Cross-Modality Medical Image Segmentation

Deep learning has achieved remarkable success in medical image segmentation, often reaching expert-level accuracy in delineating tumors and tissues. However, most existing approaches remain task-specific, showing strong performance on individual datasets but limited generalization across diverse imaging modalities. Moreover, many methods focus primarily on the encoder, relying on large pretrained backbones that increase computational complexity. In this paper, we propose a decoder-centric approach for generalized 2D medical image segmentation. The proposed Deco-Mamba follows a U-Net-like structure with a Transformer-CNN-Mamba design. The encoder combines a CNN block and Transformer backbone for efficient feature extraction, while the decoder integrates our novel Co-Attention Gate (CAG), Vision State Space Module (VSSM), and deformable convolutional refinement block to enhance multi-scale contextual representation. Additionally, a windowed distribution-aware KL-divergence loss is introduced for deep supervision across multiple decoding stages. Extensive experiments on diverse medical image segmentation benchmarks yield state-of-the-art performance and strong generalization capability while maintaining moderate model complexity. The source code will be released upon acceptance.

In interventional radiology, Cone-Beam Computed Tomography (CBCT) is a helpful imaging modality that provides guidance to practicians during minimally invasive procedures. CBCT differs from traditional Computed Tomography (CT) due to its limited reconstructed field of view, specific artefacts, and the intra-arterial administration of contrast medium. While CT benefits from abundant publicly available annotated datasets, interventional CBCT data remain scarce and largely unannotated, with existing datasets focused primarily on radiotherapy applications. To address this limitation, we leverage a proprietary collection of unannotated interventional CBCT scans in conjunction with annotated CT data, employing domain adaptation techniques to bridge the modality gap and enhance liver segmentation performance on CBCT. We propose a novel unsupervised domain adaptation (UDA) framework based on the formalism of Margin Disparity Discrepancy (MDD), which improves target domain performance through a reformulation of the original MDD optimization framework. Experimental results on CT and CBCT datasets for liver segmentation demonstrate that our method achieves state-of-the-art performance in UDA, as well as in the few-shot setting.

Modeling medical vessel-like anatomy is challenging due to its intricate topology and sensitivity to dataset shifts. Consequently, task-specific models often suffer from topological inconsistencies, including artificial disconnections and spurious merges. Motivated by the promise of multimodal large language models (MLLMs) for zero-shot generalization, we propose TubeMLLM, a unified foundation model that couples structured understanding with controllable generation for medical vessel-like anatomy. By integrating topological priors through explicit natural language prompting and aligning them with visual representations in a shared-attention architecture, TubeMLLM significantly enhances topology-aware perception. Furthermore, we construct TubeMData, a pionner multimodal benchmark comprising comprehensive topology-centric tasks, and introduce an adaptive loss weighting strategy to emphasize topology-critical regions during training. Extensive experiments on fifteen diverse datasets demonstrate our superiority. Quantitatively, TubeMLLM achieves state-of-the-art out-of-distribution performance, substantially reducing global topological discrepancies on color fundus photography (decreasing the $β_{0}$ number error from 37.42 to 8.58 compared to baselines). Notably, TubeMLLM exhibits exceptional zero-shot cross-modality transferring ability on unseen X-ray angiography, achieving a Dice score of 67.50% while significantly reducing the $β_{0}$ error to 1.21. TubeMLLM also maintains robustness against degradations such as blur, noise, and low resolution. Furthermore, in topology-aware understanding tasks, the model achieves 97.38% accuracy in evaluating mask topological quality, significantly outperforming standard vision-language baselines.

Purpose: Developing generalizable medical image segmentation models is challenging because imaging data are distributed across institutions and differ in modality and acquisition protocol. Federated learning (FL) enables collaborative training without centralizing raw medical images, but cross-modality domain shifts between computed tomography (CT) and magnetic resonance imaging (MRI) can substantially reduce model performance. This study investigates augmentation-driven cross-modality FL for abdominal organ and whole-heart segmentation. Methods: We evaluate convolution-based spatial augmentation, frequency-domain argumentation, domain-specific normalization, and global intensity nonlinear (GIN) augmentation for multimodal segmentation. Abdominal organ segmentation and whole-heart segmentation are first evaluated using a 2D U-Net framework. For whole-heart segmentation, we additionally perform native 3D experiments using a self-configuring nnU-Net architecture on the CARE-WHS 2026 dataset, enabling evaluation of whether the observed cross-modality FL behavior persists when moving from slice-based 2D segmentation to volumetric 3D segmentation. Results: GIN provides the most consistent cross-modality performance among the evaluated approaches in the original 2D experiments. For pancreas segmentation, the Dice similarity coefficient (DSC) improved from 0.073 to 0.437 when CT data were incorporated through federated cross-modality training. In 3D whole-heart segmentation, FedGIN improved mean DSC over FedAvg from 0.8696 to 0.8901 on the unseen CT center and from 0.7160 to 0.7956 on the unseen MRI center. Relative to centralized GIN training, FedGIN retained 92.4% of performance on unseen CT data and achieved comparable performance on unseen MRI data (0.7956 versus 0.7937).

We introduce a novel uncertainty-aware multimodal segmentation framework that leverages both radiological images and associated clinical text for precise medical diagnosis. We propose a Modality Decoding Attention Block (MoDAB) with a lightweight State Space Mixer (SSMix) to enable efficient cross-modal fusion and long-range dependency modelling. To guide learning under ambiguity, we propose the Spectral-Entropic Uncertainty (SEU) Loss, which jointly captures spatial overlap, spectral consistency, and predictive uncertainty in a unified objective. In complex clinical circumstances with poor image quality, this formulation improves model reliability. Extensive experiments on various publicly available medical datasets, QATA-COVID19, MosMed++, and Kvasir-SEG, demonstrate that our method achieves superior segmentation performance while being significantly more computationally efficient than existing State-of-the-Art (SoTA) approaches. Our results highlight the importance of incorporating uncertainty modelling and structured modality alignment in vision-language medical segmentation tasks. Code: https://github.com/arya-domain/UA-VLS

Robust medical image segmentation across modalities remains challenging due to severe domain shifts and the lack of target-domain labels. While diffusion models have been explored for cross-domain generation and augmentation, target-domain conditional diffusion training typically relies on highly noisy pseudo masks; naively conditioning on a single Arg-Max pseudo-label can corrupt diffusion training and downstream segmentation. We propose UPDiff-UDA, a unified UDA framework whose core is an uncertainty-guided training objective for target-domain conditional diffusion. Given an imperfect source-trained segmenter, we use its per-pixel softmax distribution to form ranked pseudo-label maps (Arg-Max, Arg-2nd, Arg-3rd, ...). Each map yields a conditional score estimate, and we aggregate them via pixel-wise confidence weighting to obtain an uncertainty-reweighted score for score matching, improving robustness to pseudo-label noise while leveraging alternative plausible labels in uncertain regions. We further provide a theoretical justification showing that confidence-weighted aggregation follows a minimum-MSE convex-combination principle under the segmenter-induced surrogate label distribution. To improve pseudo-condition quality, we also introduce a feature-guided, low-degree-of-freedom Bézier curve adaptation to reduce appearance gaps. Experiments on multiple public datasets and modality shifts show that UPDiff-UDA generates high-fidelity labeled target-style samples for augmentation and consistently outperforms strong UDA baselines. The code for this project is available at: https://github.com/superlc1995/Multi-Channel-Uncertainty-Diffusion-UDA

Lightweight 3D medical image segmentation remains constrained by a fundamental *efficiency / robustness conflict''*, particularly when processing complex anatomical structures and heterogeneous modalities. In this paper, we study how to redesign the framework based on the characteristics of high-dimensional 3D images, and explore data synergy to overcome the fragile representation of lightweight methods. Our approach, VeloxSeg, begins with a deployable and extensible dual-stream CNN-Transformer architecture composed of Paired Window Attention (PWA) and Johnson-Lindenstrauss lemma-guided convolution (JLC). For each 3D image, we invoke a glance-and-focus'' principle, where PWA rapidly retrieves multi-scale information, and JLC ensures robust local feature extraction with minimal parameters, significantly enhancing the model's ability to operate with low computational budget. Followed by an extension of the dual-stream architecture that incorporates modal interaction into the multi-scale image-retrieval process, VeloxSeg efficiently models heterogeneous modalities. Finally, Spatially Decoupled Knowledge Transfer (SDKT) via Gram matrices injects the texture prior extracted by a self-supervised network into the segmentation network, yielding stronger representations than baselines at no extra inference cost. Experimental results on multimodal benchmarks show that VeloxSeg achieves a 26% Dice improvement, alongside increasing GPU throughput by 11$\times$, CPU by 48$\times$, and reducing training peak GPU memory usage by $1/20$, inference by $1/24$. Code is available at https://github.com/JinPLu/VeloxSeg.

Subcortical segmentation in neuroimages plays an important role in understanding brain anatomy and facilitating computer-aided diagnosis of traumatic brain injuries and neurodegenerative disorders. However, training accurate automatic models requires large amounts of labelled data. Despite the availability of publicly available subcortical segmentation datasets for Magnetic Resonance Imaging (MRI), a significant gap exists for Computed Tomography (CT). This paper proposes an automatic ensemble framework to generate high-quality subcortical segmentation labels for CT scans by leveraging existing MRI-based models. We introduce a robust ensembling pipeline to integrate them and apply it to unannotated paired MRI-CT data, resulting in a comprehensive CT subcortical segmentation dataset. Extensive experiments on multiple public datasets demonstrate the superior performance of our proposed framework. Furthermore, using our generated CT dataset, we train segmentation models that achieve improved performance on related segmentation tasks. To facilitate future research, we make our source code, generated dataset, and trained models publicly available at https://github.com/alxw0671/CT_Subcortical_Segmentation, marking the first open-source release for CT subcortical segmentation to the best of our knowledge.

This paper addresses cross-modal medical image segmentation, focusing on MRI-CT transfer in a source-only domain generalization setting. During training, only source-modality samples are available, while unlabeled target-modality images are used for testing. We propose LowBridge, which builds on the observation that cross-modal images share similar low-level features (e.g. edges) as they depict the same types of anatomical structures. Specifically, we first train a generative model to recover the source images from their edge features, followed by training a segmentation model on the generated source images, separately. At test time, edge features from the target images are input to the pretrained generative model to generate source-style target domain images, which are then segmented using the pretrained segmentation network. Experiments on various public datasets demonstrate that LowBridge achieves state-of-the-art performance, outperforming ten existing approaches. Ablation studies further show that LowBridge is compatible with different types of generative and segmentation models, suggesting its generalizability and potential to benefit from future advances in these models. The code will be available at https://github.com/JoshuaLPF/LowBridge.

Fetal brain tissue segmentation from magnetic resonance imaging (MRI) is crucial for studying neurodevelopment, but remains challenging due to data heterogeneity and limited annotations. Domain randomization (DR) has recently emerged as a promising strategy for single-source domain generalization by synthesizing training images with randomized artifacts, contrast, and resolution. In this work, we investigate how to maximize the out-of-domain (OOD) generalization of DR-based methods. We evaluate several synthetic data generation strategies for DR, with a particular focus on our recently proposed framework, FetalSynthSeg. We show that simple Gaussian mixture-based intensity modeling outperforms more complex physics-based simulations, and that intensity clustering (subdividing tissue classes based on intensity) improves OOD robustness. Evaluated on 348 fetal subjects from four sites spanning 0.55-3T and both T1w and T2w contrasts, FetalSynthSeg reaches state-of-the-art performance on several FeTA 2024 testing datasets (80-85 Dice score) and, for the first time, offers robust segmentation on modalities other than T2w for fetal brain segmentation (80 Dice on dHCP-T1w dataset). Compared with state-of-the-art methods such as BOUNTI, nnU-Net ensemble, and the FeTA 2024 winner, FetalSynthSeg delivers comparable or superior accuracy while maintaining strong robustness across domain shifts. Our code, model weights, and Docker image ready for easy inference are available at https://hub.docker.com/r/vzalevskyi/fetalsynthseg.

Existing brain tumor segmentation methods usually utilize multiple Magnetic Resonance Imaging (MRI) modalities in brain tumor images for segmentation, which can achieve better segmentation performance. However, in clinical applications, some modalities are often missing due to resource constraints, resulting in significant performance degradation for methods that rely on complete modality segmentation. In this paper, we propose a Multimodal feature distillation with Mamba-Transformer hybrid network (MMTSeg) for accurate brain tumor segmentation with missing modalities. We first employ a Multimodal Feature Distillation (MFD) module to distill feature-level multimodal knowledge into different unimodalities to extract complete modality information. We further develop an Unimodal Feature Enhancement (UFE) module to model the semantic relationship between global and local information. Finally, we built a Cross-Modal Fusion (CMF) module to explicitly align the global correlations across modalities, even when some modalities are missing. Complementary features within and across modalities are refined by the Mamba-Transformer hybrid architectures in both the UFE and CMF modules, dynamically capturing long-range dependencies and global semantic information for complex spatial contexts. A boundary-wise loss function is employed as the segmentation loss of the proposed MMTSeg to minimize boundary discrepancies for a distance-based metric. Our ablation study demonstrates the importance of the proposed feature enhancement and fusion modules in the proposed network and the Transformer with Mamba block for improving the performance of brain tumor segmentation with missing modalities. Extensive experiments on the BraTS 2018 and BraTS 2020 datasets demonstrate that the proposed MMTSeg framework outperforms state-of-the-art methods when modalities are missing.

Unsupervised domain adaptation approaches have recently succeeded in various medical image segmentation tasks. The reported works often tackle the domain shift problem by aligning the domain-invariant features and minimizing the domain-specific discrepancies. That strategy works well when the difference between a specific domain and between different domains is slight. However, the generalization ability of these models on diverse imaging modalities remains a significant challenge. This paper introduces UDA-VAE++, an unsupervised domain adaptation framework for cardiac segmentation. We show that the evidence lower bound of VAE-based domain adaptation penalizes the mutual information between the image and the latent space, including the structure information that segmentation relies on. Maximizing the structure mutual information removes this penalty on the structure information, while the remaining information is still compressed. To estimate this term, we develop a novel Structure Mutual Information Estimation (SMIE) block with a global estimator, a local estimator, and a prior information matching estimator to maximize the mutual information between the reconstruction and segmentation tasks. Specifically, we design a novel sequential reparameterization scheme that enables information flow and variance correction from the low-resolution latent space to the high-resolution latent space. Comprehensive experiments on benchmark cardiac segmentation datasets demonstrate that our model outperforms previous state-of-the-art qualitatively and quantitatively. The code is available at https://github.com/LOUEY233/Toward-Mutual-Information