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arXiv2023

Non-Iterative Scribble-Supervised Learning with Pacing Pseudo-Masks for Medical Image Segmentation

Scribble-supervised medical image segmentation tackles the limitation of sparse masks. Conventional approaches alternate between: labeling pseudo-masks and optimizing network parameters. However, such iterative two-stage paradigm is unwieldy and could be trapped in poor local optima since the networks undesirably regress to the erroneous pseudo-masks. To address these issues, we propose a non-iterative method where a stream of varying (pacing) pseudo-masks teach a network via consistency training, named PacingPseudo. Our motivation lies first in a non-iterative process. Interestingly, it can be achieved gracefully by a siamese architecture, wherein a stream of pseudo-masks naturally assimilate a stream of predicted masks during training. Second, we make the consistency training effective with two necessary designs: (i) entropy regularization to obtain high-confidence pseudo-masks for effective teaching; and (ii) distorted augmentations to create discrepancy between the pseudo-mask and predicted-mask streams for consistency regularization. Third, we devise a new memory bank mechanism that provides an extra source of ensemble features to complement scarce labeled pixels. The efficacy of the proposed PacingPseudo is validated on three public medical image datasets, including the segmentation tasks of abdominal multi-organs, cardiac structures, and myocardium. Extensive experiments demonstrate our PacingPseudo improves the baseline by large margins and consistently outcompetes several previous methods. In some cases, our PacingPseudo achieves comparable performance with its fully-supervised counterparts, showing the feasibility of our method for the challenging scribble-supervised segmentation applications. The code and scribble annotations will be publicly available.

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arXiv2020

Inter-slice Context Residual Learning for 3D Medical Image Segmentation

Automated and accurate 3D medical image segmentation plays an essential role in assisting medical professionals to evaluate disease progresses and make fast therapeutic schedules. Although deep convolutional neural networks (DCNNs) have widely applied to this task, the accuracy of these models still need to be further improved mainly due to their limited ability to 3D context perception. In this paper, we propose the 3D context residual network (ConResNet) for the accurate segmentation of 3D medical images. This model consists of an encoder, a segmentation decoder, and a context residual decoder. We design the context residual module and use it to bridge both decoders at each scale. Each context residual module contains both context residual mapping and context attention mapping, the formal aims to explicitly learn the inter-slice context information and the latter uses such context as a kind of attention to boost the segmentation accuracy. We evaluated this model on the MICCAI 2018 Brain Tumor Segmentation (BraTS) dataset and NIH Pancreas Segmentation (Pancreas-CT) dataset. Our results not only demonstrate the effectiveness of the proposed 3D context residual learning scheme but also indicate that the proposed ConResNet is more accurate than six top-ranking methods in brain tumor segmentation and seven top-ranking methods in pancreas segmentation. Code is available at https://git.io/ConResNet

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arXiv2025

Distribution-aware Fairness Learning in Medical Image Segmentation From A Control-Theoretic Perspective

Ensuring fairness in medical image segmentation is critical due to biases in imbalanced clinical data acquisition caused by demographic attributes (e.g., age, sex, race) and clinical factors (e.g., disease severity). To address these challenges, we introduce Distribution-aware Mixture of Experts (dMoE), inspired by optimal control theory. We provide a comprehensive analysis of its underlying mechanisms and clarify dMoE's role in adapting to heterogeneous distributions in medical image segmentation. Furthermore, we integrate dMoE into multiple network architectures, demonstrating its broad applicability across diverse medical image analysis tasks. By incorporating demographic and clinical factors, dMoE achieves state-of-the-art performance on two 2D benchmark datasets and a 3D in-house dataset. Our results highlight the effectiveness of dMoE in mitigating biases from imbalanced distributions, offering a promising approach to bridging control theory and medical image segmentation within fairness learning paradigms. The source code will be made available. The source code is available at https://github.com/tvseg/dMoE.

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arXiv2025

RobustEMD: Domain Robust Matching for Cross-domain Few-shot Medical Image Segmentation

Few-shot medical image segmentation (FSMIS) aims to perform the limited annotated data learning in the medical image analysis scope. Despite the progress has been achieved, current FSMIS models are all trained and deployed on the same data domain, as is not consistent with the clinical reality that medical imaging data is always across different data domains (e.g. imaging modalities, institutions and equipment sequences). How to enhance the FSMIS models to generalize well across the different specific medical imaging domains? In this paper, we focus on the matching mechanism of the few-shot semantic segmentation models and introduce an Earth Mover's Distance (EMD) calculation based domain robust matching mechanism for the cross-domain scenario. Specifically, we formulate the EMD transportation process between the foreground support-query features, the texture structure aware weights generation method, which proposes to perform the sobel based image gradient calculation over the nodes, is introduced in the EMD matching flow to restrain the domain relevant nodes. Besides, the point set level distance measurement metric is introduced to calculated the cost for the transportation from support set nodes to query set nodes. To evaluate the performance of our model, we conduct experiments on three scenarios (i.e., cross-modal, cross-sequence and cross-institution), which includes eight medical datasets and involves three body regions, and the results demonstrate that our model achieves the SoTA performance against the compared models.

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arXiv2026

Beyond Visual Cues: CoT-Enhanced Reasoning for Semi-supervised Medical Image Segmentation

Semi-supervised medical image segmentation has emerged as a dominant research problem in medical image analysis, mitigating annotation scarcity by leveraging consistency regularization on unlabeled data. However, existing approaches operate predominantly via visual pattern matching, relying heavily on pixel-level similarities. This visual-centric dependency often falters in clinical scenarios characterized by the visual-semantic mismatch, where visually similar lesions warrant distinct diagnostic conclusions, thus failing to capture the underlying diagnostic logic used by experts. To address this, we move beyond visual cues and propose CERS (CoT-Enhanced Reasoning Segmentation), a framework that integrates Chain-of-Thought (CoT) reasoning to distinguish pathologically distinct cases. Specifically, we construct a knowledge pool enriched with linguistic reasoning descriptions generated by large language models (LLMs). A semantic-aware reference selection strategy is introduced to identify historical evidence, filtering candidates first by morphology, and then refining them via CoT consistency to eliminate hard negatives. Furthermore, a multi-scale coordinate attention module (MCAM) is designed to effectively fuse this reasoning-derived context into the decoding process. Extensive experiments demonstrate the superiority of CERS against state-of-the-art approaches, particularly in resolving boundary ambiguities and semantic inconsistencies. The code is available at https://github.com/cymasuna/CERS.

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arXiv2020

UXNet: Searching Multi-level Feature Aggregation for 3D Medical Image Segmentation

Aggregating multi-level feature representation plays a critical role in achieving robust volumetric medical image segmentation, which is important for the auxiliary diagnosis and treatment. Unlike the recent neural architecture search (NAS) methods that typically searched the optimal operators in each network layer, but missed a good strategy to search for feature aggregations, this paper proposes a novel NAS method for 3D medical image segmentation, named UXNet, which searches both the scale-wise feature aggregation strategies as well as the block-wise operators in the encoder-decoder network. UXNet has several appealing benefits. (1) It significantly improves flexibility of the classical UNet architecture, which only aggregates feature representations of encoder and decoder in equivalent resolution. (2) A continuous relaxation of UXNet is carefully designed, enabling its searching scheme performed in an efficient differentiable manner. (3) Extensive experiments demonstrate the effectiveness of UXNet compared with recent NAS methods for medical image segmentation. The architecture discovered by UXNet outperforms existing state-of-the-art models in terms of Dice on several public 3D medical image segmentation benchmarks, especially for the boundary locations and tiny tissues. The searching computational complexity of UXNet is cheap, enabling to search a network with the best performance less than 1.5 days on two TitanXP GPUs.

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arXiv2025

Continual Alignment for SAM: Rethinking Foundation Models for Medical Image Segmentation in Continual Learning

In medical image segmentation, heterogeneous privacy policies across institutions often make joint training on pooled datasets infeasible, motivating continual image segmentation-learning from data streams without catastrophic forgetting. While the Segment Anything Model (SAM) offers strong zero-shot priors and has been widely fine-tuned across downstream tasks, its large parameter count and computational overhead challenge practical deployment. This paper demonstrates that the SAM paradigm is highly promising once its computational efficiency and performance can be balanced. To this end, we introduce the Alignment Layer, a lightweight, plug-and-play module which aligns encoder-decoder feature distributions to efficiently adapt SAM to specific medical images, improving accuracy while reducing computation. Building on SAM and the Alignment Layer, we then propose Continual Alignment for SAM (CA-SAM), a continual learning strategy that automatically adapts the appropriate Alignment Layer to mitigate catastrophic forgetting, while leveraging SAM's zero-shot priors to preserve strong performance on unseen medical datasets. Experimented across nine medical segmentation datasets under continual-learning scenario, CA-SAM achieves state-of-the-art performance. Our code, models and datasets will be released on \mbox{https://github.com/azzzzyo/Continual-Alignment-for-SAM.}

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arXiv2025

Self-Prompt SAM: Medical Image Segmentation via Automatic Prompt SAM Adaptation

Segment Anything Model (SAM) has demonstrated impressive zero-shot performance and brought a range of unexplored capabilities to natural image segmentation tasks. However, as a very important branch of image segmentation, the performance of SAM remains uncertain when applied to medical image segmentation due to the significant differences between natural images and medical images. Meanwhile, it is harsh to meet the SAM's requirements of extra prompts provided, such as points or boxes to specify medical regions. In this paper, we propose a novel self-prompt SAM adaptation framework for medical image segmentation, named Self-Prompt-SAM. We design a multi-scale prompt generator combined with the image encoder in SAM to generate auxiliary masks. Then, we use the auxiliary masks to generate bounding boxes as box prompts and use Distance Transform to select the most central points as point prompts. Meanwhile, we design a 3D depth-fused adapter (DfusedAdapter) and inject the DFusedAdapter into each transformer in the image encoder and mask decoder to enable pre-trained 2D SAM models to extract 3D information and adapt to 3D medical images. Extensive experiments demonstrate that our method achieves state-of-the-art performance and outperforms nnUNet by 2.3% on AMOS2022, 1.6% on ACDCand 0.5% on Synapse datasets.

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arXiv2023

Finding the Most Transferable Tasks for Brain Image Segmentation

Although many studies have successfully applied transfer learning to medical image segmentation, very few of them have investigated the selection strategy when multiple source tasks are available for transfer. In this paper, we propose a prior knowledge guided and transferability based framework to select the best source tasks among a collection of brain image segmentation tasks, to improve the transfer learning performance on the given target task. The framework consists of modality analysis, RoI (region of interest) analysis, and transferability estimation, such that the source task selection can be refined step by step. Specifically, we adapt the state-of-the-art analytical transferability estimation metrics to medical image segmentation tasks and further show that their performance can be significantly boosted by filtering candidate source tasks based on modality and RoI characteristics. Our experiments on brain matter, brain tumor, and white matter hyperintensities segmentation datasets reveal that transferring from different tasks under the same modality is often more successful than transferring from the same task under different modalities. Furthermore, within the same modality, transferring from the source task that has stronger RoI shape similarity with the target task can significantly improve the final transfer performance. And such similarity can be captured using the Structural Similarity index in the label space.

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arXiv2024

SDCL: Students Discrepancy-Informed Correction Learning for Semi-supervised Medical Image Segmentation

Semi-supervised medical image segmentation (SSMIS) has been demonstrated the potential to mitigate the issue of limited medical labeled data. However, confirmation and cognitive biases may affect the prevalent teacher-student based SSMIS methods due to erroneous pseudo-labels. To tackle this challenge, we improve the mean teacher approach and propose the Students Discrepancy-Informed Correction Learning (SDCL) framework that includes two students and one non-trainable teacher, which utilizes the segmentation difference between the two students to guide the self-correcting learning. The essence of SDCL is to identify the areas of segmentation discrepancy as the potential bias areas, and then encourage the model to review the correct cognition and rectify their own biases in these areas. To facilitate the bias correction learning with continuous review and rectification, two correction loss functions are employed to minimize the correct segmentation voxel distance and maximize the erroneous segmentation voxel entropy. We conducted experiments on three public medical image datasets: two 3D datasets (CT and MRI) and one 2D dataset (MRI). The results show that our SDCL surpasses the current State-of-the-Art (SOTA) methods by 2.57\%, 3.04\%, and 2.34\% in the Dice score on the Pancreas, LA, and ACDC datasets, respectively. In addition, the accuracy of our method is very close to the fully supervised method on the ACDC dataset, and even exceeds the fully supervised method on the Pancreas and LA dataset. (Code available at \url{https://github.com/pascalcpp/SDCL}).

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arXiv2025

From Few to More: Scribble-based Medical Image Segmentation via Masked Context Modeling and Continuous Pseudo Labels

Scribble-based weakly supervised segmentation methods have shown promising results in medical image segmentation, significantly reducing annotation costs. However, existing approaches often rely on auxiliary tasks to enforce semantic consistency and use hard pseudo labels for supervision, overlooking the unique challenges faced by models trained with sparse annotations. These models must predict pixel-wise segmentation maps from limited data, making it crucial to handle varying levels of annotation richness effectively. In this paper, we propose MaCo, a weakly supervised model designed for medical image segmentation, based on the principle of "from few to more." MaCo leverages Masked Context Modeling (MCM) and Continuous Pseudo Labels (CPL). MCM employs an attention-based masking strategy to perturb the input image, ensuring that the model's predictions align with those of the original image. CPL converts scribble annotations into continuous pixel-wise labels by applying an exponential decay function to distance maps, producing confidence maps that represent the likelihood of each pixel belonging to a specific category, rather than relying on hard pseudo labels. We evaluate MaCo on three public datasets, comparing it with other weakly supervised methods. Our results show that MaCo outperforms competing methods across all datasets, establishing a new record in weakly supervised medical image segmentation.

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arXiv2020

Non-local U-Net for Biomedical Image Segmentation

Deep learning has shown its great promise in various biomedical image segmentation tasks. Existing models are typically based on U-Net and rely on an encoder-decoder architecture with stacked local operators to aggregate long-range information gradually. However, only using the local operators limits the efficiency and effectiveness. In this work, we propose the non-local U-Nets, which are equipped with flexible global aggregation blocks, for biomedical image segmentation. These blocks can be inserted into U-Net as size-preserving processes, as well as down-sampling and up-sampling layers. We perform thorough experiments on the 3D multimodality isointense infant brain MR image segmentation task to evaluate the non-local U-Nets. Results show that our proposed models achieve top performances with fewer parameters and faster computation.

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arXiv2020

ACNN: a Full Resolution DCNN for Medical Image Segmentation

Deep Convolutional Neural Networks (DCNNs) are used extensively in medical image segmentation and hence 3D navigation for robot-assisted Minimally Invasive Surgeries (MISs). However, current DCNNs usually use down sampling layers for increasing the receptive field and gaining abstract semantic information. These down sampling layers decrease the spatial dimension of feature maps, which can be detrimental to image segmentation. Atrous convolution is an alternative for the down sampling layer. It increases the receptive field whilst maintains the spatial dimension of feature maps. In this paper, a method for effective atrous rate setting is proposed to achieve the largest and fully-covered receptive field with a minimum number of atrous convolutional layers. Furthermore, a new and full resolution DCNN - Atrous Convolutional Neural Network (ACNN), which incorporates cascaded atrous II-blocks, residual learning and Instance Normalization (IN) is proposed. Application results of the proposed ACNN to Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) image segmentation demonstrate that the proposed ACNN can achieve higher segmentation Intersection over Unions (IoUs) than U-Net and Deeplabv3+, but with reduced trainable parameters.

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arXiv2021

A Weighted Difference of Anisotropic and Isotropic Total Variation for Relaxed Mumford-Shah Color and Multiphase Image Segmentation

In a class of piecewise-constant image segmentation models, we propose to incorporate a weighted difference of anisotropic and isotropic total variation (AITV) to regularize the partition boundaries in an image. In particular, we replace the total variation regularization in the Chan-Vese segmentation model and a fuzzy region competition model by the proposed AITV. To deal with the nonconvex nature of AITV, we apply the difference-of-convex algorithm (DCA), in which the subproblems can be minimized by the primal-dual hybrid gradient method with linesearch. The convergence of the DCA scheme is analyzed. In addition, a generalization to color image segmentation is discussed. In the numerical experiments, we compare the proposed models with the classic convex approaches and the two-stage segmentation methods (smoothing and then thresholding) on various images, showing that our models are effective in image segmentation and robust with respect to impulsive noises.

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arXiv2024

TG-LMM: Enhancing Medical Image Segmentation Accuracy through Text-Guided Large Multi-Modal Model

We propose TG-LMM (Text-Guided Large Multi-Modal Model), a novel approach that leverages textual descriptions of organs to enhance segmentation accuracy in medical images. Existing medical image segmentation methods face several challenges: current medical automatic segmentation models do not effectively utilize prior knowledge, such as descriptions of organ locations; previous text-visual models focus on identifying the target rather than improving the segmentation accuracy; prior models attempt to use prior knowledge to enhance accuracy but do not incorporate pre-trained models. To address these issues, TG-LMM integrates prior knowledge, specifically expert descriptions of the spatial locations of organs, into the segmentation process. Our model utilizes pre-trained image and text encoders to reduce the number of training parameters and accelerate the training process. Additionally, we designed a comprehensive image-text information fusion structure to ensure thorough integration of the two modalities of data. We evaluated TG-LMM on three authoritative medical image datasets, encompassing the segmentation of various parts of the human body. Our method demonstrated superior performance compared to existing approaches, such as MedSAM, SAM and nnUnet.

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arXiv2025

SPENet: Self-guided Prototype Enhancement Network for Few-shot Medical Image Segmentation

Few-Shot Medical Image Segmentation (FSMIS) aims to segment novel classes of medical objects using only a few labeled images. Prototype-based methods have made significant progress in addressing FSMIS. However, they typically generate a single global prototype for the support image to match with the query image, overlooking intra-class variations. To address this issue, we propose a Self-guided Prototype Enhancement Network (SPENet). Specifically, we introduce a Multi-level Prototype Generation (MPG) module, which enables multi-granularity measurement between the support and query images by simultaneously generating a global prototype and an adaptive number of local prototypes. Additionally, we observe that not all local prototypes in the support image are beneficial for matching, especially when there are substantial discrepancies between the support and query images. To alleviate this issue, we propose a Query-guided Local Prototype Enhancement (QLPE) module, which adaptively refines support prototypes by incorporating guidance from the query image, thus mitigating the negative effects of such discrepancies. Extensive experiments on three public medical datasets demonstrate that SPENet outperforms existing state-of-the-art methods, achieving superior performance.

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arXiv2022

Application of belief functions to medical image segmentation: A review

The investigation of uncertainty is of major importance in risk-critical applications, such as medical image segmentation. Belief function theory, a formal framework for uncertainty analysis and multiple evidence fusion, has made significant contributions to medical image segmentation, especially since the development of deep learning. In this paper, we provide an introduction to the topic of medical image segmentation methods using belief function theory. We classify the methods according to the fusion step and explain how information with uncertainty or imprecision is modeled and fused with belief function theory. In addition, we discuss the challenges and limitations of present belief function-based medical image segmentation and propose orientations for future research. Future research could investigate both belief function theory and deep learning to achieve more promising and reliable segmentation results.

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arXiv2014

MBIS: Multivariate Bayesian Image Segmentation Tool

We present MBIS (Multivariate Bayesian Image Segmentation tool), a clustering tool based on the mixture of multivariate normal distributions model. MBIS supports multi-channel bias field correction based on a B-spline model. A second methodological novelty is the inclusion of graph-cuts optimization for the stationary anisotropic hidden Markov random field model. Along with MBIS, we release an evaluation framework that contains three different experiments on multi-site data. We first validate the accuracy of segmentation and the estimated bias field for each channel. MBIS outperforms a widely used segmentation tool in a cross-comparison evaluation. The second experiment demonstrates the robustness of results on atlas-free segmentation of two image sets from scan-rescan protocols on 21 healthy subjects. Multivariate segmentation is more replicable than the monospectral counterpart on T1-weighted images. Finally, we provide a third experiment to illustrate how MBIS can be used in a large-scale study of tissue volume change with increasing age in 584 healthy subjects. This last result is meaningful as multivariate segmentation performs robustly without the need for prior knowledge

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