The rapid growth of multimodal medical imaging data presents significant storage and transmission challenges, particularly in resource-constrained clinical settings. We propose NEURAL, a novel framework that addresses this by using semantics-guided data compression. Our approach repurposes cross-attention scores between the image and its radiological report from a fine-tuned generative vision-language model to structurally prune chest X-rays, preserving only diagnostically critical regions. This process transforms the image into a highly compressed, graph representation. This unified graph-based representation fuses the pruned visual graph with a knowledge graph derived from the clinical report, creating a universal data structure that simplifies downstream modeling. Validated on the MIMIC-CXR and CheXpert Plus dataset for pneumonia detection, NEURAL achieves a 93.4-97.7\% reduction in image data size while maintaining a high diagnostic performance of 0.88-0.95 AUC, outperforming other baseline models that use uncompressed data. By creating a persistent, task-agnostic data asset, NEURAL resolves the trade-off between data size and clinical utility, enabling efficient workflows and teleradiology without sacrificing performance. Our NEURAL code is available at https://github.com/basiralab/NEURAL.

Advances in image registration and machine learning have recently enabled volumetric analysis of \emph{postmortem} brain tissue from conventional photographs of coronal slabs, which are routinely collected in brain banks and neuropathology laboratories worldwide. One caveat of this methodology is the requirement of segmentation of the tissue from photographs, which currently requires costly manual intervention. In this article, we present a deep learning model to automate this process. The automatic segmentation tool relies on a U-Net architecture that was trained with a combination of \textit{(i)}1,414 manually segmented images of both fixed and fresh tissue, from specimens with varying diagnoses, photographed at two different sites; and \textit{(ii)}~2,000 synthetic images with randomized contrast and corresponding masks generated from MRI scans for improved generalizability to unseen photographic setups. Automated model predictions on a subset of photographs not seen in training were analyzed to estimate performance compared to manual labels -- including both inter- and intra-rater variability. Our model achieved a median Dice score over 0.98, mean surface distance under 0.4~mm, and 95\% Hausdorff distance under 1.60~mm, which approaches inter-/intra-rater levels. Our tool is publicly available at surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools.

Generative artificial intelligence (AI) has been playing an important role in various domains. Leveraging its high capability to generate high-fidelity and diverse synthetic data, generative AI is widely applied in diagnostic tasks, such as lung cancer diagnosis using computed tomography (CT). However, existing generative models for lung cancer diagnosis suffer from low efficiency and anatomical imprecision, which limit their clinical applicability. To address these drawbacks, we propose Lung-DDPM+, an improved version of our previous model, Lung-DDPM. This novel approach is a denoising diffusion probabilistic model (DDPM) guided by nodule semantic layouts and accelerated by a pulmonary DPM-solver, enabling the method to focus on lesion areas while achieving a better trade-off between sampling efficiency and quality. Evaluation results on the public LIDC-IDRI dataset suggest that the proposed method achieves 8$\times$ fewer FLOPs (floating point operations per second), 6.8$\times$ lower GPU memory consumption, and 14$\times$ faster sampling compared to Lung-DDPM. Moreover, it maintains comparable sample quality to both Lung-DDPM and other state-of-the-art (SOTA) generative models in two downstream segmentation tasks. We also conducted a Visual Turing Test by an experienced radiologist, showing the advanced quality and fidelity of synthetic samples generated by the proposed method. These experimental results demonstrate that Lung-DDPM+ can effectively generate high-quality thoracic CT images with lung nodules, highlighting its potential for broader applications, such as general tumor synthesis and lesion generation in medical imaging. The code and pretrained models are available at https://github.com/Manem-Lab/Lung-DDPM-PLUS.

Ultrasound deformable registration estimates spatial transformations between pairs of deformed ultrasound images, which is crucial for capturing biomechanical properties and enhancing diagnostic accuracy in diseases such as thyroid nodules and breast cancer. However, ultrasound deformable registration remains highly challenging, especially under large deformation. The inherently low contrast, heavy noise and ambiguous tissue boundaries in ultrasound images severely hinder reliable feature extraction and correspondence matching. Existing methods often suffer from poor anatomical alignment and lack physical interpretability. To address the problem, we propose PADReg, a physics-aware deformable registration framework guided by contact force. PADReg leverages synchronized contact force measured by robotic ultrasound systems as a physical prior to constrain the registration. Specifically, instead of directly predicting deformation fields, we first construct a pixel-wise stiffness map utilizing the multi-modal information from contact force and ultrasound images. The stiffness map is then combined with force data to estimate a dense deformation field, through a lightweight physics-aware module inspired by Hooke's law. This design enables PADReg to achieve physically plausible registration with better anatomical alignment than previous methods relying solely on image similarity. Experiments on in-vivo datasets demonstrate that it attains a HD95 of 12.90, which is 21.34\% better than state-of-the-art methods. The source code is available at https://github.com/evelynskip/PADReg.

Despite significant progress in generative modelling, existing diffusion models often struggle to produce anatomically precise female pelvic images, limiting their application in gynaecological imaging, where data scarcity and patient privacy concerns are critical. To overcome these barriers, we introduce a novel diffusion-based framework for uterine MRI synthesis, integrating both unconditional and conditioned Denoising Diffusion Probabilistic Models (DDPMs) and Latent Diffusion Models (LDMs) in 2D and 3D. Our approach generates anatomically coherent, high fidelity synthetic images that closely mimic real scans and provide valuable resources for training robust diagnostic models. We evaluate generative quality using advanced perceptual and distributional metrics, benchmarking against standard reconstruction methods, and demonstrate substantial gains in diagnostic accuracy on a key classification task. A blinded expert evaluation further validates the clinical realism of our synthetic images. We release our models with privacy safeguards and a comprehensive synthetic uterine MRI dataset to support reproducible research and advance equitable AI in gynaecology.

The volume of image data generated in the medical field is continuously increasing. Manual annotation is both costly and prone to human error. Additionally, deep learning-based medical image algorithms rely on large, accurately annotated training datasets, which are expensive to produce and often result in instability. This study introduces LR-COBRAS, an interactive computer-aided data annotation algorithm designed for medical experts. LR-COBRAS aims to assist healthcare professionals in achieving more precise annotation outcomes through interactive processes, thereby optimizing medical image annotation tasks. The algorithm enhances must-link and cannot-link constraints during interactions through a logic reasoning module. It automatically generates potential constraint relationships, reducing the frequency of user interactions and improving clustering accuracy. By utilizing rules such as symmetry, transitivity, and consistency, LR-COBRAS effectively balances automation with clinical relevance. Experimental results based on the MedMNIST＋ dataset and ChestX-ray8 dataset demonstrate that LR-COBRAS significantly outperforms existing methods in clustering accuracy, efficiency, and interactive burden, showcasing superior robustness and applicability. This algorithm provides a novel solution for intelligent medical image analysis. The source code for our implementation is available on https://github.com/cjw-bbxc/MILR-COBRAS.

Recent innovations in medical imaging have markedly improved brain tumor identification, surpassing conventional diagnostic approaches that suffer from low resolution, radiation exposure, and limited contrast. Magnetic Resonance Imaging (MRI) is pivotal in precise and accurate tumor characterization owing to its high-resolution, non-invasive nature. This study investigates the synergy among multiple feature representation schemes such as local Binary Patterns (LBP), Gabor filters, Discrete Wavelet Transform, Fast Fourier Transform, Convolutional Neural Networks (CNN), and Gray-Level Run Length Matrix alongside five learning algorithms namely: k-nearest Neighbor, Random Forest, Support Vector Classifier (SVC), and probabilistic neural network (PNN), and CNN. Empirical findings indicate that LBP in conjunction with SVC and CNN obtained high specificity and accuracy, rendering it a promising method for MRI-based tumor diagnosis. Further to investigate the contribution of LBP, Statistical analysis chi-square and p-value tests are used to confirm the significant impact of LBP feature space for identification of brain Tumor. In addition, The SHAP analysis was used to identify the most important features in classification. In a small dataset, CNN obtained 97.8% accuracy while SVC yielded 98.06% accuracy. In subsequent analysis, a large benchmark dataset is also utilized to evaluate the performance of learning algorithms in order to investigate the generalization power of the proposed model. CNN achieves the highest accuracy of 98.9%, followed by SVC at 96.7%. These results highlight CNN's effectiveness in automated, high-precision tumor diagnosis. This achievement is ascribed with MRI-based feature extraction by combining high resolution, non-invasive imaging capabilities with the powerful analytical abilities of CNN. CNN demonstrates superiority in medical imaging owing to its ability to learn intricate spatial patterns and generalize effectively. This interaction enhances the accuracy, speed, and consistency of brain tumor detection, ultimately leading to better patient outcomes and more efficient healthcare delivery. https://github.com/asifrahman557/BrainTumorDetection .

Accelerating Magnetic Resonance Imaging (MRI) reduces scan time but often degrades image quality. While Implicit Neural Representations (INRs) show promise for MRI reconstruction, they struggle at high acceleration factors due to weak prior constraints, leading to structural loss and aliasing artefacts. To address this, we propose PrIINeR, an INR-based MRI reconstruction method that integrates prior knowledge from pre-trained deep learning models into the INR framework. By combining population-level knowledge with instance-based optimization and enforcing dual data consistency, PrIINeR aligns both with the acquired k-space data and the prior-informed reconstruction. Evaluated on the NYU fastMRI dataset, our method not only outperforms state-of-the-art INR-based approaches but also improves upon several learning-based state-of-the-art methods, significantly improving structural preservation and fidelity while effectively removing aliasing artefacts.PrIINeR bridges deep learning and INR-based techniques, offering a more reliable solution for high-quality, accelerated MRI reconstruction. The code is publicly available on https://github.com/multimodallearning/PrIINeR.

Epilepsy affects over 50 million people worldwide, with anti-seizure medications (ASMs) as the primary treatment for seizure control. However, ASM selection remains a "trial and error" process due to the lack of reliable predictors of effectiveness and tolerability. While machine learning approaches have been explored, existing models are limited to predicting outcomes only for ASMs encountered during training and have not leveraged recent biomedical foundation models for this task. This work investigates ASM outcome prediction using only patient MRI scans and reports. Specifically, we leverage biomedical vision-language foundation models and introduce a novel contextualized instruction-tuning framework that integrates expert-built knowledge trees of MRI entities to enhance their performance. Additionally, by training only on the four most commonly prescribed ASMs, our framework enables generalization to predicting outcomes and effectiveness for unseen ASMs not present during training. We evaluate our instruction-tuning framework on two retrospective epilepsy patient datasets, achieving an average AUC of 71.39 and 63.03 in predicting outcomes for four primary ASMs and three completely unseen ASMs, respectively. Our approach improves the AUC by 5.53 and 3.51 compared to standard report-based instruction tuning for seen and unseen ASMs, respectively. Our code, MRI knowledge tree, prompting templates, and TREE-TUNE generated instruction-answer tuning dataset are available at the link.

Accurate brain parcellation in diffusion MRI (dMRI) space is essential for advanced neuroimaging analyses. However, most existing approaches rely on anatomical MRI for segmentation and inter-modality registration, a process that can introduce errors and limit the versatility of the technique. In this study, we present a novel deep learning-based framework for direct parcellation based on the Desikan-Killiany (DK) atlas using only diffusion MRI data. Our method utilizes a hierarchical, two-stage segmentation network: the first stage performs coarse parcellation into broad brain regions, and the second stage refines the segmentation to delineate more detailed subregions within each coarse category. We conduct an extensive ablation study to evaluate various diffusion-derived parameter maps, identifying an optimal combination of fractional anisotropy, trace, sphericity, and maximum eigenvalue that enhances parellation accuracy. When evaluated on the Human Connectome Project and Consortium for Neuropsychiatric Phenomics datasets, our approach achieves superior Dice Similarity Coefficients compared to existing state-of-the-art models. Additionally, our method demonstrates robust generalization across different image resolutions and acquisition protocols, producing more homogeneous parcellations as measured by the relative standard deviation within regions. This work represents a significant advancement in dMRI-based brain segmentation, providing a precise, reliable, and registration-free solution that is critical for improved structural connectivity and microstructural analyses in both research and clinical applications. The implementation of our method is publicly available on github.com/xmindflow/DKParcellationdMRI.