Stroke is among the top three causes of death worldwide, and accurate identification of stroke lesion boundaries is critical for diagnosis and treatment. Supervised deep learning methods have emerged as the leading solution for stroke lesion segmentation but require large, diverse, and annotated datasets. The ISLES'24 challenge addresses this need by providing longitudinal stroke imaging data, including CT scans taken on arrival to the hospital and follow-up MRI taken 2-9 days from initial arrival, with annotations derived from follow-up MRI. Importantly, models submitted to the ISLES'24 challenge are evaluated using only CT inputs, requiring prediction of lesion progression that may not be visible in CT scans for segmentation. Our winning solution shows that a carefully designed preprocessing pipeline including deep-learning-based skull stripping and custom intensity windowing is beneficial for accurate segmentation. Combined with a standard large residual nnU-Net architecture for segmentation, this approach achieves a mean test Dice of 28.5 with a standard deviation of 21.27.
Multimodal medical image segmentation faces significant challenges in the context of gastric cancer lesion analysis. This clinical context is defined by the scarcity of independent multimodal datasets and the imperative to amalgamate inherently misaligned modalities. As a result, algorithms are constrained to train on approximate data and depend on application migration, leading to substantial resource expenditure and a potential decline in analysis accuracy. To address those challenges, we have made two major contributions: First, we publicly disseminate the GCM 2025 dataset, which serves as the first large-scale, open-source collection of gastric cancer multimodal MRI scans, featuring professionally annotated FS-T2W, CE-T1W, and ADC images from 500 patients. Second, we introduce HWA-UNETR, a novel 3D segmentation framework that employs an original HWA block with learnable window aggregation layers to establish dynamic feature correspondences between different modalities' anatomical structures, and leverages the innovative tri-orientated fusion mamba mechanism for context modeling and capturing long-range spatial dependencies. Extensive experiments on our GCM 2025 dataset and the publicly BraTS 2021 dataset validate the performance of our framework, demonstrating that the new approach surpasses existing methods by up to 1.68\% in the Dice score while maintaining solid robustness. The dataset and code are public via https://github.com/JeMing-creater/HWA-UNETR.
Camouflaged object segmentation presents unique challenges compared to traditional segmentation tasks, primarily due to the high similarity in patterns and colors between camouflaged objects and their backgrounds. Effective solutions to this problem have significant implications in critical areas such as pest control, defect detection, and lesion segmentation in medical imaging. Prior research has predominantly emphasized supervised or unsupervised pre-training methods, leaving zero-shot approaches significantly underdeveloped. Existing zero-shot techniques commonly utilize the Segment Anything Model (SAM) in automatic mode or rely on vision-language models to generate cues for segmentation; however, their performances remain unsatisfactory, likely due to the similarity of the camouflaged object and the background. Optical flow, commonly utilized for detecting moving objects, has demonstrated effectiveness even with camouflaged entities. Our method integrates optical flow, a vision-language model, and SAM 2 into a sequential pipeline. Evaluated on the MoCA-Mask dataset, our approach achieves outstanding performance improvements, significantly outperforming existing zero-shot methods by raising the F-measure ($F_\beta^w$) from 0.296 to 0.628. Remarkably, our approach also surpasses supervised methods, increasing the F-measure from 0.476 to 0.628. Additionally, evaluation on the MoCA-Filter dataset demonstrates an increase in the success rate from 0.628 to 0.697 when compared with FlowSAM, a supervised transfer method. A thorough ablation study further validates the individual contributions of each component. More details can be found on https://github.com/weathon/vcos.
Accurate segmentation of lesions plays a critical role in medical image analysis and diagnosis. Traditional segmentation approaches that rely solely on visual features often struggle with the inherent uncertainty in lesion distribution and size. To address these issues, we propose STPNet, a Scale-aware Text Prompt Network that leverages vision-language modeling to enhance medical image segmentation. Our approach utilizes multi-scale textual descriptions to guide lesion localization and employs retrieval-segmentation joint learning to bridge the semantic gap between visual and linguistic modalities. Crucially, STPNet retrieves relevant textual information from a specialized medical text repository during training, eliminating the need for text input during inference while retaining the benefits of cross-modal learning. We evaluate STPNet on three datasets: COVID-Xray, COVID-CT, and Kvasir-SEG. Experimental results show that our vision-language approach outperforms state-of-the-art segmentation methods, demonstrating the effectiveness of incorporating textual semantic knowledge into medical image analysis. The code has been made publicly on https://github.com/HUANGLIZI/STPNet.
In the setting of clinical imaging, differences in between vendors, hospitals and sequences can yield highly inhomogeneous imaging data. In MRI in particular, voxel dimension, slice spacing and acquisition plane can vary substantially. For clinical applications, therefore, algorithms must be trained to handle data with various voxel resolutions. The usual strategy to deal with heterogeneity of resolution is harmonization: resampling imaging data to a common (usually isovoxel) resolution. This can lead to loss of fidelity arising from interpolation artifacts out-of-plane and downsampling in-plane. We present in this paper a network architecture designed to be able to learn directly from spatially heterogeneous data, without resampling: a segmentation network based on the e3nn framework that leverages a spherical harmonic, rather than voxel-grid, parameterization of convolutional kernels, with a fixed physical radius. Networks based on these kernels can be resampled to their input voxel dimensions. We trained and tested our network on a publicly available dataset assembled from three centres, and on an in-house dataset of Multiple Sclerosis cases with a high degree of spatial inhomogeneity. We compared our approach to a standard U-Net with two strategies for handling inhomogeneous data: training directly on the data without resampling, and resampling to a common resolution of 1mm isovoxels. We show that our network is able to learn from various combinations of voxel sizes and outperforms classical U-Nets on 2D testing cases and most 3D testing cases. This shows an ability to generalize well when tested on image resolutions not seen during training. Our code can be found at: http://github.com/SCAN-NRAD/e3nn\_U-Net.
Traditional brain lesion segmentation models for multi-modal MRI are typically tailored to specific pathologies, relying on datasets with predefined modalities. Adapting to new MRI modalities or pathologies often requires training separate models, which contrasts with how medical professionals incrementally expand their expertise by learning from diverse datasets over time. Inspired by this human learning process, we propose a unified segmentation model capable of sequentially learning from multiple datasets with varying modalities and pathologies. Our approach leverages a privacy-aware continual learning framework that integrates a mixture-of-experts mechanism and dual knowledge distillation to mitigate catastrophic forgetting while not compromising performance on newly encountered datasets. Extensive experiments across five diverse brain MRI datasets and four dataset sequences demonstrate the effectiveness of our framework in maintaining a single adaptable model, capable of handling varying hospital protocols, imaging modalities, and disease types. Compared to widely used privacy-aware continual learning methods such as LwF, SI, EWC, and MiB, our method achieves an average Dice score improvement of approximately 11%. Our framework represents a significant step toward more versatile and practical brain lesion segmentation models, with implementation available at \href{https://github.com/xmindflow/BrainCL}{GitHub}.
Skin lesion segmentation is a critical challenge in computer vision, and it is essential to separate pathological features from healthy skin for diagnostics accurately. Traditional Convolutional Neural Networks (CNNs) are limited by narrow receptive fields, and Transformers face significant computational burdens. This paper presents a novel skin lesion segmentation framework, the Atrous Shifted Parallel Vision Mamba UNet (ASP-VMUNet), which integrates the efficient and scalable Mamba architecture to overcome limitations in traditional CNNs and computationally demanding Transformers. The framework introduces an atrous scan technique that minimizes background interference and expands the receptive field, enhancing Mamba's scanning capabilities. Additionally, the inclusion of a Parallel Vision Mamba (PVM) layer and a shift round operation optimizes feature segmentation and fosters rich inter-segment information exchange. A supplementary CNN branch with a Selective-Kernel (SK) Block further refines the segmentation by blending local and global contextual information. Tested on four benchmark datasets (ISIC16/17/18 and PH2), ASP-VMUNet demonstrates superior performance in skin lesion segmentation, validated by comprehensive ablation studies. This approach not only advances medical image segmentation but also highlights the benefits of hybrid architectures in medical imaging technology. Our code is available at https://github.com/BaoBao0926/ASP-VMUNet/tree/main.
Melanoma is a malignant tumor originating from skin cell lesions. Accurate and efficient segmentation of skin lesions is essential for quantitative medical analysis but remains challenging. To address this, we propose ScaleFusionNet, a segmentation model that integrates Cross-Attention Transformer Module (CATM) and AdaptiveFusionBlock to enhance feature extraction and fusion. The model employs a hybrid architecture encoder that effectively captures both local and global features. We introduce CATM, which utilizes Swin Transformer Blocks and Cross Attention Fusion (CAF) to adaptively refine encoder-decoder feature fusion, reducing semantic gaps and improving segmentation accuracy. Additionally, the AdaptiveFusionBlock is improved by integrating adaptive multi-scale fusion, where Swin Transformer-based attention complements deformable convolution-based multi-scale feature extraction. This enhancement refines lesion boundaries and preserves fine-grained details. ScaleFusionNet achieves Dice scores of 92.94% and 91.65% on ISIC-2016 and ISIC-2018 datasets, respectively, demonstrating its effectiveness in skin lesion analysis. Our code implementation is publicly available at GitHub.
We can achieve fast and consistent early skin cancer detection with recent developments in computer vision and deep learning techniques. However, the existing skin lesion segmentation and classification prediction models run independently, thus missing potential efficiencies from their integrated execution. To unify skin lesion analysis, our paper presents the Gaussian Splatting - Transformer UNet (GS-TransUNet), a novel approach that synergistically combines 2D Gaussian splatting with the Transformer UNet architecture for automated skin cancer diagnosis. Our unified deep learning model efficiently delivers dual-function skin lesion classification and segmentation for clinical diagnosis. Evaluated on ISIC-2017 and PH2 datasets, our network demonstrates superior performance compared to existing state-of-the-art models across multiple metrics through 5-fold cross-validation. Our findings illustrate significant advancements in the precision of segmentation and classification. This integration sets new benchmarks in the field and highlights the potential for further research into multi-task medical image analysis methodologies, promising enhancements in automated diagnostic systems.
In recent years, machine learning algorithms have achieved much success in segmenting lesions across various tissues. There is, however, not one satisfying model that works well on all tissue types universally. In response to this need, we attempt to train a model that 1) works well on all tissue types, and 2) is capable of still performing fast inferences. To this end, we design our architectures, test multiple existing architectures, compare their results, and settle upon SwinUnet. We document our rationales, successes, and failures. Finally, we propose some further directions that we think are worth exploring. codes: https://github.com/KWFredShi/ULS2023NGKD.git
Self-supervised deep learning has accelerated 2D natural image analysis but remains difficult to translate into 3D MRI, where data are scarce and pre-trained 2D backbones cannot capture volumetric context. We present a sequence-invariant self-supervised framework leveraging quantitative MRI (qMRI). By simulating multiple MRI contrasts from a single 3D qMRI scan and enforcing consistent representations across these contrasts, we learn anatomy-centric rather than sequence-specific features. This yields a robust 3D encoder that performs strongly across varied tasks and protocols. Experiments on healthy brain segmentation (IXI), stroke lesion segmentation (ARC), and MRI denoising show significant gains over baseline SSL approaches, especially in low-data settings (up to +8.3% Dice, +4.2 dB PSNR). Our model also generalises effectively to unseen sites, demonstrating potential for more scalable and clinically reliable volumetric analysis. All code and trained models are publicly available.
This study explores the potential of graph neural networks (GNNs) to enhance semantic segmentation across diverse image modalities. We evaluate the effectiveness of a novel GNN-based U-Net architecture on three distinct datasets: PascalVOC, a standard benchmark for natural image segmentation, WoodScape, a challenging dataset of fisheye images commonly used in autonomous driving, introducing significant geometric distortions; and ISIC2016, a dataset of dermoscopic images for skin lesion segmentation. We compare our proposed UNet-GNN model against established convolutional neural networks (CNNs) based segmentation models, including U-Net and U-Net++, as well as the transformer-based SwinUNet. Unlike these methods, which primarily rely on local convolutional operations or global self-attention, GNNs explicitly model relationships between image regions by constructing and operating on a graph representation of the image features. This approach allows the model to capture long-range dependencies and complex spatial relationships, which we hypothesize will be particularly beneficial for handling geometric distortions present in fisheye imagery and capturing intricate boundaries in medical images. Our analysis demonstrates the versatility of GNNs in addressing diverse segmentation challenges and highlights their potential to improve segmentation accuracy in various applications, including autonomous driving and medical image analysis.
Breast cancer lesion segmentation in DCE-MRI remains challenging due to heterogeneous tumor morphology and indistinct boundaries. To address these challenges, this study proposes a novel hybrid segmentation network, HCMA-UNet, for lesion segmentation of breast cancer. Our network consists of a lightweight CNN backbone and a Multi-view Axial Self-Attention Mamba (MISM) module. The MISM module integrates Visual State Space Block (VSSB) and Axial Self-Attention (ASA) mechanism, effectively reducing parameters through Asymmetric Split Channel (ASC) strategy to achieve efficient tri-directional feature extraction. Our lightweight model achieves superior performance with 2.87M parameters and 126.44 GFLOPs. A Feature-guided Region-aware loss function (FRLoss) is proposed to enhance segmentation accuracy. Extensive experiments on one private and two public DCE-MRI breast cancer datasets demonstrate that our approach achieves state-of-the-art performance while maintaining computational efficiency. FRLoss also exhibits good cross-architecture generalization capabilities. The source code is available at https://github.com/Haoxuanli-Thu/HCMA-UNet.
Accurate medical image segmentation is essential for effective diagnosis and treatment planning but is often challenged by domain shifts caused by variations in imaging devices, acquisition conditions, and patient-specific attributes. Traditional domain generalization methods typically require inclusion of parts of the test domain within the training set, which is not always feasible in clinical settings with limited diverse data. Additionally, although diffusion models have demonstrated strong capabilities in image generation and style transfer, they often fail to preserve the critical structural information necessary for precise medical analysis. To address these issues, we propose a novel medical image segmentation method that combines diffusion models and Structure-Preserving Network for structure-aware one-shot image stylization. Our approach effectively mitigates domain shifts by transforming images from various sources into a consistent style while maintaining the location, size, and shape of lesions. This ensures robust and accurate segmentation even when the target domain is absent from the training data. Experimental evaluations on colonoscopy polyp segmentation and skin lesion segmentation datasets show that our method enhances the robustness and accuracy of segmentation models, achieving superior performance metrics compared to baseline models without style transfer. This structure-aware stylization framework offers a practical solution for improving medical image segmentation across diverse domains, facilitating more reliable clinical diagnoses.
Segmenting stroke lesions in MRI is challenging due to diverse acquisition protocols that limit model generalisability. In this work, we introduce two physics-constrained approaches to generate synthetic quantitative MRI (qMRI) images that improve segmentation robustness across heterogeneous domains. Our first method, $\texttt{qATLAS}$, trains a neural network to estimate qMRI maps from standard MPRAGE images, enabling the simulation of varied MRI sequences with realistic tissue contrasts. The second method, $\texttt{qSynth}$, synthesises qMRI maps directly from tissue labels using label-conditioned Gaussian mixture models, ensuring physical plausibility. Extensive experiments on multiple out-of-domain datasets show that both methods outperform a baseline UNet, with $\texttt{qSynth}$ notably surpassing previous synthetic data approaches. These results highlight the promise of integrating MRI physics into synthetic data generation for robust, generalisable stroke lesion segmentation. Code is available at https://github.com/liamchalcroft/qsynth
Early detection of skin abnormalities plays a crucial role in diagnosing and treating skin cancer. Segmentation of affected skin regions using AI-powered devices is relatively common and supports the diagnostic process. However, achieving high performance remains a significant challenge due to the need for high-resolution images and the often unclear boundaries of individual lesions. At the same time, medical devices require segmentation models to have a small memory foot-print and low computational cost. Based on these requirements, we introduce a novel lightweight model called MambaU-Lite, which combines the strengths of Mamba and CNN architectures, featuring just over 400K parameters and a computational cost of more than 1G flops. To enhance both global context and local feature extraction, we propose the P-Mamba block, a novel component that incorporates VSS blocks along-side multiple pooling layers, enabling the model to effectively learn multiscale features and enhance segmentation performance. We evaluate the model's performance on two skin datasets, ISIC2018 and PH2, yielding promising results. Our source code will be made publicly available at: https://github.com/nqnguyen812/MambaU-Lite.
Segmenting glomerular intraglomerular tissue and lesions traditionally depends on detailed morphological evaluations by expert nephropathologists, a labor-intensive process susceptible to interobserver variability. Our group previously developed the Glo-In-One toolkit for integrated detection and segmentation of glomeruli. In this study, we leverage the Glo-In-One toolkit to version 2 with fine-grained segmentation capabilities, curating 14 distinct labels for tissue regions, cells, and lesions across a dataset of 23,529 annotated glomeruli across human and mouse histopathology data. To our knowledge, this dataset is among the largest of its kind to date.In this study, we present a single dynamic head deep learning architecture designed to segment 14 classes within partially labeled images of human and mouse pathology data. Our model was trained using a training set derived from 368 annotated kidney whole-slide images (WSIs) to identify 5 key intraglomerular tissues covering Bowman's capsule, glomerular tuft, mesangium, mesangial cells, and podocytes. Additionally, the network segments 9 glomerular lesion classes including adhesion, capsular drop, global sclerosis, hyalinosis, mesangial lysis, microaneurysm, nodular sclerosis, mesangial expansion, and segmental sclerosis. The glomerulus segmentation model achieved a decent performance compared with baselines, and achieved a 76.5 % average Dice Similarity Coefficient (DSC). Additional, transfer learning from rodent to human for glomerular lesion segmentation model has enhanced the average segmentation accuracy across different types of lesions by more than 3 %, as measured by Dice scores. The Glo-In-One-v2 model and trained weight have been made publicly available at https: //github.com/hrlblab/Glo-In-One_v2.
Timely and precise classification and segmentation of gastric bleeding in endoscopic imagery are pivotal for the rapid diagnosis and intervention of gastric complications, which is critical in life-saving medical procedures. Traditional methods grapple with the challenge posed by the indistinguishable intensity values of bleeding tissues adjacent to other gastric structures. Our study seeks to revolutionize this domain by introducing a novel deep learning model, the Dual Spatial Kernelized Constrained Fuzzy C-Means (Deep DuS-KFCM) clustering algorithm. This Hybrid Neuro-Fuzzy system synergizes Neural Networks with Fuzzy Logic to offer a highly precise and efficient identification of bleeding regions. Implementing a two-fold coarse-to-fine strategy for segmentation, this model initially employs the Spatial Kernelized Fuzzy C-Means (SKFCM) algorithm enhanced with spatial intensity profiles and subsequently harnesses the state-of-the-art DeepLabv3+ with ResNet50 architecture to refine the segmentation output. Through extensive experiments across mainstream gastric bleeding and red spots datasets, our Deep DuS-KFCM model demonstrated unprecedented accuracy rates of 87.95%, coupled with a specificity of 96.33%, outperforming contemporary segmentation methods. The findings underscore the model's robustness against noise and its outstanding segmentation capabilities, particularly for identifying subtle bleeding symptoms, thereby presenting a significant leap forward in medical image processing.
Automatic melanoma segmentation is essential for early skin cancer detection, yet challenges arise from the heterogeneity of melanoma, as well as interfering factors like blurred boundaries, low contrast, and imaging artifacts. While numerous algorithms have been developed to address these issues, previous approaches have often overlooked the need to jointly capture spatial and sequential features within dermatological images. This limitation hampers segmentation accuracy, especially in cases with indistinct borders or structurally similar lesions. Additionally, previous models lacked both a global receptive field and high computational efficiency. In this work, we present the xLSTM-VMUNet Model, which jointly capture spatial and sequential features within dermatological images successfully. xLSTM-VMUNet can not only specialize in extracting spatial features from images, focusing on the structural characteristics of skin lesions, but also enhance contextual understanding, allowing more effective handling of complex medical image structures. Experiment results on the ISIC2018 dataset demonstrate that xLSTM-VMUNet outperforms VMUNet by 4.85% on DSC and 6.41% on IoU on the ISIC2017 dataset, by 1.25% on DSC and 2.07% on IoU on the ISIC2018 dataset, with faster convergence and consistently high segmentation performance. Our code is available at https://github.com/FangZhuoyi/XLSTM-VMUNet.
High resolution is crucial for precise segmentation in fundus images, yet handling high-resolution inputs incurs considerable GPU memory costs, with diminishing performance gains as overhead increases. To address this issue while tackling the challenge of segmenting tiny objects, recent studies have explored local-global fusion methods. These methods preserve fine details using local regions and capture long-range context information from downscaled global images. However, the necessity of multiple forward passes inevitably incurs significant computational overhead, adversely affecting inference speed. In this paper, we propose HRDecoder, a simple High-Resolution Decoder network for fundus lesion segmentation. It integrates a high-resolution representation learning module to capture fine-grained local features and a high-resolution fusion module to fuse multi-scale predictions. Our method effectively improves the overall segmentation accuracy of fundus lesions while consuming reasonable memory and computational overhead, and maintaining satisfying inference speed. Experimental results on the IDRID and DDR datasets demonstrate the effectiveness of our method. Code is available at https://github.com/CVIU-CSU/HRDecoder.