Annotation variability remains a substantial challenge in medical image segmentation, stemming from ambiguous imaging boundaries and diverse clinical expertise. Traditional deep learning methods producing single deterministic segmentation predictions often fail to capture these annotator biases. Although recent studies have explored multi-rater segmentation, existing methods typically focus on a single perspective -- either generating a probabilistic ``gold standard'' consensus or preserving expert-specific preferences -- thus struggling to provide a more omni view. In this study, we propose DiffOSeg, a two-stage diffusion-based framework, which aims to simultaneously achieve both consensus-driven (combining all experts' opinions) and preference-driven (reflecting experts' individual assessments) segmentation. Stage I establishes population consensus through a probabilistic consensus strategy, while Stage II captures expert-specific preference via adaptive prompts. Demonstrated on two public datasets (LIDC-IDRI and NPC-170), our model outperforms existing state-of-the-art methods across all evaluated metrics. Source code is available at https://github.com/string-ellipses/DiffOSeg .
Unified Medical Image Segmentation (UMIS) is critical for comprehensive anatomical assessment but faces challenges due to multi-scale structural heterogeneity. Conventional pixel-based approaches, lacking object-level anatomical insight and inter-organ relational modeling, struggle with morphological complexity and feature conflicts, limiting their efficacy in UMIS. We propose Mamba Snake, a novel deep snake framework enhanced by state space modeling for UMIS. Mamba Snake frames multi-contour evolution as a hierarchical state space atlas, effectively modeling macroscopic inter-organ topological relationships and microscopic contour refinements. We introduce a snake-specific vision state space module, the Mamba Evolution Block (MEB), which leverages effective spatiotemporal information aggregation for adaptive refinement of complex morphologies. Energy map shape priors further ensure robust long-range contour evolution in heterogeneous data. Additionally, a dual-classification synergy mechanism is incorporated to concurrently optimize detection and segmentation, mitigating under-segmentation of microstructures in UMIS. Extensive evaluations across five clinical datasets reveal Mamba Snake's superior performance, with an average Dice improvement of 3\% over state-of-the-art methods.
Achieving equity in healthcare accessibility requires lightweight yet high-performance solutions for medical image segmentation, particularly in resource-limited settings. Existing methods like U-Net and its variants often suffer from limited global Effective Receptive Fields (ERFs), hindering their ability to capture long-range dependencies. To address this, we propose U-RWKV, a novel framework leveraging the Recurrent Weighted Key-Value(RWKV) architecture, which achieves efficient long-range modeling at O(N) computational cost. The framework introduces two key innovations: the Direction-Adaptive RWKV Module(DARM) and the Stage-Adaptive Squeeze-and-Excitation Module(SASE). DARM employs Dual-RWKV and QuadScan mechanisms to aggregate contextual cues across images, mitigating directional bias while preserving global context and maintaining high computational efficiency. SASE dynamically adapts its architecture to different feature extraction stages, balancing high-resolution detail preservation and semantic relationship capture. Experiments demonstrate that U-RWKV achieves state-of-the-art segmentation performance with high computational efficiency, offering a practical solution for democratizing advanced medical imaging technologies in resource-constrained environments. The code is available at https://github.com/hbyecoding/U-RWKV.
In medical image segmentation, convolutional neural networks (CNNs) and transformers are dominant. For CNNs, given the local receptive fields of convolutional layers, long-range spatial correlations are captured through consecutive convolutions and pooling. However, as the computational cost and memory footprint can be prohibitively large, 3D models can only afford fewer layers than 2D models with reduced receptive fields and abstract levels. For transformers, although long-range correlations can be captured by multi-head attention, its quadratic complexity with respect to input size is computationally demanding. Therefore, either model may require input size reduction to allow more filters and layers for better segmentation. Nevertheless, given their discrete nature, models trained with patch-wise training or image downsampling may produce suboptimal results when applied on higher resolutions. To address this issue, here we propose the resolution-robust HNOSeg-XS architecture. We model image segmentation by learnable partial differential equations through the Fourier neural operator which has the zero-shot super-resolution property. By replacing the Fourier transform by the Hartley transform and reformulating the problem in the frequency domain, we created the HNOSeg-XS model, which is resolution robust, fast, memory efficient, and extremely parameter efficient. When tested on the BraTS'23, KiTS'23, and MVSeg'23 datasets with a Tesla V100 GPU, HNOSeg-XS showed its superior resolution robustness with fewer than 34.7k model parameters. It also achieved the overall best inference time (< 0.24 s) and memory efficiency (< 1.8 GiB) compared to the tested CNN and transformer models.
Manual annotation of medical images is a labor-intensive and time-consuming process, posing a significant bottleneck in the development and deployment of robust medical imaging AI systems. This paper introduces a novel Human-AI collaborative framework for medical image segmentation that substantially reduces the annotation burden by eliminating the need for explicit manual pixel-level labeling. The core innovation lies in a preference learning paradigm, where human experts provide minimal, intuitive feedback -- simply indicating whether an AI-generated segmentation is better or worse than a previous version. The framework comprises four key components: (1) an adaptable foundation model (FM) for feature extraction, (2) label propagation based on feature similarity, (3) a clicking agent that learns from human better-or-worse feedback to decide where to click and with which label, and (4) a multi-round segmentation learning procedure that trains a state-of-the-art segmentation network using pseudo-labels generated by the clicking agent and FM-based label propagation. Experiments on three public datasets demonstrate that the proposed approach achieves competitive segmentation performance using only binary preference feedback, without requiring experts to directly manually annotate the images.
Recent "segment anything" efforts show promise by learning from large-scale data, but adapting such models directly to medical images remains challenging due to the complexity of medical data, noisy annotations, and continual learning requirements across diverse modalities and anatomical structures. In this work, we propose SAMed-2, a new foundation model for medical image segmentation built upon the SAM-2 architecture. Specifically, we introduce a temporal adapter into the image encoder to capture image correlations and a confidence-driven memory mechanism to store high-certainty features for later retrieval. This memory-based strategy counters the pervasive noise in large-scale medical datasets and mitigates catastrophic forgetting when encountering new tasks or modalities. To train and evaluate SAMed-2, we curate MedBank-100k, a comprehensive dataset spanning seven imaging modalities and 21 medical segmentation tasks. Our experiments on both internal benchmarks and 10 external datasets demonstrate superior performance over state-of-the-art baselines in multi-task scenarios. The code is available at: https://github.com/ZhilingYan/Medical-SAM-Bench.
The clinical utility of deep learning models for medical image segmentation is severely constrained by their inability to generalize to unseen domains. This failure is often rooted in the models learning spurious correlations between anatomical content and domain-specific imaging styles. To overcome this fundamental challenge, we introduce Causal-SAM-LLM, a novel framework that elevates Large Language Models (LLMs) to the role of causal reasoners. Our framework, built upon a frozen Segment Anything Model (SAM) encoder, incorporates two synergistic innovations. First, Linguistic Adversarial Disentanglement (LAD) employs a Vision-Language Model to generate rich, textual descriptions of confounding image styles. By training the segmentation model's features to be contrastively dissimilar to these style descriptions, it learns a representation robustly purged of non-causal information. Second, Test-Time Causal Intervention (TCI) provides an interactive mechanism where an LLM interprets a clinician's natural language command to modulate the segmentation decoder's features in real-time, enabling targeted error correction. We conduct an extensive empirical evaluation on a composite benchmark from four public datasets (BTCV, CHAOS, AMOS, BraTS), assessing generalization under cross-scanner, cross-modality, and cross-anatomy settings. Causal-SAM-LLM establishes a new state of the art in out-of-distribution (OOD) robustness, improving the average Dice score by up to 6.2 points and reducing the Hausdorff Distance by 15.8 mm over the strongest baseline, all while using less than 9% of the full model's trainable parameters. Our work charts a new course for building robust, efficient, and interactively controllable medical AI systems.
Medical image segmentation is a key task in the imaging workflow, influencing many image-based decisions. Traditional, fully-supervised segmentation models rely on large amounts of labeled training data, typically obtained through manual annotation, which can be an expensive, time-consuming, and error-prone process. This signals a need for accurate, automatic, and annotation-efficient methods of training these models. We propose ADA-SAM (automated, domain-specific, and adaptive segment anything model), a novel multitask learning framework for medical image segmentation that leverages class activation maps from an auxiliary classifier to guide the predictions of the semi-supervised segmentation branch, which is based on the Segment Anything (SAM) framework. Additionally, our ADA-SAM model employs a novel gradient feedback mechanism to create a learnable connection between the segmentation and classification branches by using the segmentation gradients to guide and improve the classification predictions. We validate ADA-SAM on real-world clinical data collected during rehabilitation trials, and demonstrate that our proposed method outperforms both fully-supervised and semi-supervised baselines by double digits in limited label settings. Our code is available at: https://github.com/tbwa233/ADA-SAM.
Medical image segmentation plays a crucial role in clinical diagnosis and treatment planning, where accurate boundary delineation is essential for precise lesion localization, organ identification, and quantitative assessment. In recent years, deep learning-based methods have significantly advanced segmentation accuracy. However, two major challenges remain. First, the performance of these methods heavily relies on large-scale annotated datasets, which are often difficult to obtain in medical scenarios due to privacy concerns and high annotation costs. Second, clinically challenging scenarios, such as low contrast in certain imaging modalities and blurry lesion boundaries caused by malignancy, still pose obstacles to precise segmentation. To address these challenges, we propose MedSAM-CA, an architecture-level fine-tuning approach that mitigates reliance on extensive manual annotations by adapting the pretrained foundation model, Medical Segment Anything (MedSAM). MedSAM-CA introduces two key components: the Convolutional Attention-Enhanced Boundary Refinement Network (CBR-Net) and the Attention-Enhanced Feature Fusion Block (Atte-FFB). CBR-Net operates in parallel with the MedSAM encoder to recover boundary information potentially overlooked by long-range attention mechanisms, leveraging hierarchical convolutional processing. Atte-FFB, embedded in the MedSAM decoder, fuses multi-level fine-grained features from skip connections in CBR-Net with global representations upsampled within the decoder to enhance boundary delineation accuracy. Experiments on publicly available datasets covering dermoscopy, CT, and MRI imaging modalities validate the effectiveness of MedSAM-CA. On dermoscopy dataset, MedSAM-CA achieves 94.43% Dice with only 2% of full training data, reaching 97.25% of full-data training performance, demonstrating strong effectiveness in low-resource clinical settings.
Although new vision foundation models such as Segment Anything Model 2 (SAM2) have significantly enhanced zero-shot image segmentation capabilities, reliance on human-provided prompts poses significant challenges in adapting SAM2 to medical image segmentation tasks. Moreover, SAM2's performance in medical image segmentation was limited by the domain shift issue, since it was originally trained on natural images and videos. To address these challenges, we proposed SAM2 with support-set guided prompting (SAM2-SGP), a framework that eliminated the need for manual prompts. The proposed model leveraged the memory mechanism of SAM2 to generate pseudo-masks using image-mask pairs from a support set via a Pseudo-mask Generation (PMG) module. We further introduced a novel Pseudo-mask Attention (PMA) module, which used these pseudo-masks to automatically generate bounding boxes and enhance localized feature extraction by guiding attention to relevant areas. Furthermore, a low-rank adaptation (LoRA) strategy was adopted to mitigate the domain shift issue. The proposed framework was evaluated on both 2D and 3D datasets across multiple medical imaging modalities, including fundus photography, X-ray, computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasound. The results demonstrated a significant performance improvement over state-of-the-art models, such as nnUNet and SwinUNet, as well as foundation models, such as SAM2 and MedSAM2, underscoring the effectiveness of the proposed approach. Our code is publicly available at https://github.com/astlian9/SAM_Support.
Medical image segmentation is challenging due to overlapping anatomies with ambiguous boundaries and a severe imbalance between the foreground and background classes, which particularly affects the delineation of small lesions. Existing methods, including encoder-decoder networks and prompt-driven variants of the Segment Anything Model (SAM), rely heavily on local cues or user prompts and lack integrated semantic priors, thus failing to generalize well to low-contrast or overlapping targets. To address these issues, we propose MedSeg-R, a lightweight, dual-stage framework inspired by inspired by clinical reasoning. Its cognitive stage interprets medical report into structured semantic priors (location, texture, shape), which are fused via transformer block. In the perceptual stage, these priors modulate the SAM backbone: spatial attention highlights likely lesion regions, dynamic convolution adapts feature filters to expected textures, and deformable sampling refines spatial support. By embedding this fine-grained guidance early, MedSeg-R disentangles inter-class confusion and amplifies minority-class cues, greatly improving sensitivity to small lesions. In challenging benchmarks, MedSeg-R produces large Dice improvements in overlapping and ambiguous structures, demonstrating plug-and-play compatibility with SAM-based systems.
Medical image segmentation has greatly aided medical diagnosis, with U-Net based architectures and nnU-Net providing state-of-the-art performance. There have been numerous general promptable models and medical variations introduced in recent years, but there is currently a lack of evaluation and comparison of these models across a variety of prompt qualities on a common medical dataset. This research uses Segment Anything Model (SAM), Segment Anything Model 2 (SAM 2), MedSAM, SAM-Med-3D, and nnU-Net to obtain zero-shot inference on the BraTS 2023 adult glioma and pediatrics dataset across multiple prompt qualities for both points and bounding boxes. Several of these models exhibit promising Dice scores, particularly SAM and SAM 2 achieving scores of up to 0.894 and 0.893, respectively when given extremely accurate bounding box prompts which exceeds nnU-Net's segmentation performance. However, nnU-Net remains the dominant medical image segmentation network due to the impracticality of providing highly accurate prompts to the models. The model and prompt evaluation, as well as the comparison, are extended through fine-tuning SAM, SAM 2, MedSAM, and SAM-Med-3D on the pediatrics dataset. The improvements in point prompt performance after fine-tuning are substantial and show promise for future investigation, but are unable to achieve better segmentation than bounding boxes or nnU-Net.
Current medical image analysis systems are typically task-specific, requiring separate models for classification and segmentation, and lack the flexibility to support user-defined workflows. To address these challenges, we introduce MedPrompt, a unified framework that combines a few-shot prompted Large Language Model (Llama-4-17B) for high-level task planning with a modular Convolutional Neural Network (DeepFusionLab) for low-level image processing. The LLM interprets user instructions and generates structured output to dynamically route task-specific pretrained weights. This weight routing approach avoids retraining the entire framework when adding new tasks-only task-specific weights are required, enhancing scalability and deployment. We evaluated MedPrompt across 19 public datasets, covering 12 tasks spanning 5 imaging modalities. The system achieves a 97% end-to-end correctness in interpreting and executing prompt-driven instructions, with an average inference latency of 2.5 seconds, making it suitable for near real-time applications. DeepFusionLab achieves competitive segmentation accuracy (e.g., Dice 0.9856 on lungs) and strong classification performance (F1 0.9744 on tuberculosis). Overall, MedPrompt enables scalable, prompt-driven medical imaging by combining the interpretability of LLMs with the efficiency of modular CNNs.
Foundation models for volumetric medical image segmentation have emerged as powerful tools in clinical workflows, enabling radiologists to delineate regions of interest through intuitive clicks. While these models demonstrate promising capabilities in segmenting previously unseen anatomical structures, their performance is strongly influenced by prompt quality. In clinical settings, radiologists often provide suboptimal prompts, which affects segmentation reliability and accuracy. To address this limitation, we present SafeClick, an error-tolerant interactive segmentation approach for medical volumes based on hierarchical expert consensus. SafeClick operates as a plug-and-play module compatible with foundation models including SAM 2 and MedSAM 2. The framework consists of two key components: a collaborative expert layer (CEL) that generates diverse feature representations through specialized transformer modules, and a consensus reasoning layer (CRL) that performs cross-referencing and adaptive integration of these features. This architecture transforms the segmentation process from a prompt-dependent operation to a robust framework capable of producing accurate results despite imperfect user inputs. Extensive experiments across 15 public datasets demonstrate that our plug-and-play approach consistently improves the performance of base foundation models, with particularly significant gains when working with imperfect prompts. The source code is available at https://github.com/yifangao112/SafeClick.
Segmenting biomarkers in medical images is crucial for various biotech applications. Despite advances, Transformer and CNN based methods often struggle with variations in staining and morphology, limiting feature extraction. In medical image segmentation, where datasets often have limited sample availability, recent state-of-the-art (SOTA) methods achieve higher accuracy by leveraging pre-trained encoders, whereas end-to-end methods tend to underperform. This is due to challenges in effectively transferring rich multiscale features from encoders to decoders, as well as limitations in decoder efficiency. To address these issues, we propose an architecture that captures multi-scale local and global contextual information and a novel decoder design, which effectively integrates features from the encoder, emphasizes important channels and regions, and reconstructs spatial dimensions to enhance segmentation accuracy. Our method, compatible with various encoders, outperforms SOTA methods, as demonstrated by experiments on four datasets and ablation studies. Specifically, our method achieves absolute performance gains of 2.76% on MoNuSeg, 3.12% on DSB, 2.87% on Electron Microscopy, and 4.03% on TNBC datasets compared to existing SOTA methods. Code: https://github.com/saadwazir/MCADS-Decoder
Class imbalance and the difficulty imbalance are the two types of data imbalance that affect the performance of neural networks in medical segmentation tasks. In class imbalance the loss is dominated by the majority classes and in difficulty imbalance the loss is dominated by easy to classify pixels. This leads to an ineffective training. Dice loss, which is based on a geometrical metric, is very effective in addressing the class imbalance compared to the cross entropy (CE) loss, which is adopted directly from classification tasks. To address the difficulty imbalance, the common approach is employing a re-weighted CE loss or a modified Dice loss to focus the training on difficult to classify areas. The existing modification methods are computationally costly and with limited success. In this study we propose a simple modification to the Dice loss with minimal computational cost. With a pixel level modulating term, we take advantage of the effectiveness of Dice loss in handling the class imbalance to also handle the difficulty imbalance. Results on three commonly used medical segmentation tasks show that the proposed Pixel-wise Modulated Dice loss (PM Dice loss) outperforms other methods, which are designed to tackle the difficulty imbalance problem.
Cancer is an abnormal growth with potential to invade locally and metastasize to distant organs. Accurate auto-segmentation of the tumor and surrounding normal tissues is required for radiotherapy treatment plan optimization. Recent AI-based segmentation models are generally trained on large public datasets, which lack the heterogeneity of local patient populations. While these studies advance AI-based medical image segmentation, research on local datasets is necessary to develop and integrate AI tumor segmentation models directly into hospital software for efficient and accurate oncology treatment planning and execution. This study enhances tumor segmentation using computationally efficient hybrid UNet-Transformer models on magnetic resonance imaging (MRI) datasets acquired from a local hospital under strict privacy protection. We developed a robust data pipeline for seamless DICOM extraction and preprocessing, followed by extensive image augmentation to ensure model generalization across diverse clinical settings, resulting in a total dataset of 6080 images for training. Our novel architecture integrates UNet-based convolutional neural networks with a transformer bottleneck and complementary attention modules, including efficient attention, Squeeze-and-Excitation (SE) blocks, Convolutional Block Attention Module (CBAM), and ResNeXt blocks. To accelerate convergence and reduce computational demands, we used a maximum batch size of 8 and initialized the encoder with pretrained ImageNet weights, training the model on dual NVIDIA T4 GPUs via checkpointing to overcome Kaggle's runtime limits. Quantitative evaluation on the local MRI dataset yielded a Dice similarity coefficient of 0.764 and an Intersection over Union (IoU) of 0.736, demonstrating competitive performance despite limited data and underscoring the importance of site-specific model development for clinical deployment.
With the advancement of Large Language Model (LLM) for natural language processing, this paper presents an intriguing finding: a frozen pre-trained LLM layer can process visual tokens for medical image segmentation tasks. Specifically, we propose a simple hybrid structure that integrates a pre-trained, frozen LLM layer within the CNN encoder-decoder segmentation framework (LLM4Seg). Surprisingly, this design improves segmentation performance with a minimal increase in trainable parameters across various modalities, including ultrasound, dermoscopy, polypscopy, and CT scans. Our in-depth analysis reveals the potential of transferring LLM's semantic awareness to enhance segmentation tasks, offering both improved global understanding and better local modeling capabilities. The improvement proves robust across different LLMs, validated using LLaMA and DeepSeek.
Deep learning has demonstrated remarkable success in medical image segmentation and computer-aided diagnosis. In particular, numerous advanced methods have achieved state-of-the-art performance in brain tumor segmentation from MRI scans. While recent studies in other medical imaging domains have revealed that integrating textual reports with visual data can enhance segmentation accuracy, the field of brain tumor analysis lacks a comprehensive dataset that combines radiological images with corresponding textual annotations. This limitation has hindered the exploration of multimodal approaches that leverage both imaging and textual data. To bridge this critical gap, we introduce the TextBraTS dataset, the first publicly available volume-level multimodal dataset that contains paired MRI volumes and rich textual annotations, derived from the widely adopted BraTS2020 benchmark. Building upon this novel dataset, we propose a novel baseline framework and sequential cross-attention method for text-guided volumetric medical image segmentation. Through extensive experiments with various text-image fusion strategies and templated text formulations, our approach demonstrates significant improvements in brain tumor segmentation accuracy, offering valuable insights into effective multimodal integration techniques. Our dataset, implementation code, and pre-trained models are publicly available at https://github.com/Jupitern52/TextBraTS.
While modern segmentation models often prioritize performance over practicality, we advocate a design philosophy prioritizing simplicity and efficiency, and attempted high performance segmentation model design. This paper presents SimpleUNet, a scalable ultra-lightweight medical image segmentation model with three key innovations: (1) A partial feature selection mechanism in skip connections for redundancy reduction while enhancing segmentation performance; (2) A fixed-width architecture that prevents exponential parameter growth across network stages; (3) An adaptive feature fusion module achieving enhanced representation with minimal computational overhead. With a record-breaking 16 KB parameter configuration, SimpleUNet outperforms LBUNet and other lightweight benchmarks across multiple public datasets. The 0.67 MB variant achieves superior efficiency (8.60 GFLOPs) and accuracy, attaining a mean DSC/IoU of 85.76%/75.60% on multi-center breast lesion datasets, surpassing both U-Net and TransUNet. Evaluations on skin lesion datasets (ISIC 2017/2018: mDice 84.86%/88.77%) and endoscopic polyp segmentation (KVASIR-SEG: 86.46%/76.48% mDice/mIoU) confirm consistent dominance over state-of-the-art models. This work demonstrates that extreme model compression need not compromise performance, providing new insights for efficient and accurate medical image segmentation. Codes can be found at https://github.com/Frankyu5666666/SimpleUNet.