Due to the association with higher incidence of left ventricular dysfunction and complications, segmentation of left ventricle and related pathological tissues: microvascular obstruction and myocardial infarction from late gadolinium enhancement cardiac magnetic resonance images is crucially important. However, lack of datasets, diverse shapes and locations, extreme imbalanced class, severe intensity distribution overlapping are the main challenges. We first release a late gadolinium enhancement cardiac magnetic resonance benchmark dataset LGE-LVP containing 140 patients with left ventricle myocardial infarction and concomitant microvascular obstruction. Then, a progressive deep learning model LVPSegNet is proposed to segment the left ventricle and its pathologies via adaptive region of interest extraction, sample augmentation, curriculum learning, and multiple receptive field fusion in dealing with the challenges. Comprehensive comparisons with state-of-the-art models on the internal and external datasets demonstrate that the proposed model performs the best on both geometric and clinical metrics and it most closely matched the clinician's performance. Overall, the released LGE-LVP dataset alongside the LVPSegNet we proposed offer a practical solution for automated left ventricular and its pathologies segmentation by providing data support and facilitating effective segmentation. The dataset and source codes will be released via https://github.com/DFLAG-NEU/LVPSegNet.

Most publicly available medical segmentation datasets are only partially labeled, with annotations provided for a subset of anatomical structures. When multiple datasets are combined for training, this incomplete annotation poses challenges, as it limits the model's ability to learn shared anatomical representations among datasets. Furthermore, vision-only frameworks often fail to capture complex anatomical relationships and task-specific distinctions, leading to reduced segmentation accuracy and poor generalizability to unseen datasets. In this study, we proposed a novel CLIP-DINO Prompt-Driven Segmentation Network (CDPDNet), which combined a self-supervised vision transformer with CLIP-based text embedding and introduced task-specific text prompts to tackle these challenges. Specifically, the framework was constructed upon a convolutional neural network (CNN) and incorporated DINOv2 to extract both fine-grained and global visual features, which were then fused using a multi-head cross-attention module to overcome the limited long-range modeling capability of CNNs. In addition, CLIP-derived text embeddings were projected into the visual space to help model complex relationships among organs and tumors. To further address the partial label challenge and enhance inter-task discriminative capability, a Text-based Task Prompt Generation (TTPG) module that generated task-specific prompts was designed to guide the segmentation. Extensive experiments on multiple medical imaging datasets demonstrated that CDPDNet consistently outperformed existing state-of-the-art segmentation methods. Code and pretrained model are available at: https://github.com/wujiong-hub/CDPDNet.git.

Most publicly available medical segmentation datasets are only partially labeled, with annotations provided for a subset of anatomical structures. When multiple datasets are combined for training, this incomplete annotation poses challenges, as it limits the model's ability to learn shared anatomical representations among datasets. Furthermore, vision-only frameworks often fail to capture complex anatomical relationships and task-specific distinctions, leading to reduced segmentation accuracy and poor generalizability to unseen datasets. In this study, we proposed a novel CLIP-DINO Prompt-Driven Segmentation Network (CDPDNet), which combined a self-supervised vision transformer with CLIP-based text embedding and introduced task-specific text prompts to tackle these challenges. Specifically, the framework was constructed upon a convolutional neural network (CNN) and incorporated DINOv2 to extract both fine-grained and global visual features, which were then fused using a multi-head cross-attention module to overcome the limited long-range modeling capability of CNNs. In addition, CLIP-derived text embeddings were projected into the visual space to help model complex relationships among organs and tumors. To further address the partial label challenge and enhance inter-task discriminative capability, a Text-based Task Prompt Generation (TTPG) module that generated task-specific prompts was designed to guide the segmentation. Extensive experiments on multiple medical imaging datasets demonstrated that CDPDNet consistently outperformed existing state-of-the-art segmentation methods. Code and pretrained model are available at: https://github.com/wujiong-hub/CDPDNet.git.

Advanced autoregressive models have reshaped multimodal AI. However, their transformative potential in medical imaging remains largely untapped due to the absence of a unified visual tokenizer -- one capable of capturing fine-grained visual structures for faithful image reconstruction and realistic image synthesis, as well as rich semantics for accurate diagnosis and image interpretation. To this end, we present MedITok, the first unified tokenizer tailored for medical images, encoding both low-level structural details and high-level clinical semantics within a unified latent space. To balance these competing objectives, we introduce a novel two-stage training framework: a visual representation alignment stage that cold-starts the tokenizer reconstruction learning with a visual semantic constraint, followed by a textual semantic representation alignment stage that infuses detailed clinical semantics into the latent space. Trained on the meticulously collected large-scale dataset with over 30 million medical images and 2 million image-caption pairs, MedITok achieves state-of-the-art performance on more than 30 datasets across 9 imaging modalities and 4 different tasks. By providing a unified token space for autoregressive modeling, MedITok supports a wide range of tasks in clinical diagnostics and generative healthcare applications. Model and code will be made publicly available at: https://github.com/Masaaki-75/meditok.

3D medical image segmentation is vital for clinical diagnosis and treatment but is challenged by high-dimensional data and complex spatial dependencies. Traditional single-modality networks, such as CNNs and Transformers, are often limited by computational inefficiency and constrained contextual modeling in 3D settings. We introduce a novel multimodal framework that leverages Mamba and Kolmogorov-Arnold Networks (KAN) as an efficient backbone for long-sequence modeling. Our approach features three key innovations: First, an EGSC (Enhanced Gated Spatial Convolution) module captures spatial information when unfolding 3D images into 1D sequences. Second, we extend Group-Rational KAN (GR-KAN), a Kolmogorov-Arnold Networks variant with rational basis functions, into 3D-Group-Rational KAN (3D-GR-KAN) for 3D medical imaging - its first application in this domain - enabling superior feature representation tailored to volumetric data. Third, a dual-branch text-driven strategy leverages CLIP's text embeddings: one branch swaps one-hot labels for semantic vectors to preserve inter-organ semantic relationships, while the other aligns images with detailed organ descriptions to enhance semantic alignment. Experiments on the Medical Segmentation Decathlon (MSD) and KiTS23 datasets show our method achieving state-of-the-art performance, surpassing existing approaches in accuracy and efficiency. This work highlights the power of combining advanced sequence modeling, extended network architectures, and vision-language synergy to push forward 3D medical image segmentation, delivering a scalable solution for clinical use. The source code is openly available at https://github.com/yhy-whu/TK-Mamba.

To introduce MATI (Microstructural Analysis Toolbox for Imaging), a versatile MATLAB-based toolbox that combines both simulation and data fitting capabilities for microstructural dMRI research. MATI provides a user-friendly, graphical user interface that enables researchers, including those without much programming experience, to perform advanced simulations and data analyses for microstructural MRI research. For simulation, MATI supports arbitrary microstructural tissues and pulse sequences. For data fitting, MATI supports a range of fitting methods, including traditional non-linear least squares, Bayesian approaches, machine learning, and dictionary matching methods, allowing users to tailor analyses based on specific research needs. Optimized with vectorized matrix operations and high-performance numerical libraries, MATI achieves high computational efficiency, enabling rapid simulations and data fitting on CPU and GPU hardware. While designed for microstructural dMRI, MATI's generalized framework can be extended to other imaging methods, making it a flexible and scalable tool for quantitative MRI research. MATI offers a significant step toward translating advanced microstructural MRI techniques into clinical applications.

Both CNN-based and Transformer-based methods have achieved remarkable success in medical image segmentation tasks. However, CNN-based methods struggle to effectively capture global contextual information due to the inherent limitations of convolution operations. Meanwhile, Transformer-based methods suffer from insufficient local feature modeling and face challenges related to the high computational complexity caused by the self-attention mechanism. To address these limitations, we propose a novel hybrid CNN-Transformer architecture, named MSLAU-Net, which integrates the strengths of both paradigms. The proposed MSLAU-Net incorporates two key ideas. First, it introduces Multi-Scale Linear Attention, designed to efficiently extract multi-scale features from medical images while modeling long-range dependencies with low computational complexity. Second, it adopts a top-down feature aggregation mechanism, which performs multi-level feature aggregation and restores spatial resolution using a lightweight structure. Extensive experiments conducted on benchmark datasets covering three imaging modalities demonstrate that the proposed MSLAU-Net outperforms other state-of-the-art methods on nearly all evaluation metrics, validating the superiority, effectiveness, and robustness of our approach. Our code is available at https://github.com/Monsoon49/MSLAU-Net.

Intraventricular hemorrhage (IVH) is a severe neurological complication among premature infants, necessitating early and accurate detection from brain ultrasound (US) images to improve clinical outcomes. While recent deep learning methods offer promise for computer-aided diagnosis, challenges remain in capturing both local spatial details and global contextual dependencies critical for segmenting brain anatomies. In this work, we propose an enhanced Residual U-Net architecture incorporating two complementary attention mechanisms: the Convolutional Block Attention Module (CBAM) and a Sparse Attention Layer (SAL). The CBAM improves the model's ability to refine spatial and channel-wise features, while the SAL introduces a dual-branch design, sparse attention filters out low-confidence query-key pairs to suppress noise, and dense attention ensures comprehensive information propagation. Extensive experiments on the Brain US dataset demonstrate that our method achieves state-of-the-art segmentation performance, with a Dice score of 89.04% and IoU of 81.84% for ventricle region segmentation. These results highlight the effectiveness of integrating spatial refinement and attention sparsity for robust brain anatomy detection. Code is available at: https://github.com/DanYuan001/BrainImgSegment.

Lung cancer has been one of the major threats across the world with the highest mortalities. Computer-aided detection (CAD) can help in early detection and thus can help increase the survival rate. Accurate lung parenchyma segmentation (to include the juxta-pleural nodules) and lung nodule segmentation, the primary symptom of lung cancer, play a crucial role in the overall accuracy of the Lung CAD pipeline. Lung nodule segmentation is quite challenging because of the diverse nodule types and other inhibit structures present within the lung lobes. Traditional machine/deep learning methods suffer from generalization and robustness. Recent Vision Language Models/Foundation Models perform well on the anatomical level, but they suffer on fine-grained segmentation tasks, and their semi-automatic nature limits their effectiveness in real-time clinical scenarios. In this paper, we propose a novel method for accurate 3D segmentation of lung parenchyma and lung nodules. The proposed architecture is an attention-based network with residual blocks at each encoder-decoder state. Max pooling is replaced by strided convolutions at the encoder, and trilinear interpolation is replaced by transposed convolutions at the decoder to maximize the number of learnable parameters. Dilated convolutions at each encoder-decoder stage allow the model to capture the larger context without increasing computational costs. The proposed method has been evaluated extensively on one of the largest publicly available datasets, namely LUNA16, and is compared with recent notable work in the domain using standard performance metrics like Dice score, IOU, etc. It can be seen from the results that the proposed method achieves better performance than state-of-the-art methods. The source code, datasets, and pre-processed data can be accessed using the link: https://github.com/EMeRALDsNRPU/Attention-Based-3D-ResUNet.

Low-quality pseudo labels pose a significant obstacle in semi-supervised medical image segmentation (SSMIS), impeding consistency learning on unlabeled data. Leveraging vision-language model (VLM) holds promise in ameliorating pseudo label quality by employing textual prompts to delineate segmentation regions, but it faces the challenge of cross-modal alignment uncertainty due to multiple correspondences (multiple images/texts tend to correspond to one text/image). Existing VLMs address this challenge by modeling semantics as distributions but such distributions lead to semantic degradation. To address these problems, we propose Alignment-Multiplicity Aware Vision-Language Model (AMVLM), a new VLM pre-training paradigm with two novel similarity metric strategies. (i) Cross-modal Similarity Supervision (CSS) proposes a probability distribution transformer to supervise similarity scores across fine-granularity semantics through measuring cross-modal distribution disparities, thus learning cross-modal multiple alignments. (ii) Intra-modal Contrastive Learning (ICL) takes into account the similarity metric of coarse-fine granularity information within each modality to encourage cross-modal semantic consistency. Furthermore, using the pretrained AMVLM, we propose a pioneering text-guided SSMIS network to compensate for the quality deficiencies of pseudo-labels. This network incorporates a text mask generator to produce multimodal supervision information, enhancing pseudo label quality and the model's consistency learning. Extensive experimentation validates the efficacy of our AMVLM-driven SSMIS, showcasing superior performance across four publicly available datasets. The code will be available at: https://github.com/QingtaoPan/AMVLM.