Ultrasound is widely used in clinical care, yet standard deep learning methods often struggle with full video analysis due to non-standardized acquisition and operator bias. We offer a new perspective on ultrasound video analysis through implicit neural representations (INRs). We build on Functa, an INR framework in which each image is represented by a modulation vector that conditions a shared neural network. However, its extension to the temporal domain of medical videos remains unexplored. To address this gap, we propose VidFuncta, a novel framework that leverages Functa to encode variable-length ultrasound videos into compact, time-resolved representations. VidFuncta disentangles each video into a static video-specific vector and a sequence of time-dependent modulation vectors, capturing both temporal dynamics and dataset-level redundancies. Our method outperforms 2D and 3D baselines on video reconstruction and enables downstream tasks to directly operate on the learned 1D modulation vectors. We validate VidFuncta on three public ultrasound video datasets -- cardiac, lung, and breast -- and evaluate its downstream performance on ejection fraction prediction, B-line detection, and breast lesion classification. These results highlight the potential of VidFuncta as a generalizable and efficient representation framework for ultrasound videos. Our code is publicly available under https://github.com/JuliaWolleb/VidFuncta_public.

Deep learning techniques have become pivotal in medical image segmentation, but their success often relies on large, manually annotated datasets, which are expensive and labor-intensive to obtain. Additionally, different segmentation tasks frequently require retraining models from scratch, resulting in substantial computational costs. To address these limitations, we propose PDoRA, an innovative parameter-efficient fine-tuning method that leverages knowledge transfer from a pre-trained SwinUNETR model for a wide range of brain image segmentation tasks. PDoRA minimizes the reliance on extensive data annotation and computational resources by decomposing model weights into principal and residual weights. The principal weights are further divided into magnitude and direction, enabling independent fine-tuning to enhance the model's ability to capture task-specific features. The residual weights remain fixed and are later fused with the updated principal weights, ensuring model stability while enhancing performance. We evaluated PDoRA on three diverse medical image datasets for brain structure and metastasis segmentation. The results demonstrate that PDoRA consistently outperforms existing parameter-efficient fine-tuning methods, achieving superior segmentation accuracy and efficiency. Our code is available at https://github.com/Perfect199001/PDoRA/tree/main .

Magnetic resonance imaging (MRI) is a crucial medical imaging modality. However, long acquisition times remain a significant challenge, leading to increased costs, and reduced patient comfort. Recent studies have shown the potential of using deep learning models that incorporate information from prior subject-specific MRI scans to improve reconstruction quality of present scans. Integrating this prior information requires registration of the previous scan to the current image reconstruction, which can be time-consuming. We propose a novel deep-learning-based MRI reconstruction framework which consists of an initial reconstruction network, a deep registration model, and a transformer-based enhancement network. We validated our method on a longitudinal dataset of T1-weighted MRI scans with 2,808 images from 18 subjects at four acceleration factors (R5, R10, R15, R20). Quantitative metrics confirmed our approach's superiority over existing methods (p < 0.05, Wilcoxon signed-rank test). Furthermore, we analyzed the impact of our MRI reconstruction method on the downstream task of brain segmentation and observed improved accuracy and volumetric agreement with reference segmentations. Our approach also achieved a substantial reduction in total reconstruction time compared to methods that use traditional registration algorithms, making it more suitable for real-time clinical applications. The code associated with this work is publicly available at https://github.com/amirshamaei/longitudinal-mri-deep-recon.

Generating high-fidelity dental radiographs is essential for training diagnostic models. Despite the development of numerous methods for other medical data, generative approaches in dental radiology remain unexplored. Due to the intricate tooth structures and specialized terminology, these methods often yield ambiguous tooth regions and incorrect dental concepts when applied to dentistry. In this paper, we take the first attempt to investigate diffusion-based teeth X-ray image generation and propose ToothMaker, a novel framework specifically designed for the dental domain. Firstly, to synthesize X-ray images that possess accurate tooth structures and realistic radiological styles simultaneously, we design control-disentangled fine-tuning (CDFT) strategy. Specifically, we present two separate controllers to handle style and layout control respectively, and introduce a gradient-based decoupling method that optimizes each using their corresponding disentangled gradients. Secondly, to enhance model's understanding of dental terminology, we propose prior-disentangled guidance module (PDGM), enabling precise synthesis of dental concepts. It utilizes large language model to decompose dental terminology into a series of meta-knowledge elements and performs interactions and refinements through hypergraph neural network. These elements are then fed into the network to guide the generation of dental concepts. Extensive experiments demonstrate the high fidelity and diversity of the images synthesized by our approach. By incorporating the generated data, we achieve substantial performance improvements on downstream segmentation and visual question answering tasks, indicating that our method can greatly reduce the reliance on manually annotated data. Code will be public available at https://github.com/CUHK-AIM-Group/ToothMaker.

Anomaly detection in medical imaging plays a crucial role in identifying pathological regions across various imaging modalities, such as brain MRI, liver CT, and carotid ultrasound (US). However, training fully supervised segmentation models is often hindered by the scarcity of expert annotations and the complexity of diverse anatomical structures. To address these issues, we propose a novel unsupervised anomaly detection framework based on a diffusion model that incorporates a synthetic anomaly (Synomaly) noise function and a multi-stage diffusion process. Synomaly noise introduces synthetic anomalies into healthy images during training, allowing the model to effectively learn anomaly removal. The multi-stage diffusion process is introduced to progressively denoise images, preserving fine details while improving the quality of anomaly-free reconstructions. The generated high-fidelity counterfactual healthy images can further enhance the interpretability of the segmentation models, as well as provide a reliable baseline for evaluating the extent of anomalies and supporting clinical decision-making. Notably, the unsupervised anomaly detection model is trained purely on healthy images, eliminating the need for anomalous training samples and pixel-level annotations. We validate the proposed approach on brain MRI, liver CT datasets, and carotid US. The experimental results demonstrate that the proposed framework outperforms existing state-of-the-art unsupervised anomaly detection methods, achieving performance comparable to fully supervised segmentation models in the US dataset. Ablation studies further highlight the contributions of Synomaly noise and the multi-stage diffusion process in improving anomaly segmentation. These findings underscore the potential of our approach as a robust and annotation-efficient alternative for medical anomaly detection. Code:https://github.com/yuan-12138/Synomaly.

Medical image segmentation plays an important role in computer-aided diagnosis. Traditional convolution-based U-shape segmentation architectures are usually limited by the local receptive field. Existing vision transformers have been widely applied to diverse medical segmentation frameworks due to their superior capabilities of capturing global contexts. Despite the advantage, the real-world application of vision transformers is challenged by their non-linear self-attention mechanism, requiring huge computational costs. To address this issue, the selective state space model (SSM) Mamba has gained recognition for its adeptness in modeling long-range dependencies in sequential data, particularly noted for its efficient memory costs. In this paper, we propose MambaVesselNet++, a Hybrid CNN-Mamba framework for medical image segmentation. Our MambaVesselNet++ is comprised of a hybrid image encoder (Hi-Encoder) and a bifocal fusion decoder (BF-Decoder). In Hi-Encoder, we first devise the texture-aware layer to capture low-level semantic features by leveraging convolutions. Then, we utilize Mamba to effectively model long-range dependencies with linear complexity. The Bi-Decoder adopts skip connections to combine local and global information of the Hi-Encoder for the accurate generation of segmentation masks. Extensive experiments demonstrate that MambaVesselNet++ outperforms current convolution-based, transformer-based, and Mamba-based state-of-the-arts across diverse medical 2D, 3D, and instance segmentation tasks. The code is available at https://github.com/CC0117/MambaVesselNet.

Computed tomography (CT) images are reconstructed from raw datasets including sinogram using various convolution kernels through back projection. Kernels are typically chosen depending on the anatomical structure being imaged and the specific purpose of the scan, balancing the trade-off between image sharpness and pixel noise. Generally, a sinogram requires large storage capacity, and storage space is often limited in clinical settings. Thus, CT images are generally reconstructed with only one specific kernel in clinical settings, and the sinogram is typically discarded after a week. Therefore, many researchers have proposed deep learning-based image-to-image translation methods for CT kernel conversion. However, transferring the style of the target kernel while preserving anatomical structure remains challenging, particularly when translating CT images from a source domain to a target domain in an unpaired manner, which is often encountered in real-world settings. Thus, we propose a novel kernel conversion method using unpaired image-to-image translation (KC-UNIT). This approach utilizes discriminator regularization, using feature maps from the generator to improve semantic representation learning. To capture content and style features, cosine similarity content and contrastive style losses were defined between the feature map of generator and semantic label map of discriminator. This can be easily incorporated by modifying the discriminator's architecture without requiring any additional learnable or pre-trained networks. The KC-UNIT demonstrated the ability to preserve fine-grained anatomical structure from the source domain during transfer. Our method outperformed existing generative adversarial network-based methods across most kernel conversion methods in three kernel domains. The code is available at https://github.com/cychoi97/KC-UNIT.

Data scarcity is a major challenge in medical imaging, particularly for deep learning models. While data pooling (combining datasets from multiple sources) and data addition (adding more data from a new dataset) have been shown to enhance model performance, they are not without complications. Specifically, increasing the size of the training dataset through pooling or addition can induce distributional shifts, negatively affecting downstream model performance, a phenomenon known as the "Data Addition Dilemma". While the traditional i.i.d. assumption may not hold in multi-source contexts, assuming exchangeability across datasets provides a more practical framework for data pooling. In this work, we investigate medical image segmentation under these conditions, drawing insights from causal frameworks to propose a method for controlling foreground-background feature discrepancies across all layers of deep networks. This approach improves feature representations, which are crucial in data-addition scenarios. Our method achieves state-of-the-art segmentation performance on histopathology and ultrasound images across five datasets, including a novel ultrasound dataset that we have curated and contributed. Qualitative results demonstrate more refined and accurate segmentation maps compared to prominent baselines across three model architectures. The code will be available on Github.

Unsupervised anomaly detection (UAD) aims to detect anomalies without labeled data, a necessity in many machine learning applications where anomalous samples are rare or not available. Most state-of-the-art methods fall into two categories: reconstruction-based approaches, which often reconstruct anomalies too well, and decoupled representation learning with density estimators, which can suffer from suboptimal feature spaces. While some recent methods attempt to couple feature learning and anomaly detection, they often rely on surrogate objectives, restrict kernel choices, or introduce approximations that limit their expressiveness and robustness. To address this challenge, we propose a novel method that tightly couples representation learning with an analytically solvable one-class SVM (OCSVM), through a custom loss formulation that directly aligns latent features with the OCSVM decision boundary. The model is evaluated on two tasks: a new benchmark based on MNIST-C, and a challenging brain MRI subtle lesion detection task. Unlike most methods that focus on large, hyperintense lesions at the image level, our approach succeeds to target small, non-hyperintense lesions, while we evaluate voxel-wise metrics, addressing a more clinically relevant scenario. Both experiments evaluate a form of robustness to domain shifts, including corruption types in MNIST-C and scanner/age variations in MRI. Results demonstrate performance and robustness of our proposed mode,highlighting its potential for general UAD and real-world medical imaging applications. The source code is available at https://github.com/Nicolas-Pinon/uad_ocsvm_guided_repr_learning

Medical image segmentation continues to advance rapidly, yet rigorous comparison between methods remains challenging due to a lack of standardized and customizable tooling. In this work, we present the current state of the Medical Imaging Segmentation Toolkit (MIST), with a particular focus on its flexible and modular postprocessing framework designed for the BraTS 2025 pre- and post-treatment glioma segmentation challenge. Since its debut in the 2024 BraTS adult glioma post-treatment segmentation challenge, MIST's postprocessing module has been significantly extended to support a wide range of transforms, including removal or replacement of small objects, extraction of the largest connected components, and morphological operations such as hole filling and closing. These transforms can be composed into user-defined strategies, enabling fine-grained control over the final segmentation output. We evaluate three such strategies - ranging from simple small-object removal to more complex, class-specific pipelines - and rank their performance using the BraTS ranking protocol. Our results highlight how MIST facilitates rapid experimentation and targeted refinement, ultimately producing high-quality segmentations for the BraTS 2025 challenge. MIST remains open source and extensible, supporting reproducible and scalable research in medical image segmentation.