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arXiv2026

ProGeo-RC: Prototype-guided Semantic Reliability and Geometric Error Calibration for Semi-supervised Cardiac Image Segmentation

Semi-supervised medical image segmentation aims to train reliable segmentation models using limited labeled data and abundant unlabeled data. However, existing methods typically rely on prediction confidence or model consistency to estimate pseudo-label reliability, but these criteria are insufficient to characterize both semantic reliability and geometric plausibility. To address this issue, we propose ProGeo-RC, a prototype-guided semantic reliability and geometric error calibration framework for semi-supervised medical image segmentation. ProGeo-RC consists of two key modules: Prototype-guided Semantic Reliability Estimation (PSRE) and Structured Semantic-Geometric Error Calibration (S-SGEC). PSRE uses probabilistic class prototypes to estimate the semantic reliability of unlabeled predictions and calibrate pixel-wise teacher pseudo labels, while S-SGEC introduces signed-distance-field-based geometric constraints to refine ambiguous boundaries and suppress spurious foreground responses outside target structures. Experiments on the ACDC and MVAA-CT datasets show that ProGeo-RC achieves better performance compared with representative semi-supervised segmentation methods. Under the 10\% labeled setting on ACDC, ProGeo-RC improves DSC and Jaccard by 0.37\% and 0.49\% over the corresponding second-best results, while reducing 95HD and ASD by 0.61 and 0.21, respectively. These results indicate that joint semantic reliability estimation and geometric error calibration can provide more reliable pseudo supervision for semi-supervised medical image segmentation.

cs.CV↗

arXiv2017

Interactive Medical Image Segmentation using Deep Learning with Image-specific Fine-tuning

Convolutional neural networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they have not demonstrated sufficiently accurate and robust results for clinical use. In addition, they are limited by the lack of image-specific adaptation and the lack of generalizability to previously unseen object classes. To address these problems, we propose a novel deep learning-based framework for interactive segmentation by incorporating CNNs into a bounding box and scribble-based segmentation pipeline. We propose image-specific fine-tuning to make a CNN model adaptive to a specific test image, which can be either unsupervised (without additional user interactions) or supervised (with additional scribbles). We also propose a weighted loss function considering network and interaction-based uncertainty for the fine-tuning. We applied this framework to two applications: 2D segmentation of multiple organs from fetal MR slices, where only two types of these organs were annotated for training; and 3D segmentation of brain tumor core (excluding edema) and whole brain tumor (including edema) from different MR sequences, where only tumor cores in one MR sequence were annotated for training. Experimental results show that 1) our model is more robust to segment previously unseen objects than state-of-the-art CNNs; 2) image-specific fine-tuning with the proposed weighted loss function significantly improves segmentation accuracy; and 3) our method leads to accurate results with fewer user interactions and less user time than traditional interactive segmentation methods.

cs.CV↗

arXiv2025

From Claims to Evidence: A Unified Framework and Critical Analysis of CNN vs. Transformer vs. Mamba in Medical Image Segmentation

While numerous architectures for medical image segmentation have been proposed, achieving competitive performance with state-of-the-art models networks such as nnUNet, still leave room for further innovation. In this work, we introduce nnUZoo, an open source benchmarking framework built upon nnUNet, which incorporates various deep learning architectures, including CNNs, Transformers, and Mamba-based models. Using this framework, we provide a fair comparison to demystify performance claims across different medical image segmentation tasks. Additionally, in an effort to enrich the benchmarking, we explored five new architectures based on Mamba and Transformers, collectively named X2Net, and integrated them into nnUZoo for further evaluation. The proposed models combine the features of conventional U2Net, nnUNet, CNN, Transformer, and Mamba layers and architectures, called X2Net (UNETR2Net (UNETR), SwT2Net (SwinTransformer), SS2D2Net (SwinUMamba), Alt1DM2Net (LightUMamba), and MambaND2Net (MambaND)). We extensively evaluate the performance of different models on six diverse medical image segmentation datasets, including microscopy, ultrasound, CT, MRI, and PET, covering various body parts, organs, and labels. We compare their performance, in terms of dice score and computational efficiency, against their baseline models, U2Net, and nnUNet. CNN models like nnUNet and U2Net demonstrated both speed and accuracy, making them effective choices for medical image segmentation tasks. Transformer-based models, while promising for certain imaging modalities, exhibited high computational costs. Proposed Mamba-based X2Net architecture (SS2D2Net) achieved competitive accuracy with no significantly difference from nnUNet and U2Net, while using fewer parameters. However, they required significantly longer training time, highlighting a trade-off between model efficiency and computational cost.

eess.IV↗

arXiv2024

VM-UNet: Vision Mamba UNet for Medical Image Segmentation

In the realm of medical image segmentation, both CNN-based and Transformer-based models have been extensively explored. However, CNNs exhibit limitations in long-range modeling capabilities, whereas Transformers are hampered by their quadratic computational complexity. Recently, State Space Models (SSMs), exemplified by Mamba, have emerged as a promising approach. They not only excel in modeling long-range interactions but also maintain a linear computational complexity. In this paper, leveraging state space models, we propose a U-shape architecture model for medical image segmentation, named Vision Mamba UNet (VM-UNet). Specifically, the Visual State Space (VSS) block is introduced as the foundation block to capture extensive contextual information, and an asymmetrical encoder-decoder structure is constructed with fewer convolution layers to save calculation cost. We conduct comprehensive experiments on the ISIC17, ISIC18, and Synapse datasets, and the results indicate that VM-UNet performs competitively in medical image segmentation tasks. To our best knowledge, this is the first medical image segmentation model constructed based on the pure SSM-based model. We aim to establish a baseline and provide valuable insights for the future development of more efficient and effective SSM-based segmentation systems. Our code is available at https://github.com/JCruan519/VM-UNet.

eess.IV↗

arXiv2021

Generative Synthetic Augmentation using Label-to-Image Translation for Nuclei Image Segmentation

In medical image diagnosis, pathology image analysis using semantic segmentation becomes important for efficient screening as a field of digital pathology. The spatial augmentation is ordinary used for semantic segmentation. Tumor images under malignant are rare and to annotate the labels of nuclei region takes much time-consuming. We require an effective use of dataset to maximize the segmentation accuracy. It is expected that some augmentation to transform generalized images influence the segmentation performance. We propose a synthetic augmentation using label-to-image translation, mapping from a semantic label with the edge structure to a real image. Exactly this paper deal with stain slides of nuclei in tumor. Actually, we demonstrate several segmentation algorithms applied to the initial dataset that contains real images and labels using synthetic augmentation in order to add their generalized images. We computes and reports that a proposed synthetic augmentation procedure improve their accuracy.

cs.LG↗

arXiv2025

Generalist Models in Medical Image Segmentation: A Survey and Performance Comparison with Task-Specific Approaches

Following the successful paradigm shift of large language models, leveraging pre-training on a massive corpus of data and fine-tuning on different downstream tasks, generalist models have made their foray into computer vision. The introduction of Segment Anything Model (SAM) set a milestone on segmentation of natural images, inspiring the design of a multitude of architectures for medical image segmentation. In this survey we offer a comprehensive and in-depth investigation on generalist models for medical image segmentation. We start with an introduction on the fundamentals concepts underpinning their development. Then, we provide a taxonomy on the different declinations of SAM in terms of zero-shot, few-shot, fine-tuning, adapters, on the recent SAM 2, on other innovative models trained on images alone, and others trained on both text and images. We thoroughly analyze their performances at the level of both primary research and best-in-literature, followed by a rigorous comparison with the state-of-the-art task-specific models. We emphasize the need to address challenges in terms of compliance with regulatory frameworks, privacy and security laws, budget, and trustworthy artificial intelligence (AI). Finally, we share our perspective on future directions concerning synthetic data, early fusion, lessons learnt from generalist models in natural language processing, agentic AI and physical AI, and clinical translation.

eess.IV↗

arXiv2025

Interactive 3D Medical Image Segmentation with SAM 2

Interactive medical image segmentation (IMIS) has shown significant potential in enhancing segmentation accuracy by integrating iterative feedback from medical professionals. However, the limited availability of enough 3D medical data restricts the generalization and robustness of most IMIS methods. The Segment Anything Model (SAM), though effective for 2D images, requires expensive semi-auto slice-by-slice annotations for 3D medical images. In this paper, we explore the zero-shot capabilities of SAM 2, the next-generation Meta SAM model trained on videos, for 3D medical image segmentation. By treating sequential 2D slices of 3D images as video frames, SAM 2 can fully automatically propagate annotations from a single frame to the entire 3D volume. We propose a practical pipeline for using SAM 2 in 3D medical image segmentation and present key findings highlighting its efficiency and potential for further optimization. Concretely, numerical experiments on the BraTS2020 and the medical segmentation decathlon datasets demonstrate that SAM 2 still has a gap with supervised methods but can narrow the gap in specific settings and organ types, significantly reducing the annotation burden on medical professionals. Our code will be open-sourced and available at https://github.com/Chuyun-Shen/SAM_2_Medical_3D.

cs.CV↗

arXiv2020

Image Segmentation Using Deep Learning: A Survey

Image segmentation is a key topic in image processing and computer vision with applications such as scene understanding, medical image analysis, robotic perception, video surveillance, augmented reality, and image compression, among many others. Various algorithms for image segmentation have been developed in the literature. Recently, due to the success of deep learning models in a wide range of vision applications, there has been a substantial amount of works aimed at developing image segmentation approaches using deep learning models. In this survey, we provide a comprehensive review of the literature at the time of this writing, covering a broad spectrum of pioneering works for semantic and instance-level segmentation, including fully convolutional pixel-labeling networks, encoder-decoder architectures, multi-scale and pyramid based approaches, recurrent networks, visual attention models, and generative models in adversarial settings. We investigate the similarity, strengths and challenges of these deep learning models, examine the most widely used datasets, report performances, and discuss promising future research directions in this area.

cs.CV↗

arXiv2020

EDC3: Ensemble of Deep-Classifiers using Class-specific Copula functions to Improve Semantic Image Segmentation

In the literature, many fusion techniques are registered for the segmentation of images, but they primarily focus on observed output or belief score or probability score of the output classes. In the present work, we have utilized inter source statistical dependency among different classifiers for ensembling of different deep learning techniques for semantic segmentation of images. For this purpose, in the present work, a class-wise Copula-based ensembling method is newly proposed for solving the multi-class segmentation problem. Experimentally, it is observed that the performance has improved more for semantic image segmentation using the proposed class-specific Copula function than the traditionally used single Copula function for the problem. The performance is also compared with three state-of-the-art ensembling methods.

cs.CV↗

arXiv2025

Semantic Localization Guiding Segment Anything Model For Reference Remote Sensing Image Segmentation

The Reference Remote Sensing Image Segmentation (RRSIS) task generates segmentation masks for specified objects in images based on textual descriptions, which has attracted widespread attention and research interest. Current RRSIS methods rely on multi-modal fusion backbones and semantic segmentation heads but face challenges like dense annotation requirements and complex scene interpretation. To address these issues, we propose a framework named \textit{prompt-generated semantic localization guiding Segment Anything Model}(PSLG-SAM), which decomposes the RRSIS task into two stages: coarse localization and fine segmentation. In coarse localization stage, a visual grounding network roughly locates the text-described object. In fine segmentation stage, the coordinates from the first stage guide the Segment Anything Model (SAM), enhanced by a clustering-based foreground point generator and a mask boundary iterative optimization strategy for precise segmentation. Notably, the second stage can be train-free, significantly reducing the annotation data burden for the RRSIS task. Additionally, decomposing the RRSIS task into two stages allows for focusing on specific region segmentation, avoiding interference from complex scenes.We further contribute a high-quality, multi-category manually annotated dataset. Experimental validation on two datasets (RRSIS-D and RRSIS-M) demonstrates that PSLG-SAM achieves significant performance improvements and surpasses existing state-of-the-art models.Our code will be made publicly available.

cs.CV↗

arXiv2026

CoMLP: Cooperatively-Gated MLPs for Fine-Grained Cross-Modal Information Fusion in Medical Image Segmentation

Multi-modal medical images and clinical reports provide complementary anatomical, functional, and semantic information for medical image segmentation. Effectively exploiting these heterogeneous sources requires fine-grained cross-modal information fusion that preserves subtle spatial details while capturing semantic dependencies across modalities. Existing fusion approaches frequently rely on cross-attention, whose computational burden increases rapidly with spatial resolution, making dense cross-modal interaction difficult on high-resolution feature maps, particularly for volumetric medical images. In this work, we propose CoMLP, a cooperatively-gated MLP module for fine-grained cross-modal information fusion in medical image segmentation. CoMLP models cross-modal dependencies through cooperative cross-gating, built upon complementary regional and dilated MLP interactions, to capture local and global cross-modal dependencies. We further develop a multi-source fusion architecture in which CoMLP performs both inter-image fusion across imaging modalities and vision-language fusion between visual features and textual reports, enabling heterogeneous information to be integrated without relying on dense cross-attention. Extensive experiments on five medical segmentation benchmarks, covering 2D/3D images, clinical reports, multiple imaging modalities, and diverse anatomical regions, demonstrate consistent improvements over state-of-the-art multi-modal and language-guided segmentation methods. Ablation studies further show that fine-grained interaction at high spatial resolutions and complementary local-global fusion are critical to the performance gains. These results demonstrate the potential of MLP-based interaction as an effective alternative for fine-grained cross-modal information fusion in medical image segmentation.

cs.CV↗

arXiv2026

Segment Anything Model Based Context Guided Mamba Unet for Medical Image Segmentation

Medical image segmentation is crucial for clinical diagnosis and treatment planning, requiring both global contextual understanding and fine-grained structural precision. While the Segment Anything Model (SAM) demonstrates strong generalization capabilities, its direct application to medical images often lacks domain-specific adaptability. Meanwhile, State Space Models (SSMs)-based methods, such as Mamba, efficiently capture long-range dependencies but may struggle with preserving fine anatomical details. To address these challenges, we propose a segment anything model based context guided mamba unet, SAMBA-UNet, a novel framework that integrates SAM's context knowledge with Mamba's hierarchical feature learning to enhance both global representation and local detail refinement. Specifically, we introduce the Hierarchical Context Enhancement Module (HCEM), an attention-based fusion module that deeply incorporates the multi-level features of SAM and Mamba to improve detail perception and segmentation precision. Additionally, we employ LoRA and Adapter-based fine-tuning to adapt SAM to medical imaging tasks, further enhancing its domain-specific segmentation capability and robustness. We conducted a comprehensive study on several medical segmentation datasets, including Synapse, ISIC17, and ISIC18, evaluating our method across multiple metrics. Experimental results demonstrate that SAMBA-UNet achieves state-of-the-art performance, effectively balancing generalization, segmentation accuracy, and computational efficiency. Our code will be released upon acceptance.

cs.CV↗

arXiv2023

3D TransUNet: Advancing Medical Image Segmentation through Vision Transformers

Medical image segmentation plays a crucial role in advancing healthcare systems for disease diagnosis and treatment planning. The u-shaped architecture, popularly known as U-Net, has proven highly successful for various medical image segmentation tasks. However, U-Net's convolution-based operations inherently limit its ability to model long-range dependencies effectively. To address these limitations, researchers have turned to Transformers, renowned for their global self-attention mechanisms, as alternative architectures. One popular network is our previous TransUNet, which leverages Transformers' self-attention to complement U-Net's localized information with the global context. In this paper, we extend the 2D TransUNet architecture to a 3D network by building upon the state-of-the-art nnU-Net architecture, and fully exploring Transformers' potential in both the encoder and decoder design. We introduce two key components: 1) A Transformer encoder that tokenizes image patches from a convolution neural network (CNN) feature map, enabling the extraction of global contexts, and 2) A Transformer decoder that adaptively refines candidate regions by utilizing cross-attention between candidate proposals and U-Net features. Our investigations reveal that different medical tasks benefit from distinct architectural designs. The Transformer encoder excels in multi-organ segmentation, where the relationship among organs is crucial. On the other hand, the Transformer decoder proves more beneficial for dealing with small and challenging segmented targets such as tumor segmentation. Extensive experiments showcase the significant potential of integrating a Transformer-based encoder and decoder into the u-shaped medical image segmentation architecture. TransUNet outperforms competitors in various medical applications.

cs.CV↗

arXiv2023

Segment Together: A Versatile Paradigm for Semi-Supervised Medical Image Segmentation

Annotation scarcity has become a major obstacle for training powerful deep-learning models for medical image segmentation, restricting their deployment in clinical scenarios. To address it, semi-supervised learning by exploiting abundant unlabeled data is highly desirable to boost the model training. However, most existing works still focus on limited medical tasks and underestimate the potential of learning across diverse tasks and multiple datasets. Therefore, in this paper, we introduce a \textbf{Ver}satile \textbf{Semi}-supervised framework (VerSemi) to point out a new perspective that integrates various tasks into a unified model with a broad label space, to exploit more unlabeled data for semi-supervised medical image segmentation. Specifically, we introduce a dynamic task-prompted design to segment various targets from different datasets. Next, this unified model is used to identify the foreground regions from all labeled data, to capture cross-dataset semantics. Particularly, we create a synthetic task with a cutmix strategy to augment foreground targets within the expanded label space. To effectively utilize unlabeled data, we introduce a consistency constraint. This involves aligning aggregated predictions from various tasks with those from the synthetic task, further guiding the model in accurately segmenting foreground regions during training. We evaluated our VerSemi model on four public benchmarking datasets. Extensive experiments demonstrated that VerSemi can consistently outperform the second-best method by a large margin (e.g., an average 2.69\% Dice gain on four datasets), setting new SOTA performance for semi-supervised medical image segmentation. The code will be released.

cs.CV↗

arXiv2024

HResFormer: Hybrid Residual Transformer for Volumetric Medical Image Segmentation

Vision Transformer shows great superiority in medical image segmentation due to the ability in learning long-range dependency. For medical image segmentation from 3D data, such as computed tomography (CT), existing methods can be broadly classified into 2D-based and 3D-based methods. One key limitation in 2D-based methods is that the intra-slice information is ignored, while the limitation in 3D-based methods is the high computation cost and memory consumption, resulting in a limited feature representation for inner-slice information. During the clinical examination, radiologists primarily use the axial plane and then routinely review both axial and coronal planes to form a 3D understanding of anatomy. Motivated by this fact, our key insight is to design a hybrid model which can first learn fine-grained inner-slice information and then generate a 3D understanding of anatomy by incorporating 3D information. We present a novel \textbf{H}ybrid \textbf{Res}idual trans\textbf{Former} \textbf{(HResFormer)} for 3D medical image segmentation. Building upon standard 2D and 3D Transformer backbones, HResFormer involves two novel key designs: \textbf{(1)} a \textbf{H}ybrid \textbf{L}ocal-\textbf{G}lobal fusion \textbf{M}odule \textbf{(HLGM)} to effectively and adaptively fuse inner-slice information from 2D Transformer and intra-slice information from 3D volumes for 3D Transformer with local fine-grained and global long-range representation. \textbf{(2)} a residual learning of the hybrid model, which can effectively leverage the inner-slice and intra-slice information for better 3D understanding of anatomy. Experiments show that our HResFormer outperforms prior art on widely-used medical image segmentation benchmarks. This paper sheds light on an important but neglected way to design Transformers for 3D medical image segmentation.

cs.CV↗

arXiv2024

FAMNet: Frequency-aware Matching Network for Cross-domain Few-shot Medical Image Segmentation

Existing few-shot medical image segmentation (FSMIS) models fail to address a practical issue in medical imaging: the domain shift caused by different imaging techniques, which limits the applicability to current FSMIS tasks. To overcome this limitation, we focus on the cross-domain few-shot medical image segmentation (CD-FSMIS) task, aiming to develop a generalized model capable of adapting to a broader range of medical image segmentation scenarios with limited labeled data from the novel target domain. Inspired by the characteristics of frequency domain similarity across different domains, we propose a Frequency-aware Matching Network (FAMNet), which includes two key components: a Frequency-aware Matching (FAM) module and a Multi-Spectral Fusion (MSF) module. The FAM module tackles two problems during the meta-learning phase: 1) intra-domain variance caused by the inherent support-query bias, due to the different appearances of organs and lesions, and 2) inter-domain variance caused by different medical imaging techniques. Additionally, we design an MSF module to integrate the different frequency features decoupled by the FAM module, and further mitigate the impact of inter-domain variance on the model's segmentation performance. Combining these two modules, our FAMNet surpasses existing FSMIS models and Cross-domain Few-shot Semantic Segmentation models on three cross-domain datasets, achieving state-of-the-art performance in the CD-FSMIS task.

cs.CV↗

arXiv2020

Uncertainty quantification in medical image segmentation with normalizing flows

Medical image segmentation is inherently an ambiguous task due to factors such as partial volumes and variations in anatomical definitions. While in most cases the segmentation uncertainty is around the border of structures of interest, there can also be considerable inter-rater differences. The class of conditional variational autoencoders (cVAE) offers a principled approach to inferring distributions over plausible segmentations that are conditioned on input images. Segmentation uncertainty estimated from samples of such distributions can be more informative than using pixel level probability scores. In this work, we propose a novel conditional generative model that is based on conditional Normalizing Flow (cFlow). The basic idea is to increase the expressivity of the cVAE by introducing a cFlow transformation step after the encoder. This yields improved approximations of the latent posterior distribution, allowing the model to capture richer segmentation variations. With this we show that the quality and diversity of samples obtained from our conditional generative model is enhanced. Performance of our model, which we call cFlow Net, is evaluated on two medical imaging datasets demonstrating substantial improvements in both qualitative and quantitative measures when compared to a recent cVAE based model.

stat.ML↗

arXiv2025

Rethinking Query-based Transformer for Continual Image Segmentation

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.

cs.CV↗