state-of-the-art performance on tabletop scenes and show that GraphSeg enables improved performance on downstream robotic manipulation tasks. Code available at https://github.com/tomtang502/graphseg.git.
Recent advances in zero-shot referring image segmentation (RIS), driven by models such as the Segment Anything Model (SAM) and CLIP, have made substantial progress in aligning visual and textual information. Despite these successes, the extraction of precise and high-quality mask region representations remains a critical challenge, limiting the full potential of RIS tasks. In this paper, we introduce a training-free, hybrid global-local feature extraction approach that integrates detailed mask-specific features with contextual information from the surrounding area, enhancing mask region representation. To further strengthen alignment between mask regions and referring expressions, we propose a spatial guidance augmentation strategy that improves spatial coherence, which is essential for accurately localizing described areas. By incorporating multiple spatial cues, this approach facilitates more robust and precise referring segmentation. Extensive experiments on standard RIS benchmarks demonstrate that our method significantly outperforms existing zero-shot RIS models, achieving substantial performance gains. We believe our approach advances RIS tasks and establishes a versatile framework for region-text alignment, offering broader implications for cross-modal understanding and interaction. Code is available at https://github.com/fhgyuanshen/HybridGL .
Supervised deep learning for semantic segmentation has achieved excellent results in accurately identifying anatomical and pathological structures in medical images. However, it often requires large annotated training datasets, which limits its scalability in clinical settings. To address this challenge, semi-supervised learning is a well-established approach that leverages both labeled and unlabeled data. In this paper, we introduce a novel semi-supervised teacher-student framework for biomedical image segmentation, inspired by the recent success of generative models. Our approach leverages denoising diffusion probabilistic models (DDPMs) to generate segmentation masks by progressively refining noisy inputs conditioned on the corresponding images. The teacher model is first trained in an unsupervised manner using a cycle-consistency constraint based on noise-corrupted image reconstruction, enabling it to generate informative semantic masks. Subsequently, the teacher is integrated into a co-training process with a twin-student network. The student learns from ground-truth labels when available and from teacher-generated pseudo-labels otherwise, while the teacher continuously improves its pseudo-labeling capabilities. Finally, to further enhance performance, we introduce a multi-round pseudo-label generation strategy that iteratively improves the pseudo-labeling process. We evaluate our approach on multiple biomedical imaging benchmarks, spanning multiple imaging modalities and segmentation tasks. Experimental results show that our method consistently outperforms state-of-the-art semi-supervised techniques, highlighting its effectiveness in scenarios with limited annotated data. The code to replicate our experiments can be found at https://github.com/ciampluca/diffusion_semi_supervised_biomedical_image_segmentation
Accurate segmentation of lesions plays a critical role in medical image analysis and diagnosis. Traditional segmentation approaches that rely solely on visual features often struggle with the inherent uncertainty in lesion distribution and size. To address these issues, we propose STPNet, a Scale-aware Text Prompt Network that leverages vision-language modeling to enhance medical image segmentation. Our approach utilizes multi-scale textual descriptions to guide lesion localization and employs retrieval-segmentation joint learning to bridge the semantic gap between visual and linguistic modalities. Crucially, STPNet retrieves relevant textual information from a specialized medical text repository during training, eliminating the need for text input during inference while retaining the benefits of cross-modal learning. We evaluate STPNet on three datasets: COVID-Xray, COVID-CT, and Kvasir-SEG. Experimental results show that our vision-language approach outperforms state-of-the-art segmentation methods, demonstrating the effectiveness of incorporating textual semantic knowledge into medical image analysis. The code has been made publicly on https://github.com/HUANGLIZI/STPNet.
While convolutional neural networks (CNNs) and vision transformers (ViTs) have advanced medical image segmentation, they face inherent limitations such as local receptive fields in CNNs and high computational complexity in ViTs. This paper introduces Deconver, a novel network that integrates traditional deconvolution techniques from image restoration as a core learnable component within a U-shaped architecture. Deconver replaces computationally expensive attention mechanisms with efficient nonnegative deconvolution (NDC) operations, enabling the restoration of high-frequency details while suppressing artifacts. Key innovations include a backpropagation-friendly NDC layer based on a provably monotonic update rule and a parameter-efficient design. Evaluated across four datasets (ISLES'22, BraTS'23, GlaS, FIVES) covering both 2D and 3D segmentation tasks, Deconver achieves state-of-the-art performance in Dice scores and Hausdorff distance while reducing computational costs (FLOPs) by up to 90% compared to leading baselines. By bridging traditional image restoration with deep learning, this work offers a practical solution for high-precision segmentation in resource-constrained clinical workflows. The project is available at https://github.com/pashtari/deconver.
Vision Transformers (ViTs) have shown remarkable performance and scalability across various computer vision tasks. To apply single-scale ViTs to image segmentation, existing methods adopt a convolutional adapter to generate multi-scale features, a pixel decoder to fuse these features, and a Transformer decoder that uses the fused features to make predictions. In this paper, we show that the inductive biases introduced by these task-specific components can instead be learned by the ViT itself, given sufficiently large models and extensive pre-training. Based on these findings, we introduce the Encoder-only Mask Transformer (EoMT), which repurposes the plain ViT architecture to conduct image segmentation. With large-scale models and pre-training, EoMT obtains a segmentation accuracy similar to state-of-the-art models that use task-specific components. At the same time, EoMT is significantly faster than these methods due to its architectural simplicity, e.g., up to 4x faster with ViT-L. Across a range of model sizes, EoMT demonstrates an optimal balance between segmentation accuracy and prediction speed, suggesting that compute resources are better spent on scaling the ViT itself rather than adding architectural complexity. Code: https://www.tue-mps.org/eomt/.
Medical image segmentation typically relies solely on visual data, overlooking the rich textual information clinicians use for diagnosis. Vision-language models attempt to bridge this gap, but existing approaches often process visual and textual features independently, resulting in weak cross-modal alignment. Simple fusion techniques fail due to the inherent differences between spatial visual features and sequential text embeddings. Additionally, medical terminology deviates from general language, limiting the effectiveness of off-the-shelf text encoders and further hindering vision-language alignment. We propose BiPVL-Seg, an end-to-end framework that integrates vision-language fusion and embedding alignment through architectural and training innovations, where both components reinforce each other to enhance medical image segmentation. BiPVL-Seg introduces bidirectional progressive fusion in the architecture, which facilitates stage-wise information exchange between vision and text encoders. Additionally, it incorporates global-local contrastive alignment, a training objective that enhances the text encoder's comprehension by aligning text and vision embeddings at both class and concept levels. Extensive experiments on diverse medical imaging benchmarks across CT and MR modalities demonstrate BiPVL-Seg's superior performance when compared with state-of-the-art methods in complex multi-class segmentation. Source code is available in this GitHub repository.
Despite the significant advancements in general image segmentation achieved by large-scale pre-trained foundation models (such as Meta's Segment Any-thing Model (SAM) series and DINOv2), their performance in specialized fields remains limited by two critical issues: the excessive training costs due to large model parameters, and the insufficient ability to represent specific domain characteristics. This paper proposes a multi-scale feature collabora-tion framework guided by DINOv2 for SAM2, with core innovations in three aspects: (1) Establishing a feature collaboration mechanism between DINOv2 and SAM2 backbones, where high-dimensional semantic features extracted by the self-supervised model guide multi-scale feature fusion; (2) Designing lightweight adapter modules and cross-modal, cross-layer feature fusion units to inject cross-domain knowledge while freezing the base model parameters; (3) Constructing a U-shaped network structure based on U-net, which utilizes attention mechanisms to achieve adaptive aggregation decoding of multi-granularity features. This framework surpasses existing state-of-the-art meth-ods in downstream tasks such as camouflage target detection and salient ob-ject detection, without requiring costly training processes. It provides a tech-nical pathway for efficient deployment of visual image segmentation, demon-strating significant application value in a wide range of downstream tasks and specialized fields within image segmentation.Project page: https://github.com/CheneyXuYiMin/SAM2DINO-Seg
Skin lesion segmentation is a critical challenge in computer vision, and it is essential to separate pathological features from healthy skin for diagnostics accurately. Traditional Convolutional Neural Networks (CNNs) are limited by narrow receptive fields, and Transformers face significant computational burdens. This paper presents a novel skin lesion segmentation framework, the Atrous Shifted Parallel Vision Mamba UNet (ASP-VMUNet), which integrates the efficient and scalable Mamba architecture to overcome limitations in traditional CNNs and computationally demanding Transformers. The framework introduces an atrous scan technique that minimizes background interference and expands the receptive field, enhancing Mamba's scanning capabilities. Additionally, the inclusion of a Parallel Vision Mamba (PVM) layer and a shift round operation optimizes feature segmentation and fosters rich inter-segment information exchange. A supplementary CNN branch with a Selective-Kernel (SK) Block further refines the segmentation by blending local and global contextual information. Tested on four benchmark datasets (ISIC16/17/18 and PH2), ASP-VMUNet demonstrates superior performance in skin lesion segmentation, validated by comprehensive ablation studies. This approach not only advances medical image segmentation but also highlights the benefits of hybrid architectures in medical imaging technology. Our code is available at https://github.com/BaoBao0926/ASP-VMUNet/tree/main.
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 .
Segment Anything Model (SAM) demonstrates powerful zero-shot capabilities; however, its accuracy and robustness significantly decrease when applied to medical image segmentation. Existing methods address this issue through modality fusion, integrating textual and image information to provide more detailed priors. In this study, we argue that the granularity of text and the domain gap affect the accuracy of the priors. Furthermore, the discrepancy between high-level abstract semantics and pixel-level boundary details in images can introduce noise into the fusion process. To address this, we propose Prior-Guided SAM (PG-SAM), which employs a fine-grained modality prior aligner to leverage specialized medical knowledge for better modality alignment. The core of our method lies in efficiently addressing the domain gap with fine-grained text from a medical LLM. Meanwhile, it also enhances the priors' quality after modality alignment, ensuring more accurate segmentation. In addition, our decoder enhances the model's expressive capabilities through multi-level feature fusion and iterative mask optimizer operations, supporting unprompted learning. We also propose a unified pipeline that effectively supplies high-quality semantic information to SAM. Extensive experiments on the Synapse dataset demonstrate that the proposed PG-SAM achieves state-of-the-art performance. Our code is released at https://github.com/logan-0623/PG-SAM.
Medical image segmentation is crucial for enhancing diagnostic accuracy and treatment planning in Magnetic Resonance Imaging (MRI). However, acquiring precise lesion masks for segmentation model training demands specialized expertise and significant time investment, leading to a small dataset scale in clinical practice. In this paper, we present ZECO, a ZeroFusion guided 3D MRI conditional generation framework that extracts, compresses, and generates high-fidelity MRI images with corresponding 3D segmentation masks to mitigate data scarcity. To effectively capture inter-slice relationships within volumes, we introduce a Spatial Transformation Module that encodes MRI images into a compact latent space for the diffusion process. Moving beyond unconditional generation, our novel ZeroFusion method progressively maps 3D masks to MRI images in latent space, enabling robust training on limited datasets while avoiding overfitting. ZECO outperforms state-of-the-art models in both quantitative and qualitative evaluations on Brain MRI datasets across various modalities, showcasing its exceptional capability in synthesizing high-quality MRI images conditioned on segmentation masks.
Artificial intelligence (AI) is increasingly being used for medical imaging tasks. However, there can be biases in the resulting models, particularly when they were trained using imbalanced training datasets. One such example has been the strong race bias effect in cardiac magnetic resonance (CMR) image segmentation models. Although this phenomenon has been reported in a number of publications, little is known about the effectiveness of bias mitigation algorithms in this domain. We aim to investigate the impact of common bias mitigation methods to address bias between Black and White subjects in AI-based CMR segmentation models. Specifically, we use oversampling, importance reweighing and Group DRO as well as combinations of these techniques to mitigate the race bias. Furthermore, motivated by recent findings on the root causes of AI-based CMR segmentation bias, we evaluate the same methods using models trained and evaluated on cropped CMR images. We find that bias can be mitigated using oversampling, significantly improving performance for the underrepresented Black subjects whilst not significantly reducing the majority White subjects' performance. Group DRO also improves performance for Black subjects but not significantly, while reweighing decreases performance for Black subjects. Using a combination of oversampling and Group DRO also improves performance for Black subjects but not significantly. Using cropped images increases performance for both races and reduces the bias, whilst adding oversampling as a bias mitigation technique with cropped images reduces the bias further.
Lung cancer is a leading cause of cancer-related deaths globally. PET-CT is crucial for imaging lung tumors, providing essential metabolic and anatomical information, while it faces challenges such as poor image quality, motion artifacts, and complex tumor morphology. Deep learning-based models are expected to address these problems, however, existing small-scale and private datasets limit significant performance improvements for these methods. Hence, we introduce a large-scale PET-CT lung tumor segmentation dataset, termed PCLT20K, which comprises 21,930 pairs of PET-CT images from 605 patients. Furthermore, we propose a cross-modal interactive perception network with Mamba (CIPA) for lung tumor segmentation in PET-CT images. Specifically, we design a channel-wise rectification module (CRM) that implements a channel state space block across multi-modal features to learn correlated representations and helps filter out modality-specific noise. A dynamic cross-modality interaction module (DCIM) is designed to effectively integrate position and context information, which employs PET images to learn regional position information and serves as a bridge to assist in modeling the relationships between local features of CT images. Extensive experiments on a comprehensive benchmark demonstrate the effectiveness of our CIPA compared to the current state-of-the-art segmentation methods. We hope our research can provide more exploration opportunities for medical image segmentation. The dataset and code are available at https://github.com/mj129/CIPA.
Referring medical image segmentation targets delineating lesions indicated by textual descriptions. Aligning visual and textual cues is challenging due to their distinct data properties. Inspired by large-scale pre-trained vision-language models, we propose CausalCLIPSeg, an end-to-end framework for referring medical image segmentation that leverages CLIP. Despite not being trained on medical data, we enforce CLIP's rich semantic space onto the medical domain by a tailored cross-modal decoding method to achieve text-to-pixel alignment. Furthermore, to mitigate confounding bias that may cause the model to learn spurious correlations instead of meaningful causal relationships, CausalCLIPSeg introduces a causal intervention module which self-annotates confounders and excavates causal features from inputs for segmentation judgments. We also devise an adversarial min-max game to optimize causal features while penalizing confounding ones. Extensive experiments demonstrate the state-of-the-art performance of our proposed method. Code is available at https://github.com/WUTCM-Lab/CausalCLIPSeg.
Semantic segmentation from RGB cameras is essential to the perception of autonomous flying vehicles. The stability of predictions through the captured videos is paramount to their reliability and, by extension, to the trustworthiness of the agents. In this paper, we propose a lightweight video semantic segmentation approach-suited to onboard real-time inference-achieving high temporal consistency on aerial data through Semantic Similarity Propagation across frames. SSP temporally propagates the predictions of an efficient image segmentation model with global registration alignment to compensate for camera movements. It combines the current estimation and the prior prediction with linear interpolation using weights computed from the features similarities of the two frames. Because data availability is a challenge in this domain, we propose a consistency-aware Knowledge Distillation training procedure for sparsely labeled datasets with few annotations. Using a large image segmentation model as a teacher to train the efficient SSP, we leverage the strong correlations between labeled and unlabeled frames in the same training videos to obtain high-quality supervision on all frames. KD-SSP obtains a significant temporal consistency increase over the base image segmentation model of 12.5% and 6.7% TC on UAVid and RuralScapes respectively, with higher accuracy and comparable inference speed. On these aerial datasets, KD-SSP provides a superior segmentation quality and inference speed trade-off than other video methods proposed for general applications and shows considerably higher consistency. The code will be made publicly available upon acceptance.
The complex nature of medical image segmentation calls for models that are specifically designed to capture detailed, domain-specific features. Large foundation models offer considerable flexibility, yet the cost of fine-tuning these models remains a significant barrier. Parameter-Efficient Fine-Tuning (PEFT) methods, such as Low-Rank Adaptation (LoRA), efficiently update model weights with low-rank matrices but may suffer from underfitting when the chosen rank is insufficient to capture domain-specific nuances. Conversely, full-rank Singular Value Decomposition (SVD) based methods provide comprehensive updates by modifying all singular values, yet they often lack flexibility and exhibit variable performance across datasets. We propose SALT (Singular Value Adaptation with Low-Rank Transformation), a method that selectively adapts the most influential singular values using trainable scale and shift parameters while complementing this with a low-rank update for the remaining subspace. This hybrid approach harnesses the advantages of both LoRA and SVD, enabling effective adaptation without relying on increasing model size or depth. Evaluated on 5 challenging medical datasets, ranging from as few as 20 samples to 1000, SALT outperforms state-of-the-art PEFT (LoRA and SVD) by 2% to 5% in Dice with only 3.9% trainable parameters, demonstrating robust adaptation even in low-resource settings. The code for SALT is available at: https://github.com/BioMedIA-MBZUAI/SALT
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.