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.
Spacecraft deployed in outer space are routinely subjected to various forms of damage due to exposure to hazardous environments. In addition, there are significant risks to the subsequent process of in-space repairs through human extravehicular activity or robotic manipulation, incurring substantial operational costs. Recent developments in image segmentation could enable the development of reliable and cost-effective autonomous inspection systems. While these models often require large amounts of training data to achieve satisfactory results, publicly available annotated spacecraft segmentation data are very scarce. Here, we present a new dataset of nearly 64k annotated spacecraft images that was created using real spacecraft models, superimposed on a mixture of real and synthetic backgrounds generated using NASA's TTALOS pipeline. To mimic camera distortions and noise in real-world image acquisition, we also added different types of noise and distortion to the images. Finally, we finetuned YOLOv8 and YOLOv11 segmentation models to generate performance benchmarks for the dataset under well-defined hardware and inference time constraints to mimic real-world image segmentation challenges for real-time onboard applications in space on NASA's inspector spacecraft. The resulting models, when tested under these constraints, achieved a Dice score of 0.92, Hausdorff distance of 0.69, and an inference time of about 0.5 second. The dataset and models for performance benchmark are available at https://github.com/RiceD2KLab/SWiM.
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.
Medical language-guided segmentation, integrating textual clinical reports as auxiliary guidance to enhance image segmentation, has demonstrated significant improvements over unimodal approaches. However, its inherent reliance on paired image-text input, which we refer to as ``textual reliance", presents two fundamental limitations: 1) many medical segmentation datasets lack paired reports, leaving a substantial portion of image-only data underutilized for training; and 2) inference is limited to retrospective analysis of cases with paired reports, limiting its applicability in most clinical scenarios where segmentation typically precedes reporting. To address these limitations, we propose ProLearn, the first Prototype-driven Learning framework for language-guided segmentation that fundamentally alleviates textual reliance. At its core, we introduce a novel Prototype-driven Semantic Approximation (PSA) module to enable approximation of semantic guidance from textual input. PSA initializes a discrete and compact prototype space by distilling segmentation-relevant semantics from textual reports. Once initialized, it supports a query-and-respond mechanism which approximates semantic guidance for images without textual input, thereby alleviating textual reliance. Extensive experiments on QaTa-COV19, MosMedData+ and Kvasir-SEG demonstrate that ProLearn outperforms state-of-the-art language-guided methods when limited text is available.
Batch normalization (BN) is a ubiquitous operation in deep neural networks used primarily to achieve stability and regularization during network training. BN involves feature map centering and scaling using sample means and variances, respectively. Since these statistics are being estimated across the feature maps within a batch, this problem is ideally suited for the application of Stein's shrinkage estimation, which leads to a better, in the mean-squared-error sense, estimate of the mean and variance of the batch. In this paper, we prove that the Stein shrinkage estimator for the mean and variance dominates over the sample mean and variance estimators in the presence of adversarial attacks when modeling these attacks using sub-Gaussian distributions. This facilitates and justifies the application of Stein shrinkage to estimate the mean and variance parameters in BN and use it in image classification (segmentation) tasks with and without adversarial attacks. We present SOTA performance results using this Stein corrected batch norm in a standard ResNet architecture applied to the task of image classification using CIFAR-10 data, 3D CNN on PPMI (neuroimaging) data and image segmentation using HRNet on Cityscape data with and without adversarial attacks.
The Segment Anything Model (SAM) has revolutionized image segmentation through its innovative prompt-based approach, yet the critical role of prompt engineering in its success remains underexplored. This paper presents the first comprehensive survey focusing specifically on prompt engineering techniques for SAM and its variants. We systematically organize and analyze the rapidly growing body of work in this emerging field, covering fundamental methodologies, practical applications, and key challenges. Our review reveals how prompt engineering has evolved from simple geometric inputs to sophisticated multimodal approaches, enabling SAM's adaptation across diverse domains including medical imaging and remote sensing. We identify unique challenges in prompt optimization and discuss promising research directions. This survey fills an important gap in the literature by providing a structured framework for understanding and advancing prompt engineering in foundation models for segmentation.
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.
The remarkable performance of large multimodal models (LMMs) has attracted significant interest from the image segmentation community. To align with the next-token-prediction paradigm, current LMM-driven segmentation methods either use object boundary points to represent masks or introduce special segmentation tokens, whose hidden states are decoded by a segmentation model requiring the original image as input. However, these approaches often suffer from inadequate mask representation and complex architectures, limiting the potential of LMMs. In this work, we propose the Hierarchical Mask Tokenizer (HiMTok), which represents segmentation masks with up to 32 tokens and eliminates the need for the original image during mask de-tokenization. HiMTok allows for compact and coarse-to-fine mask representations, aligning well with the LLM next-token-prediction paradigm and facilitating the direct acquisition of segmentation capabilities. We develop a 3-stage training recipe for progressive learning of segmentation and visual capabilities, featuring a hierarchical mask loss for effective coarse-to-fine learning. Additionally, we enable bidirectional information flow, allowing conversion between bounding boxes and mask tokens to fully leverage multi-task training potential. Extensive experiments demonstrate that our method achieves state-of-the-art performance across various segmentation tasks,while also enhancing visual grounding and maintaining overall visual understanding.
Referring Image Segmentation (RIS) is a challenging task that aims to segment objects in an image based on natural language expressions. While prior studies have predominantly concentrated on improving vision-language interactions and achieving fine-grained localization, a systematic analysis of the fundamental bottlenecks in existing RIS frameworks remains underexplored. To bridge this gap, we propose DeRIS, a novel framework that decomposes RIS into two key components: perception and cognition. This modular decomposition facilitates a systematic analysis of the primary bottlenecks impeding RIS performance. Our findings reveal that the predominant limitation lies not in perceptual deficiencies, but in the insufficient multi-modal cognitive capacity of current models. To mitigate this, we propose a Loopback Synergy mechanism, which enhances the synergy between the perception and cognition modules, thereby enabling precise segmentation while simultaneously improving robust image-text comprehension. Additionally, we analyze and introduce a simple non-referent sample conversion data augmentation to address the long-tail distribution issue related to target existence judgement in general scenarios. Notably, DeRIS demonstrates inherent adaptability to both non- and multi-referents scenarios without requiring specialized architectural modifications, enhancing its general applicability. The codes and models are available at https://github.com/Dmmm1997/DeRIS.
Class-incremental/Continual image segmentation (CIS) aims to train an image segmenter in stages, where the set of available categories differs at each stage. To leverage the built-in objectness of query-based transformers, which mitigates catastrophic forgetting of mask proposals, current methods often decouple mask generation from the continual learning process. This study, however, identifies two key issues with decoupled frameworks: loss of plasticity and heavy reliance on input data order. To address these, we conduct an in-depth investigation of the built-in objectness and find that highly aggregated image features provide a shortcut for queries to generate masks through simple feature alignment. Based on this, we propose SimCIS, a simple yet powerful baseline for CIS. Its core idea is to directly select image features for query assignment, ensuring "perfect alignment" to preserve objectness, while simultaneously allowing queries to select new classes to promote plasticity. To further combat catastrophic forgetting of categories, we introduce cross-stage consistency in selection and an innovative "visual query"-based replay mechanism. Experiments demonstrate that SimCIS consistently outperforms state-of-the-art methods across various segmentation tasks, settings, splits, and input data orders. All models and codes will be made publicly available at https://github.com/SooLab/SimCIS.
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.
Image segmentation plays a vital role in the medical field by isolating organs or regions of interest from surrounding areas. Traditionally, segmentation models are trained on a specific organ or a disease, limiting their ability to handle other organs and diseases. At present, few advanced models can perform multi-organ or multi-disease segmentation, offering greater flexibility. Also, recently, prompt-based image segmentation has gained attention as a more flexible approach. It allows models to segment areas based on user-provided prompts. Despite these advances, there has been no dedicated work on prompt-based interactive multi-organ and multi-disease segmentation, especially for Chest X-rays. This work presents two main contributions: first, generating doodle prompts by medical experts of a collection of datasets from multiple sources with 23 classes, including 6 organs and 17 diseases, specifically designed for prompt-based Chest X-ray segmentation. Second, we introduce Prompt2SegCXR, a lightweight model for accurately segmenting multiple organs and diseases from Chest X-rays. The model incorporates multi-stage feature fusion, enabling it to combine features from various network layers for better spatial and semantic understanding, enhancing segmentation accuracy. Compared to existing pre-trained models for prompt-based image segmentation, our model scores well, providing a reliable solution for segmenting Chest X-rays based on user prompts.
The recent advancements in large foundation models have driven the success of open-set image segmentation, a task focused on segmenting objects beyond predefined categories. Among various prompt types (such as points, boxes, texts, and visual references), visual reference segmentation stands out for its unique flexibility and strong zero-shot capabilities. Recently, several SAM-based methods have made notable progress in this task by automatically generating prompts to guide SAM. However, these methods often generate prompts at object boundaries due to suboptimal prompt encoder, which results in instability and reduced robustness. In this work, we introduce ProSAM, a simple but effective method to address the stability challenges we identified in existing SAM-based visual reference segmentation approaches. By learning a variational prompt encoder to predict multivariate prompt distributions, ProSAM avoids generating prompts that lie in unstable regions, overcoming the instability caused by less robust prompts. Our approach consistently surpasses state-of-the-art methods on the Pascal-5$^i$ and COCO-20$^i$ datasets, providing a more robust solution for visual reference segmentation.
Referring Remote Sensing Image Segmentation provides a flexible and fine-grained framework for remote sensing scene analysis via vision-language collaborative interpretation. Current approaches predominantly utilize a three-stage pipeline encompassing dual-modal encoding, cross-modal interaction, and pixel decoding. These methods demonstrate significant limitations in managing complex semantic relationships and achieving precise cross-modal alignment, largely due to their coupled processing mechanism that conflates target localization with boundary delineation. This architectural coupling amplifies error propagation under semantic ambiguity while restricting model generalizability and interpretability. To address these issues, we propose RSRefSeg 2, a decoupling paradigm that reformulates the conventional workflow into a collaborative dual-stage framework: coarse localization followed by fine segmentation. RSRefSeg 2 integrates CLIP's cross-modal alignment strength with SAM's segmentation generalizability through strategic foundation model collaboration. Specifically, CLIP is employed as the dual-modal encoder to activate target features within its pre-aligned semantic space and generate localization prompts. To mitigate CLIP's misactivation challenges in multi-entity scenarios described by referring texts, a cascaded second-order prompter is devised, which enhances precision through implicit reasoning via decomposition of text embeddings into complementary semantic subspaces. These optimized semantic prompts subsequently direct the SAM to generate pixel-level refined masks, thereby completing the semantic transmission pipeline. Extensive experiments (RefSegRS, RRSIS-D, and RISBench) demonstrate that RSRefSeg 2 surpasses contemporary methods in segmentation accuracy (+~3% gIoU) and complex semantic interpretation. Code is available at: https://github.com/KyanChen/RSRefSeg2.
The ability to segment objects based on open-ended language prompts remains a critical challenge, requiring models to ground textual semantics into precise spatial masks while handling diverse and unseen categories. We present OpenWorldSAM, a framework that extends the prompt-driven Segment Anything Model v2 (SAM2) to open-vocabulary scenarios by integrating multi-modal embeddings extracted from a lightweight vision-language model (VLM). Our approach is guided by four key principles: i) Unified prompting: OpenWorldSAM supports a diverse range of prompts, including category-level and sentence-level language descriptions, providing a flexible interface for various segmentation tasks. ii) Efficiency: By freezing the pre-trained components of SAM2 and the VLM, we train only 4.5 million parameters on the COCO-stuff dataset, achieving remarkable resource efficiency. iii) Instance Awareness: We enhance the model's spatial understanding through novel positional tie-breaker embeddings and cross-attention layers, enabling effective segmentation of multiple instances. iv) Generalization: OpenWorldSAM exhibits strong zero-shot capabilities, generalizing well on unseen categories and an open vocabulary of concepts without additional training. Extensive experiments demonstrate that OpenWorldSAM achieves state-of-the-art performance in open-vocabulary semantic, instance, and panoptic segmentation across multiple benchmarks, including ADE20k, PASCAL, ScanNet, and SUN-RGBD.
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.