Daily Papers

Compressed Sensing (CS) significantly speeds up Magnetic Resonance Image (MRI) processing and achieves accurate MRI reconstruction from under-sampled k-space data. According to the current research, there are still several problems with dynamic MRI k-space reconstruction based on CS. 1) There are differences between the Fourier domain and the Image domain, and the differences between MRI processing of different domains need to be considered. 2) As three-dimensional data, dynamic MRI has its spatial-temporal characteristics, which need to calculate the difference and consistency of surface textures while preserving structural integrity and uniqueness. 3) Dynamic MRI reconstruction is time-consuming and computationally resource-dependent. In this paper, we propose a novel robust low-rank dynamic MRI reconstruction optimization model via highly under-sampled and Discrete Fourier Transform (DFT) called the Robust Depth Linear Error Decomposition Model (RDLEDM). Our method mainly includes linear decomposition, double Total Variation (TV), and double Nuclear Norm (NN) regularizations. By adding linear image domain error analysis, the noise is reduced after under-sampled and DFT processing, and the anti-interference ability of the algorithm is enhanced. Double TV and NN regularizations can utilize both spatial-temporal characteristics and explore the complementary relationship between different dimensions in dynamic MRI sequences. In addition, Due to the non-smoothness and non-convexity of TV and NN terms, it is difficult to optimize the unified objective model. To address this issue, we utilize a fast algorithm by solving a primal-dual form of the original problem. Compared with five state-of-the-art methods, extensive experiments on dynamic MRI data demonstrate the superior performance of the proposed method in terms of both reconstruction accuracy and time complexity.

Background: Accelerating dynamic MRI is vital for advancing clinical applications and improving patient comfort. Commonly, deep learning (DL) methods for accelerated dynamic MRI reconstruction typically rely on uniformly applying non-adaptive predetermined or random subsampling patterns across all temporal frames of the dynamic acquisition. This approach fails to exploit temporal correlations or optimize subsampling on a case-by-case basis. Purpose: To develop an end-to-end approach for adaptive dynamic MRI subsampling and reconstruction, capable of generating customized sampling patterns maximizing at the same time reconstruction quality. Methods: We introduce the End-to-end Adaptive Dynamic Sampling and Reconstruction (E2E-ADS-Recon) for MRI framework, which integrates an adaptive dynamic sampler (ADS) that adapts the acquisition trajectory to each case for a given acceleration factor with a state-of-the-art dynamic reconstruction network, vSHARP, for reconstructing the adaptively sampled data into a dynamic image. The ADS can produce either frame-specific patterns or unified patterns applied to all temporal frames. E2E-ADS-Recon is evaluated under both frame-specific and unified 1D or 2D sampling settings, using dynamic cine cardiac MRI data and compared with vSHARP models employing standard subsampling trajectories, as well as pipelines where ADS was replaced by parameterized samplers optimized for dataset-specific schemes. Results: E2E-ADS-Recon exhibited superior reconstruction quality, especially at high accelerations, in terms of standard quantitative metrics (SSIM, pSNR, NMSE). Conclusion: The proposed framework improves reconstruction quality, highlighting the importance of case-specific subsampling optimization in dynamic MRI applications.

Dynamic imaging is a beneficial tool for interventions to assess physiological changes. Nonetheless during dynamic MRI, while achieving a high temporal resolution, the spatial resolution is compromised. To overcome this spatio-temporal trade-off, this research presents a super-resolution (SR) MRI reconstruction with prior knowledge based fine-tuning to maximise spatial information while reducing the required scan-time for dynamic MRIs. An U-Net based network with perceptual loss is trained on a benchmark dataset and fine-tuned using one subject-specific static high resolution MRI as prior knowledge to obtain high resolution dynamic images during the inference stage. 3D dynamic data for three subjects were acquired with different parameters to test the generalisation capabilities of the network. The method was tested for different levels of in-plane undersampling for dynamic MRI. The reconstructed dynamic SR results after fine-tuning showed higher similarity with the high resolution ground-truth, while quantitatively achieving statistically significant improvement. The average SSIM of the lowest resolution experimented during this research (6.25~\% of the k-space) before and after fine-tuning were 0.939 pm 0.008 and 0.957 pm 0.006 respectively. This could theoretically result in an acceleration factor of 16, which can potentially be acquired in less than half a second. The proposed approach shows that the super-resolution MRI reconstruction with prior-information can alleviate the spatio-temporal trade-off in dynamic MRI, even for high acceleration factors.

Medical Imaging (MI) tasks, such as accelerated parallel Magnetic Resonance Imaging (MRI), often involve reconstructing an image from noisy or incomplete measurements. This amounts to solving ill-posed inverse problems, where a satisfactory closed-form analytical solution is not available. Traditional methods such as Compressed Sensing (CS) in MRI reconstruction can be time-consuming or prone to obtaining low-fidelity images. Recently, a plethora of Deep Learning (DL) approaches have demonstrated superior performance in inverse-problem solving, surpassing conventional methods. In this study, we propose vSHARP (variable Splitting Half-quadratic ADMM algorithm for Reconstruction of inverse Problems), a novel DL-based method for solving ill-posed inverse problems arising in MI. vSHARP utilizes the Half-Quadratic Variable Splitting method and employs the Alternating Direction Method of Multipliers (ADMM) to unroll the optimization process. For data consistency, vSHARP unrolls a differentiable gradient descent process in the image domain, while a DL-based denoiser, such as a U-Net architecture, is applied to enhance image quality. vSHARP also employs a dilated-convolution DL-based model to predict the Lagrange multipliers for the ADMM initialization. We evaluate vSHARP on tasks of accelerated parallel MRI Reconstruction using two distinct datasets and on accelerated parallel dynamic MRI Reconstruction using another dataset. Our comparative analysis with state-of-the-art methods demonstrates the superior performance of vSHARP in these applications.

Off-resonance artifacts in magnetic resonance imaging (MRI) are visual distortions that occur when the actual resonant frequencies of spins within the imaging volume differ from the expected frequencies used to encode spatial information. These discrepancies can be caused by a variety of factors, including magnetic field inhomogeneities, chemical shifts, or susceptibility differences within the tissues. Such artifacts can manifest as blurring, ghosting, or misregistration of the reconstructed image, and they often compromise its diagnostic quality. We propose to resolve these artifacts by lifting the 2D MRI reconstruction problem to 3D, introducing an additional "spectral" dimension to model this off-resonance. Our approach is inspired by recent progress in modeling radiance fields, and is capable of reconstructing both static and dynamic MR images as well as separating fat and water, which is of independent clinical interest. We demonstrate our approach in the context of PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) MRI acquisitions, which are popular for their robustness to motion artifacts. Our method operates in a few minutes on a single GPU, and to our knowledge is the first to correct for chemical shift in gradient echo PROPELLER MRI reconstruction without additional measurements or pretraining data.

Dynamic MRI enables a range of clinical applications, including cardiac function assessment, organ motion tracking, and radiotherapy guidance. However, fully sampling the dynamic k-space data is often infeasible due to time constraints and physiological motion such as respiratory and cardiac motion. This necessitates undersampling, which degrades the quality of reconstructed images. Poor image quality not only hinders visualization but also impairs the estimation of deformation fields, crucial for registering dynamic (moving) images to a static reference image. This registration enables tasks such as motion correction, treatment planning, and quantitative analysis in applications like cardiac imaging and MR-guided radiotherapy. To overcome the challenges posed by undersampling and motion, we introduce an end-to-end deep learning (DL) framework that integrates adaptive dynamic k-space sampling, reconstruction, and registration. Our approach begins with a DL-based adaptive sampling strategy, optimizing dynamic k-space acquisition to capture the most relevant data for each specific case. This is followed by a DL-based reconstruction module that produces images optimized for accurate deformation field estimation from the undersampled moving data. Finally, a registration module estimates the deformation fields aligning the reconstructed dynamic images with a static reference. The proposed framework is independent of specific reconstruction and registration modules allowing for plug-and-play integration of these components. The entire framework is jointly trained using a combination of supervised and unsupervised loss functions, enabling end-to-end optimization for improved performance across all components. Through controlled experiments and ablation studies, we validate each component, demonstrating that each choice contributes to robust motion estimation from undersampled dynamic data.

Magnetic Resonance Imaging can produce detailed images of the anatomy and physiology of the human body that can assist doctors in diagnosing and treating pathologies such as tumours. However, MRI suffers from very long acquisition times that make it susceptible to patient motion artifacts and limit its potential to deliver dynamic treatments. Conventional approaches such as Parallel Imaging and Compressed Sensing allow for an increase in MRI acquisition speed by reconstructing MR images from sub-sampled MRI data acquired using multiple receiver coils. Recent advancements in Deep Learning combined with Parallel Imaging and Compressed Sensing techniques have the potential to produce high-fidelity reconstructions from highly accelerated MRI data. In this work we present a novel Deep Learning-based Inverse Problem solver applied to the task of Accelerated MRI Reconstruction, called the Recurrent Variational Network (RecurrentVarNet), by exploiting the properties of Convolutional Recurrent Neural Networks and unrolled algorithms for solving Inverse Problems. The RecurrentVarNet consists of multiple recurrent blocks, each responsible for one iteration of the unrolled variational optimization scheme for solving the inverse problem of multi-coil Accelerated MRI Reconstruction. Contrary to traditional approaches, the optimization steps are performed in the observation domain (k-space) instead of the image domain. Each block of the RecurrentVarNet refines the observed k-space and comprises a data consistency term and a recurrent unit which takes as input a learned hidden state and the prediction of the previous block. Our proposed method achieves new state of the art qualitative and quantitative reconstruction results on 5-fold and 10-fold accelerated data from a public multi-coil brain dataset, outperforming previous conventional and deep learning-based approaches.

Dynamic MRI is a technique of acquiring a series of images continuously to follow the physiological changes over time. However, such fast imaging results in low resolution images. In this work, abdominal deformation model computed from dynamic low resolution images have been applied to high resolution image, acquired previously, to generate dynamic high resolution MRI. Dynamic low resolution images were simulated into different breathing phases (inhale and exhale). Then, the image registration between breathing time points was performed using the B-spline SyN deformable model and using cross-correlation as a similarity metric. The deformation model between different breathing phases were estimated from highly undersampled data. This deformation model was then applied to the high resolution images to obtain high resolution images of different breathing phases. The results indicated that the deformation model could be computed from relatively very low resolution images.

Magnetic resonance imaging (MRI) provides high spatial resolution and excellent soft-tissue contrast without using harmful ionising radiation. Dynamic MRI is an essential tool for interventions to visualise movements or changes of the target organ. However, such MRI acquisition with high temporal resolution suffers from limited spatial resolution - also known as the spatio-temporal trade-off of dynamic MRI. Several approaches, including deep learning based super-resolution approaches, have been proposed to mitigate this trade-off. Nevertheless, such an approach typically aims to super-resolve each time-point separately, treating them as individual volumes. This research addresses the problem by creating a deep learning model which attempts to learn both spatial and temporal relationships. A modified 3D UNet model, DDoS-UNet, is proposed - which takes the low-resolution volume of the current time-point along with a prior image volume. Initially, the network is supplied with a static high-resolution planning scan as the prior image along with the low-resolution input to super-resolve the first time-point. Then it continues step-wise by using the super-resolved time-points as the prior image while super-resolving the subsequent time-points. The model performance was tested with 3D dynamic data that was undersampled to different in-plane levels. The proposed network achieved an average SSIM value of 0.951pm0.017 while reconstructing the lowest resolution data (i.e. only 4\% of the k-space acquired) - which could result in a theoretical acceleration factor of 25. The proposed approach can be used to reduce the required scan-time while achieving high spatial resolution.

Brain-to-image decoding has been recently propelled by the progress in generative AI models and the availability of large ultra-high field functional Magnetic Resonance Imaging (fMRI). However, current approaches depend on complicated multi-stage pipelines and preprocessing steps that typically collapse the temporal dimension of brain recordings, thereby limiting time-resolved brain decoders. Here, we introduce Dynadiff (Dynamic Neural Activity Diffusion for Image Reconstruction), a new single-stage diffusion model designed for reconstructing images from dynamically evolving fMRI recordings. Our approach offers three main contributions. First, Dynadiff simplifies training as compared to existing approaches. Second, our model outperforms state-of-the-art models on time-resolved fMRI signals, especially on high-level semantic image reconstruction metrics, while remaining competitive on preprocessed fMRI data that collapse time. Third, this approach allows a precise characterization of the evolution of image representations in brain activity. Overall, this work lays the foundation for time-resolved brain-to-image decoding.

Dynamic imaging addresses the recovery of a time-varying 2D or 3D object at each time instant using its undersampled measurements. In particular, in the case of dynamic tomography, only a single projection at a single view angle may be available at a time, making the problem severely ill-posed. In this work, we propose an approach, RED-PSM, which combines for the first time two powerful techniques to address this challenging imaging problem. The first, are partially separable models, which have been used to efficiently introduce a low-rank prior for the spatio-temporal object. The second is the recent Regularization by Denoising (RED), which provides a flexible framework to exploit the impressive performance of state-of-the-art image denoising algorithms, for various inverse problems. We propose a partially separable objective with RED and a computationally efficient and scalable optimization scheme with variable splitting and ADMM. Theoretical analysis proves the convergence of our objective to a value corresponding to a stationary point satisfying the first-order optimality conditions. Convergence is accelerated by a particular projection-domain-based initialization. We demonstrate the performance and computational improvements of our proposed RED-PSM with a learned image denoiser by comparing it to a recent deep-prior-based method known as TD-DIP. Although the main focus is on dynamic tomography, we also show the performance advantages of RED-PSM in a cardiac dynamic MRI setting.

Magnetic resonance imaging (MRI) super-resolution is vital for improving diagnostic accessibility, yet most methods treat it as a deterministic mapping from a fixed low-resolution input to a high-resolution target. This overlooks a key property of MRI acquisition physics: spatial resolution and signal-to-noise ratio (SNR) are inherently coupled, making any given low-resolution scan merely one of many possible realizations under varying acquisition trade-offs. We rethink MRI super-resolution as a physics-aware reconstruction problem, in which the goal is to identify the optimal resolution-SNR configuration and then super-resolve it to obtain high-quality MRI results. A key implication of this formulation is that MRI resolution becomes dynamic rather than fixed. To handle such resolution-heterogeneous inputs, we adapt 2D Gaussian Splatting (2D GS) to MRI by formulating reconstruction as a coordinate-based, resolution-agnostic rendering problem. To further enhance fidelity, we introduce three innovations: (1) a prior-aware Gaussian representation that combines an Anatomical Structure Prior for tissue-specific kernel initialization with an Imaging System Prior that captures hardware characteristics via a covariance dictionary; (2) a physics-constrained signal modeling scheme that predicts intrinsic tissue parameters (proton density rho and effective relaxation rate R2) and synthesizes intensities through governing physical equations, ensuring biophysically plausible contrast; and (3) a meta-learning framework that alleviates paired-data scarcity by pretraining on simulated data and adapting to real-world conditions. Extensive experiments on dynamic-resolution datasets and standard benchmarks demonstrate that our method achieves state-of-the-art performance, highlighting its strong potential for clinical deployment.

Although deep learning (DL) has received much attention in accelerated magnetic resonance imaging (MRI), recent studies show that tiny input perturbations may lead to instabilities of DL-based MRI reconstruction models. However, the approaches of robustifying these models are underdeveloped. Compared to image classification, it could be much more challenging to achieve a robust MRI image reconstruction network considering its regression-based learning objective, limited amount of training data, and lack of efficient robustness metrics. To circumvent the above limitations, our work revisits the problem of DL-based image reconstruction through the lens of robust machine learning. We find a new instability source of MRI image reconstruction, i.e., the lack of reconstruction robustness against spatial transformations of an input, e.g., rotation and cutout. Inspired by this new robustness metric, we develop a robustness-aware image reconstruction method that can defend against both pixel-wise adversarial perturbations as well as spatial transformations. Extensive experiments are also conducted to demonstrate the effectiveness of our proposed approaches.

MRI is an indispensable clinical tool, offering a rich variety of tissue contrasts to support broad diagnostic and research applications. Clinical exams routinely acquire multiple structural sequences that provide complementary information for differential diagnosis, while research protocols often incorporate advanced functional, diffusion, spectroscopic, and relaxometry sequences to capture multidimensional insights into tissue structure and composition. However, these capabilities come at the cost of prolonged scan times, which reduce patient throughput, increase susceptibility to motion artifacts, and may require trade-offs in image quality or diagnostic scope. Over the last two decades, advances in image reconstruction algorithms--alongside improvements in hardware and pulse sequence design--have made it possible to accelerate acquisitions while preserving diagnostic quality. Central to this progress is the ability to incorporate prior information to regularize the solutions to the reconstruction problem. In this tutorial, we overview the basics of MRI reconstruction and highlight state-of-the-art approaches, beginning with classical methods that rely on explicit hand-crafted priors, and then turning to deep learning methods that leverage a combination of learned and crafted priors to further push the performance envelope. We also explore the translational aspects and eventual clinical implications of these methods. We conclude by discussing future directions to address remaining challenges in MRI reconstruction. The tutorial is accompanied by a Python toolbox (https://github.com/tutorial-MRI-recon/tutorial) to demonstrate select methods discussed in the article.

MRI reconstruction is an inherently ill-posed inverse problem, since incomplete measurements admit many plausible solutions. This ambiguity becomes more severe under high acceleration, where pixel-domain continuous predictors tend to average over feasible reconstructions and suppress high-frequency anatomy. We address this limitation by moving reconstruction to discrete multi-scale latent space and posing it as autoregressive next-acceleration-scale prediction. Leveraging discrete priors proven effective in visual autoregressive modeling, our method restricts the solution to compact sequences of codebook tokens, enabling sharp reconstructions even from extremely sparse measurements. This discrete autoregressive formulation also aligns naturally with modern large language model post-training techniques. Building on this observation, we introduce on-policy privileged information distillation for visual autoregressive modeling, where a teacher is provided training only privileged context that is unavailable at inference, in our case fully sampled acquisitions, and supervises a student trained on its own rollouts, leading to consistent reconstruction gains. Through extensive experiments on the fastMRI benchmark, we show that our approach delivers improved reconstruction performance across diverse sampling patterns under extreme undersampling. Project website is https://yilmazkorkmaz1.github.io/discrete-mri-reconstruction-opd/{here}.

Cardiac Magnetic Resonance (CMR) imaging is a critical tool for diagnosing and managing cardiovascular disease, yet its utility is often limited by the sparse acquisition of 2D short-axis slices, resulting in incomplete volumetric information. Accurate 3D reconstruction from these sparse slices is essential for comprehensive cardiac assessment, but existing methods face challenges, including reliance on predefined interpolation schemes (e.g., linear or spherical), computational inefficiency, and dependence on additional semantic inputs such as segmentation labels or motion data. To address these limitations, we propose a novel Cardiac Latent Interpolation Diffusion (CaLID) framework that introduces three key innovations. First, we present a data-driven interpolation scheme based on diffusion models, which can capture complex, non-linear relationships between sparse slices and improves reconstruction accuracy. Second, we design a computationally efficient method that operates in the latent space and speeds up 3D whole-heart upsampling time by a factor of 24, reducing computational overhead compared to previous methods. Third, with only sparse 2D CMR images as input, our method achieves SOTA performance against baseline methods, eliminating the need for auxiliary input such as morphological guidance, thus simplifying workflows. We further extend our method to 2D+T data, enabling the effective modeling of spatiotemporal dynamics and ensuring temporal coherence. Extensive volumetric evaluations and downstream segmentation tasks demonstrate that CaLID achieves superior reconstruction quality and efficiency. By addressing the fundamental limitations of existing approaches, our framework advances the state of the art for spatio and spatiotemporal whole-heart reconstruction, offering a robust and clinically practical solution for cardiovascular imaging.

Magnetic resonance imaging (MRI) is highly susceptible to patient motion due to its relatively long acquisition times and the fact that data are acquired sequentially in k-space. Even small patient movements introduce phase inconsistencies across measurements, leading to severe artifacts such as blurring, ghosting, and geometric distortions that can compromise diagnostic quality. Retrospective motion compensation remains challenging, particularly in accelerated acquisitions, due to the ill-posed nature of the joint reconstruction and motion estimation problem. In this work, we propose a unified Bayesian framework for motion-compensated 3D MRI that jointly estimates the anatomical image, rigid-body motion parameters, and coil sensitivity maps directly from motion-corrupted k-space data. Our approach integrates pretrained 3D complex-valued score-based diffusion models as expressive anatomical image priors within a physics-based forward model. Inference is performed by alternating diffusion posterior image updates with efficient proximal optimization steps for motion and coil sensitivity estimation, enabling fully unsupervised reconstruction without the need for paired motion-free training data. Experiments on simulated and real-motion brain MRI datasets demonstrate that the proposed method achieves improved image quality and motion robustness compared to state-of-the-art classical and learning-based motion correction techniques, particularly in the presence of severe motion and high acceleration.

Machine Learning methods can learn how to reconstruct Magnetic Resonance Images and thereby accelerate acquisition, which is of paramount importance to the clinical workflow. Physics-informed networks incorporate the forward model of accelerated MRI reconstruction in the learning process. With increasing network complexity, robustness is not ensured when reconstructing data unseen during training. We aim to embed data consistency (DC) in deep networks while balancing the degree of network complexity. While doing so, we will assess whether either explicit or implicit enforcement of DC in varying network architectures is preferred to optimize performance. We propose a scheme called Cascades of Independently Recurrent Inference Machines (CIRIM) to assess DC through unrolled optimization. Herein we assess DC both implicitly by gradient descent and explicitly by a designed term. Extensive comparison of the CIRIM to CS as well as to other methods is performed: the E2EVN, CascadeNet, KIKINet, LPDNet, RIM, IRIM, and UNet. Models were trained and evaluated on T1-weighted and FLAIR contrast brain data, and T2-weighted knee data. Both 1D and 2D undersampling patterns were evaluated. Robustness was tested by reconstructing 7.5x prospectively undersampled 3D FLAIR MRI data of Multiple Sclerosis (MS) patients with white matter lesions. The CIRIM performed best when implicitly enforcing DC, while the E2EVN required an explicit DC formulation. In reconstructing MS patient data, prospectively acquired with a sampling pattern unseen during model training, the CIRIM maintained lesion contrast while efficiently denoising the images. The CIRIM showed highly promising generalization capabilities maintaining a very fair trade-off between reconstructed image quality and fast reconstruction times, which is crucial in the clinical workflow.

Deep-learning-based brain magnetic resonance imaging (MRI) reconstruction methods have the potential to accelerate the MRI acquisition process. Nevertheless, the scientific community lacks appropriate benchmarks to assess MRI reconstruction quality of high-resolution brain images, and evaluate how these proposed algorithms will behave in the presence of small, but expected data distribution shifts. The Multi-Coil Magnetic Resonance Image (MC-MRI) Reconstruction Challenge provides a benchmark that aims at addressing these issues, using a large dataset of high-resolution, three-dimensional, T1-weighted MRI scans. The challenge has two primary goals: 1) to compare different MRI reconstruction models on this dataset and 2) to assess the generalizability of these models to data acquired with a different number of receiver coils. In this paper, we describe the challenge experimental design, and summarize the results of a set of baseline and state of the art brain MRI reconstruction models. We provide relevant comparative information on the current MRI reconstruction state-of-the-art and highlight the challenges of obtaining generalizable models that are required prior to broader clinical adoption. The MC-MRI benchmark data, evaluation code and current challenge leaderboard are publicly available. They provide an objective performance assessment for future developments in the field of brain MRI reconstruction.

A major challenge of the long measurement times in magnetic resonance imaging (MRI), an important medical imaging technology, is that patients may move during data acquisition. This leads to severe motion artifacts in the reconstructed images and volumes. In this paper, we propose a deep learning-based test-time-training method for accurate motion estimation. The key idea is that a neural network trained for motion-free reconstruction has a small loss if there is no motion, thus optimizing over motion parameters passed through the reconstruction network enables accurate estimation of motion. The estimated motion parameters enable to correct for the motion and to reconstruct accurate motion-corrected images. Our method uses 2D reconstruction networks to estimate rigid motion in 3D, and constitutes the first deep learning based method for 3D rigid motion estimation towards 3D-motion-corrected MRI. We show that our method can provably reconstruct motion parameters for a simple signal and neural network model. We demonstrate the effectiveness of our method for both retrospectively simulated motion and prospectively collected real motion-corrupted data.

Compressed Sensing MRI reconstructs images of the body's internal anatomy from undersampled measurements, thereby reducing scan time. Recently, deep learning has shown great potential for reconstructing high-fidelity images from highly undersampled measurements. However, one needs to train multiple models for different undersampling patterns and desired output image resolutions, since most networks operate on a fixed discretization. Such approaches are highly impractical in clinical settings, where undersampling patterns and image resolutions are frequently changed to accommodate different real-time imaging and diagnostic requirements. We propose a unified MRI reconstruction model robust to various measurement undersampling patterns and image resolutions. Our approach uses neural operators, a discretization-agnostic architecture applied in both image and measurement spaces, to capture local and global features. Empirically, our model improves SSIM by 11% and PSNR by 4 dB over a state-of-the-art CNN (End-to-End VarNet), with 600times faster inference than diffusion methods. The resolution-agnostic design also enables zero-shot super-resolution and extended field-of-view reconstruction, offering a versatile and efficient solution for clinical MR imaging. Our unified model offers a versatile solution for MRI, adapting seamlessly to various measurement undersampling and imaging resolutions, making it highly effective for flexible and reliable clinical imaging. Our code is available at https://armeet.ca/nomri.

MRI is an inherently slow process, which leads to long scan time for high-resolution imaging. The speed of acquisition can be increased by ignoring parts of the data (undersampling). Consequently, this leads to the degradation of image quality, such as loss of resolution or introduction of image artefacts. This work aims to reconstruct highly undersampled Cartesian or radial MR acquisitions, with better resolution and with less to no artefact compared to conventional techniques like compressed sensing. In recent times, deep learning has emerged as a very important area of research and has shown immense potential in solving inverse problems, e.g. MR image reconstruction. In this paper, a deep learning based MR image reconstruction framework is proposed, which includes a modified regularised version of ResNet as the network backbone to remove artefacts from the undersampled image, followed by data consistency steps that fusions the network output with the data already available from undersampled k-space in order to further improve reconstruction quality. The performance of this framework for various undersampling patterns has also been tested, and it has been observed that the framework is robust to deal with various sampling patterns, even when mixed together while training, and results in very high quality reconstruction, in terms of high SSIM (highest being 0.990pm0.006 for acceleration factor of 3.5), while being compared with the fully sampled reconstruction. It has been shown that the proposed framework can successfully reconstruct even for an acceleration factor of 20 for Cartesian (0.968pm0.005) and 17 for radially (0.962pm0.012) sampled data. Furthermore, it has been shown that the framework preserves brain pathology during reconstruction while being trained on healthy subjects.

Dynamic scene reconstruction from multi-view videos remains a fundamental challenge in computer vision. While recent neural surface reconstruction methods have achieved remarkable results in static 3D reconstruction, extending these approaches with comparable quality for dynamic scenes introduces significant computational and representational challenges. Existing dynamic methods focus on novel-view synthesis, therefore, their extracted meshes tend to be noisy. Even approaches aiming for geometric fidelity often result in too smooth meshes due to the ill-posedness of the problem. We present a novel framework for highly detailed dynamic reconstruction that extends the static 3D reconstruction method NeuralAngelo to work in dynamic settings. To that end, we start with a high-quality template scene reconstruction from the initial frame using NeuralAngelo, and then jointly optimize deformation fields that track the template and refine it based on the temporal sequence. This flexible template allows updating the geometry to include changes that cannot be modeled with the deformation field, for instance occluded parts or the changes in the topology. We show superior reconstruction accuracy in comparison to previous state-of-the-art methods on the ActorsHQ dataset.

Recently, Spectral Compressive Imaging (SCI) has achieved remarkable success, unlocking significant potential for dynamic spectral vision. However, existing reconstruction methods, primarily image-based, suffer from two limitations: (i) Encoding process masks spatial-spectral features, leading to uncertainty in reconstructing missing information from single compressed measurements, and (ii) The frame-by-frame reconstruction paradigm fails to ensure temporal consistency, which is crucial in the video perception. To address these challenges, this paper seeks to advance spectral reconstruction from the image level to the video level, leveraging the complementary features and temporal continuity across adjacent frames in dynamic scenes. Initially, we construct the first high-quality dynamic hyperspectral image dataset (DynaSpec), comprising 30 sequences obtained through frame-scanning acquisition. Subsequently, we propose the Propagation-Guided Spectral Video Reconstruction Transformer (PG-SVRT), which employs a spatial-then-temporal attention to effectively reconstruct spectral features from abundant video information, while using a bridged token to reduce computational complexity. Finally, we conduct simulation experiments to assess the performance of four SCI systems, and construct a DD-CASSI prototype for real-world data collection and benchmarking. Extensive experiments demonstrate that PG-SVRT achieves superior performance in reconstruction quality, spectral fidelity, and temporal consistency, while maintaining minimal FLOPs. Project page: https://github.com/nju-cite/DynaSpec

Cardiac MRI, crucial for evaluating heart structure and function, faces limitations like slow imaging and motion artifacts. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on MICCAI. CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techniques, physical modeling, and model complexity, thereby providing valuable insights for further developments in this field.

Deep learning (DL) has recently emerged as a pivotal technology for enhancing magnetic resonance imaging (MRI), a critical tool in diagnostic radiology. This review paper provides a comprehensive overview of recent advances in DL for MRI reconstruction. It focuses on DL approaches and architectures designed to improve image quality, accelerate scans, and address data-related challenges. These include end-to-end neural networks, pre-trained networks, generative models, and self-supervised methods. The paper also discusses the role of DL in optimizing acquisition protocols, enhancing robustness against distribution shifts, and tackling subtle bias. Drawing on the extensive literature and practical insights, it outlines current successes, limitations, and future directions for leveraging DL in MRI reconstruction, while emphasizing the potential of DL to significantly impact clinical imaging practices.

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.

We present a new neural network, the XPDNet, for MRI reconstruction from periodically under-sampled multi-coil data. We inform the design of this network by taking best practices from MRI reconstruction and computer vision. We show that this network can achieve state-of-the-art reconstruction results, as shown by its ranking of second in the fastMRI 2020 challenge.

Diffusion models have emerged as the new state-of-the-art generative model with high quality samples, with intriguing properties such as mode coverage and high flexibility. They have also been shown to be effective inverse problem solvers, acting as the prior of the distribution, while the information of the forward model can be granted at the sampling stage. Nonetheless, as the generative process remains in the same high dimensional (i.e. identical to data dimension) space, the models have not been extended to 3D inverse problems due to the extremely high memory and computational cost. In this paper, we combine the ideas from the conventional model-based iterative reconstruction with the modern diffusion models, which leads to a highly effective method for solving 3D medical image reconstruction tasks such as sparse-view tomography, limited angle tomography, compressed sensing MRI from pre-trained 2D diffusion models. In essence, we propose to augment the 2D diffusion prior with a model-based prior in the remaining direction at test time, such that one can achieve coherent reconstructions across all dimensions. Our method can be run in a single commodity GPU, and establishes the new state-of-the-art, showing that the proposed method can perform reconstructions of high fidelity and accuracy even in the most extreme cases (e.g. 2-view 3D tomography). We further reveal that the generalization capacity of the proposed method is surprisingly high, and can be used to reconstruct volumes that are entirely different from the training dataset.

Dynamic radiance field reconstruction methods aim to model the time-varying structure and appearance of a dynamic scene. Existing methods, however, assume that accurate camera poses can be reliably estimated by Structure from Motion (SfM) algorithms. These methods, thus, are unreliable as SfM algorithms often fail or produce erroneous poses on challenging videos with highly dynamic objects, poorly textured surfaces, and rotating camera motion. We address this robustness issue by jointly estimating the static and dynamic radiance fields along with the camera parameters (poses and focal length). We demonstrate the robustness of our approach via extensive quantitative and qualitative experiments. Our results show favorable performance over the state-of-the-art dynamic view synthesis methods.

Longitudinal medical imaging captures temporal evolution of lesions, yet extracting the underlying dynamical parameters governing this evolution remains challenging. We propose an inverse Bayesian framework for inferring lesion dynamics from longitudinal spectral CT. We decompose spectral feature (x) evolution into three components: equation* dx_i{dt} = A_i x_i + B \cdot n + C \cdot Δx_{sat} equation* where A_i captures intrinsic dynamics (lesion-autonomous evolution), B captures local environment tumour burden (organ tumour burden through satellite count coupling), and C captures environment/satellite state change (i.e., whether surrounding lesions move similarly or not). We demonstrate the framework on photon-counting NSCLC CT data from metastases, recovering distinct dynamical regimes: lung lesions exhibit significant satellite count coupling (B=-0.34, p<0.05) suggesting competitive dynamics, while liver lesions show synergistic satellite behaviour coupling (Capprox+1.0, p<0.05). Synthetic validation confirms parameter recovery, and cross-coupling analysis validates that our method detects non-zero coupling when present. This work establishes inverse dynamical inference as a principled methodology for extracting interpretable parameters from longitudinal imaging, moving beyond static feature extraction toward mechanistic characterisation of lesion behaviour. The code and data are available at: https://github.com/lukasf98/inverse-bayesian-inference

Four-dimensional computed tomography (4D CT) reconstruction is crucial for capturing dynamic anatomical changes but faces inherent limitations from conventional phase-binning workflows. Current methods discretize temporal resolution into fixed phases with respiratory gating devices, introducing motion misalignment and restricting clinical practicality. In this paper, We propose X^2-Gaussian, a novel framework that enables continuous-time 4D-CT reconstruction by integrating dynamic radiative Gaussian splatting with self-supervised respiratory motion learning. Our approach models anatomical dynamics through a spatiotemporal encoder-decoder architecture that predicts time-varying Gaussian deformations, eliminating phase discretization. To remove dependency on external gating devices, we introduce a physiology-driven periodic consistency loss that learns patient-specific breathing cycles directly from projections via differentiable optimization. Extensive experiments demonstrate state-of-the-art performance, achieving a 9.93 dB PSNR gain over traditional methods and 2.25 dB improvement against prior Gaussian splatting techniques. By unifying continuous motion modeling with hardware-free period learning, X^2-Gaussian advances high-fidelity 4D CT reconstruction for dynamic clinical imaging. Code is publicly available at: https://x2-gaussian.github.io/.

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation regularization. The experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise.

Magnetic Resonance Imaging (MRI) is a critical tool in modern medical diagnostics, yet its prolonged acquisition time remains a critical limitation, especially in time-sensitive clinical scenarios. While undersampling strategies can accelerate image acquisition, they often result in image artifacts and degraded quality. Recent diffusion models have shown promise for reconstructing high-fidelity images from undersampled data by learning powerful image priors; however, most existing approaches either (i) rely on unsupervised score functions without paired supervision or (ii) apply data consistency only as a post-processing step. In this work, we introduce a conditional denoising diffusion framework with iterative data-consistency correction, which differs from prior methods by embedding the measurement model directly into every reverse diffusion step and training the model on paired undersampled-ground truth data. This hybrid design bridges generative flexibility with explicit enforcement of MRI physics. Experiments on the fastMRI dataset demonstrate that our framework consistently outperforms recent state-of-the-art deep learning and diffusion-based methods in SSIM, PSNR, and LPIPS, with LPIPS capturing perceptual improvements more faithfully. These results demonstrate that integrating conditional supervision with iterative consistency updates yields substantial improvements in both pixel-level fidelity and perceptual realism, establishing a principled and practical advance toward robust, accelerated MRI reconstruction.

While highly accelerated non-Cartesian acquisition protocols significantly reduce scan time, they often entail long reconstruction delays. Deep learning based reconstruction methods can alleviate this, but often lack stability and robustness to distribution shifts. As an alternative, we train a rotation invariant weakly convex ridge regularizer (WCRR). The resulting variational reconstruction approach is benchmarked against state of the art methods on retrospectively simulated data and (out of distribution) on prospective GoLF SPARKLING and CAIPIRINHA acquisitions. Our approach consistently outperforms widely used baselines and achieves performance comparable to Plug and Play reconstruction with a state of the art 3D DRUNet denoiser, while offering substantially improved computational efficiency and robustness to acquisition changes. In summary, WCRR unifies the strengths of principled variational methods and modern deep learning based approaches.

Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clinical deployment and clinician trust. To mitigate this challenge, we present the Stanford Knee MRI with Multi-Task Evaluation (SKM-TEA) dataset, a collection of quantitative knee MRI (qMRI) scans that enables end-to-end, clinically-relevant evaluation of MRI reconstruction and analysis tools. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies. We provide a framework for using qMRI parameter maps, along with image reconstructions and dense image labels, for measuring the quality of qMRI biomarker estimates extracted from MRI reconstruction, segmentation, and detection techniques. Finally, we use this framework to benchmark state-of-the-art baselines on this dataset. We hope our SKM-TEA dataset and code can enable a broad spectrum of research for modular image reconstruction and image analysis in a clinically informed manner. Dataset access, code, and benchmarks are available at https://github.com/StanfordMIMI/skm-tea.

This paper considers the problem of undersampled MRI reconstruction. We propose a novel Transformer-based framework for directly processing signal in k-space, going beyond the limitation of regular grids as ConvNets do. We adopt an implicit representation of k-space spectrogram, treating spatial coordinates as inputs, and dynamically query the sparsely sampled points to reconstruct the spectrogram, i.e. learning the inductive bias in k-space. To strike a balance between computational cost and reconstruction quality, we build the decoder with hierarchical structure to generate low-resolution and high-resolution outputs respectively. To validate the effectiveness of our proposed method, we have conducted extensive experiments on two public datasets, and demonstrate superior or comparable performance to state-of-the-art approaches.

High-resolution (HR) magnetic resonance imaging (MRI) is crucial for many clinical and research applications. However, achieving it remains costly and constrained by technical trade-offs and experimental limitations. Super-resolution (SR) presents a promising computational approach to overcome these challenges by generating HR images from more affordable low-resolution (LR) scans, potentially improving diagnostic accuracy and efficiency without requiring additional hardware. This survey reviews recent advances in MRI SR techniques, with a focus on deep learning (DL) approaches. It examines DL-based MRI SR methods from the perspectives of computer vision, computational imaging, inverse problems, and MR physics, covering theoretical foundations, architectural designs, learning strategies, benchmark datasets, and performance metrics. We propose a systematic taxonomy to categorize these methods and present an in-depth study of both established and emerging SR techniques applicable to MRI, considering unique challenges in clinical and research contexts. We also highlight open challenges and directions that the community needs to address. Additionally, we provide a collection of essential open-access resources, tools, and tutorials, available on our GitHub: https://github.com/mkhateri/Awesome-MRI-Super-Resolution. IEEE keywords: MRI, Super-Resolution, Deep Learning, Computational Imaging, Inverse Problem, Survey.

Clinical MRI encompasses diverse imaging protocols--spanning anatomical targets (cardiac, brain, knee), contrasts (T1, T2, mapping), sampling patterns (Cartesian, radial, spiral, kt-space), and acceleration factors--yet current deep learning reconstructions are typically protocol-specific, hindering generalization and deployment. We introduce Scalable Deep Unrolled Model (SDUM), a universal framework combining a Restormer-based reconstructor, a learned coil sensitivity map estimator (CSME), sampling-aware weighted data consistency (SWDC), universal conditioning (UC) on cascade index and protocol metadata, and progressive cascade expansion training. SDUM exhibits foundation-model-like scaling behavior: reconstruction quality follows PSNR {sim} log(parameters) with correlation r{=}0.986 (R^2{=}0.973) up to 18 cascades, demonstrating predictable performance gains with model depth. A single SDUM trained on heterogeneous data achieves state-of-the-art results across all four CMRxRecon2025 challenge tracks--multi-center, multi-disease, 5T, and pediatric--without task-specific fine-tuning, surpassing specialized baselines by up to {+}1.0~dB. On CMRxRecon2024, SDUM outperforms the winning method PromptMR+ by {+}0.55~dB; on fastMRI brain, it exceeds PC-RNN by {+}1.8~dB. Ablations validate each component: SWDC {+}0.43~dB over standard DC, per-cascade CSME {+}0.51~dB, UC {+}0.38~dB. These results establish SDUM as a practical path toward universal, scalable MRI reconstruction.

Accelerating MRI scans is one of the principal outstanding problems in the MRI research community. Towards this goal, we hosted the second fastMRI competition targeted towards reconstructing MR images with subsampled k-space data. We provided participants with data from 7,299 clinical brain scans (de-identified via a HIPAA-compliant procedure by NYU Langone Health), holding back the fully-sampled data from 894 of these scans for challenge evaluation purposes. In contrast to the 2019 challenge, we focused our radiologist evaluations on pathological assessment in brain images. We also debuted a new Transfer track that required participants to submit models evaluated on MRI scanners from outside the training set. We received 19 submissions from eight different groups. Results showed one team scoring best in both SSIM scores and qualitative radiologist evaluations. We also performed analysis on alternative metrics to mitigate the effects of background noise and collected feedback from the participants to inform future challenges. Lastly, we identify common failure modes across the submissions, highlighting areas of need for future research in the MRI reconstruction community.

Complex, temporally evolving phenomena, from climate to brain activity, are governed by dynamical systems (DS). DS reconstruction (DSR) seeks to infer generative surrogate models of these from observed data, reproducing their long-term behavior. Existing DSR approaches require purpose-training for any new system observed, lacking the zero-shot and in-context inference capabilities known from LLMs. Here we introduce DynaMix, a novel multivariate ALRNN-based mixture-of-experts architecture pre-trained for DSR, the first DSR model able to generalize zero-shot to out-of-domain DS. Just from a provided context signal, without any re-training, DynaMix faithfully forecasts the long-term evolution of novel DS where existing time series (TS) foundation models, like Chronos, fail -- at a fraction of the number of parameters and orders of magnitude faster inference times. DynaMix outperforms TS foundation models in terms of long-term statistics, and often also short-term forecasts, even on real-world time series, like traffic or weather data, typically used for training and evaluating TS models, but not at all part of DynaMix' training corpus. We illustrate some of the failure modes of TS models for DSR problems, and conclude that models built on DS principles may bear a huge potential also for advancing the TS prediction field.

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework. This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr/

Contrast agents in dynamic contrast enhanced magnetic resonance imaging allow to localize tumors and observe their contrast kinetics, which is essential for cancer characterization and respective treatment decision-making. However, contrast agent administration is not only associated with adverse health risks, but also restricted for patients during pregnancy, and for those with kidney malfunction, or other adverse reactions. With contrast uptake as key biomarker for lesion malignancy, cancer recurrence risk, and treatment response, it becomes pivotal to reduce the dependency on intravenous contrast agent administration. To this end, we propose a multi-conditional latent diffusion model capable of acquisition time-conditioned image synthesis of DCE-MRI temporal sequences. To evaluate medical image synthesis, we additionally propose and validate the Fréchet radiomics distance as an image quality measure based on biomarker variability between synthetic and real imaging data. Our results demonstrate our method's ability to generate realistic multi-sequence fat-saturated breast DCE-MRI and uncover the emerging potential of deep learning based contrast kinetics simulation. We publicly share our accessible codebase at https://github.com/RichardObi/ccnet and provide a user-friendly library for Fréchet radiomics distance calculation at https://pypi.org/project/frd-score.

Dynamic reconstruction of deformable tissues in endoscopic video is a key technology for robot-assisted surgery. Recent reconstruction methods based on neural radiance fields (NeRFs) have achieved remarkable results in the reconstruction of surgical scenes. However, based on implicit representation, NeRFs struggle to capture the intricate details of objects in the scene and cannot achieve real-time rendering. In addition, restricted single view perception and occluded instruments also propose special challenges in surgical scene reconstruction. To address these issues, we develop SurgicalGaussian, a deformable 3D Gaussian Splatting method to model dynamic surgical scenes. Our approach models the spatio-temporal features of soft tissues at each time stamp via a forward-mapping deformation MLP and regularization to constrain local 3D Gaussians to comply with consistent movement. With the depth initialization strategy and tool mask-guided training, our method can remove surgical instruments and reconstruct high-fidelity surgical scenes. Through experiments on various surgical videos, our network outperforms existing method on many aspects, including rendering quality, rendering speed and GPU usage. The project page can be found at https://surgicalgaussian.github.io.

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. The result is a single 3D encoder that excels across 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). It also generalises to unseen sites, supporting scalable clinical use. Code and trained models are publicly available at https://github.com/liamchalcroft/contrast-squared

Accurate 3D cardiac reconstruction from cine magnetic resonance imaging (cMRI) is crucial for improved cardiovascular disease diagnosis and understanding of the heart's motion. However, current cardiac MRI-based reconstruction technology used in clinical settings is 2D with limited through-plane resolution, resulting in low-quality reconstructed cardiac volumes. To better reconstruct 3D cardiac volumes from sparse 2D image stacks, we propose a morphology-guided diffusion model for 3D cardiac volume reconstruction, DMCVR, that synthesizes high-resolution 2D images and corresponding 3D reconstructed volumes. Our method outperforms previous approaches by conditioning the cardiac morphology on the generative model, eliminating the time-consuming iterative optimization process of the latent code, and improving generation quality. The learned latent spaces provide global semantics, local cardiac morphology and details of each 2D cMRI slice with highly interpretable value to reconstruct 3D cardiac shape. Our experiments show that DMCVR is highly effective in several aspects, such as 2D generation and 3D reconstruction performance. With DMCVR, we can produce high-resolution 3D cardiac MRI reconstructions, surpassing current techniques. Our proposed framework has great potential for improving the accuracy of cardiac disease diagnosis and treatment planning. Code can be accessed at https://github.com/hexiaoxiao-cs/DMCVR.

Dynamic contrast-enhanced (DCE) MRI is essential for breast cancer diagnosis and treatment. However, its reliance on contrast agents introduces safety concerns, contraindications, increased cost, and workflow complexity. To this end, we present pre-contrast conditioned denoising diffusion probabilistic models to synthesize DCE-MRI, introducing, evaluating, and comparing a total of 22 generative model variants in both single-breast and full breast settings. Towards enhancing lesion fidelity, we introduce both tumor-aware loss functions and explicit tumor segmentation mask conditioning. Using a public multicenter dataset and comparing to respective pre-contrast baselines, we observe that subtraction image-based models consistently outperform post-contrast-based models across five complementary evaluation metrics. Apart from assessing the entire image, we also separately evaluate the region of interest, where both tumor-aware losses and segmentation mask inputs improve evaluation metrics. The latter notably enhance qualitative results capturing contrast uptake, albeit assuming access to tumor localization inputs that are not guaranteed to be available in screening settings. A reader study involving 2 radiologists and 4 MRI technologists confirms the high realism of the synthetic images, indicating an emerging clinical potential of generative contrast-enhancement. We share our codebase at https://github.com/sebastibar/conditional-diffusion-breast-MRI.

In the realm of robot-assisted minimally invasive surgery, dynamic scene reconstruction can significantly enhance downstream tasks and improve surgical outcomes. Neural Radiance Fields (NeRF)-based methods have recently risen to prominence for their exceptional ability to reconstruct scenes but are hampered by slow inference speed, prolonged training, and inconsistent depth estimation. Some previous work utilizes ground truth depth for optimization but is hard to acquire in the surgical domain. To overcome these obstacles, we present Endo-4DGS, a real-time endoscopic dynamic reconstruction approach that utilizes 3D Gaussian Splatting (GS) for 3D representation. Specifically, we propose lightweight MLPs to capture temporal dynamics with Gaussian deformation fields. To obtain a satisfactory Gaussian Initialization, we exploit a powerful depth estimation foundation model, Depth-Anything, to generate pseudo-depth maps as a geometry prior. We additionally propose confidence-guided learning to tackle the ill-pose problems in monocular depth estimation and enhance the depth-guided reconstruction with surface normal constraints and depth regularization. Our approach has been validated on two surgical datasets, where it can effectively render in real-time, compute efficiently, and reconstruct with remarkable accuracy.

Dynamic and static components in scenes often exhibit distinct properties, yet most 4D reconstruction methods treat them indiscriminately, leading to suboptimal performance in both cases. This work introduces SDD-4DGS, the first framework for static-dynamic decoupled 4D scene reconstruction based on Gaussian Splatting. Our approach is built upon a novel probabilistic dynamic perception coefficient that is naturally integrated into the Gaussian reconstruction pipeline, enabling adaptive separation of static and dynamic components. With carefully designed implementation strategies to realize this theoretical framework, our method effectively facilitates explicit learning of motion patterns for dynamic elements while maintaining geometric stability for static structures. Extensive experiments on five benchmark datasets demonstrate that SDD-4DGS consistently outperforms state-of-the-art methods in reconstruction fidelity, with enhanced detail restoration for static structures and precise modeling of dynamic motions. The code will be released.

Existing methods for the 4D reconstruction of general, non-rigidly deforming objects focus on novel-view synthesis and neglect correspondences. However, time consistency enables advanced downstream tasks like 3D editing, motion analysis, or virtual-asset creation. We propose SceNeRFlow to reconstruct a general, non-rigid scene in a time-consistent manner. Our dynamic-NeRF method takes multi-view RGB videos and background images from static cameras with known camera parameters as input. It then reconstructs the deformations of an estimated canonical model of the geometry and appearance in an online fashion. Since this canonical model is time-invariant, we obtain correspondences even for long-term, long-range motions. We employ neural scene representations to parametrize the components of our method. Like prior dynamic-NeRF methods, we use a backwards deformation model. We find non-trivial adaptations of this model necessary to handle larger motions: We decompose the deformations into a strongly regularized coarse component and a weakly regularized fine component, where the coarse component also extends the deformation field into the space surrounding the object, which enables tracking over time. We show experimentally that, unlike prior work that only handles small motion, our method enables the reconstruction of studio-scale motions.

Deep neural networks have enabled improved image quality and fast inference times for various inverse problems, including accelerated magnetic resonance imaging (MRI) reconstruction. However, such models require a large number of fully-sampled ground truth datasets, which are difficult to curate, and are sensitive to distribution drifts. In this work, we propose applying physics-driven data augmentations for consistency training that leverage our domain knowledge of the forward MRI data acquisition process and MRI physics to achieve improved label efficiency and robustness to clinically-relevant distribution drifts. Our approach, termed VORTEX, (1) demonstrates strong improvements over supervised baselines with and without data augmentation in robustness to signal-to-noise ratio change and motion corruption in data-limited regimes; (2) considerably outperforms state-of-the-art purely image-based data augmentation techniques and self-supervised reconstruction methods on both in-distribution and out-of-distribution data; and (3) enables composing heterogeneous image-based and physics-driven data augmentations. Our code is available at https://github.com/ad12/meddlr.

Reconstruction of magnetic resonance imaging (MRI) data has been positively affected by deep learning. A key challenge remains: to improve generalisation to distribution shifts between the training and testing data. Most approaches aim to address this via inductive design or data augmentation. However, they can be affected by misleading data, e.g. random noise, and cases where the inference stage data do not match assumptions in the modelled shifts. In this work, by employing a conditional hyperparameter network, we eliminate the need of augmentation, yet maintain robust performance under various levels of Gaussian noise. We demonstrate that our model withstands various input noise levels while producing high-definition reconstructions during the test stage. Moreover, we present a hyperparameter sampling strategy that accelerates the convergence of training. Our proposed method achieves the highest accuracy and image quality in all settings compared to baseline methods.

Hyperthermia (HT) in combination with radio- and/or chemotherapy has become an accepted cancer treatment for distinct solid tumour entities. In HT, tumour tissue is exogenously heated to temperatures between 39 and 43 ^circC for 60 minutes. Temperature monitoring can be performed non-invasively using dynamic magnetic resonance imaging (MRI). However, the slow nature of MRI leads to motion artefacts in the images due to the movements of patients during image acquisition. By discarding parts of the data, the speed of the acquisition can be increased - known as undersampling. However, due to the invalidation of the Nyquist criterion, the acquired images might be blurry and can also produce aliasing artefacts. The aim of this work was, therefore, to reconstruct highly undersampled MR thermometry acquisitions with better resolution and with fewer artefacts compared to conventional methods. The use of deep learning in the medical field has emerged in recent times, and various studies have shown that deep learning has the potential to solve inverse problems such as MR image reconstruction. However, most of the published work only focuses on the magnitude images, while the phase images are ignored, which are fundamental requirements for MR thermometry. This work, for the first time, presents deep learning-based solutions for reconstructing undersampled MR thermometry data. Two different deep learning models have been employed here, the Fourier Primal-Dual network and the Fourier Primal-Dual UNet, to reconstruct highly undersampled complex images of MR thermometry. The method reduced the temperature difference between the undersampled MRIs and the fully sampled MRIs from 1.3 ^circC to 0.6 ^circC in full volume and 0.49 ^circC to 0.06 ^circC in the tumour region for an acceleration factor of 10.

Deep learning (DL) has shown promise for faster, high quality accelerated MRI reconstruction. However, supervised DL methods depend on extensive amounts of fully-sampled (labeled) data and are sensitive to out-of-distribution (OOD) shifts, particularly low signal-to-noise ratio (SNR) acquisitions. To alleviate this challenge, we propose Noise2Recon, a model-agnostic, consistency training method for joint MRI reconstruction and denoising that can use both fully-sampled (labeled) and undersampled (unlabeled) scans in semi-supervised and self-supervised settings. With limited or no labeled training data, Noise2Recon outperforms compressed sensing and deep learning baselines, including supervised networks, augmentation-based training, fine-tuned denoisers, and self-supervised methods, and matches performance of supervised models, which were trained with 14x more fully-sampled scans. Noise2Recon also outperforms all baselines, including state-of-the-art fine-tuning and augmentation techniques, among low-SNR scans and when generalizing to other OOD factors, such as changes in acceleration factors and different datasets. Augmentation extent and loss weighting hyperparameters had negligible impact on Noise2Recon compared to supervised methods, which may indicate increased training stability. Our code is available at https://github.com/ad12/meddlr.

Typical quantitative MRI (qMRI) methods estimate parameter maps after image reconstructing, which is prone to biases and error propagation. We propose a Nonlinear Conjugate Gradient (NLCG) optimizer for model-based T2/T1 estimation, which incorporates U-Net regularization trained in a scan-specific manner. This end-to-end method directly estimates qMRI maps from undersampled k-space data using mono-exponential signal modeling with zero-shot scan-specific neural network regularization to enable high fidelity T1 and T2 mapping. T2 and T1 mapping results demonstrate the ability of the proposed NLCG-Net to improve estimation quality compared to subspace reconstruction at high accelerations.

Magnetic Resonance Imaging (MRI), including diffusion MRI (dMRI), serves as a ``microscope'' for anatomical structures and routinely mitigates the influence of low signal-to-noise ratio scans by compromising temporal or spatial resolution. However, these compromises fail to meet clinical demands for both efficiency and precision. Consequently, denoising is a vital preprocessing step, particularly for dMRI, where clean data is unavailable. In this paper, we introduce Di-Fusion, a fully self-supervised denoising method that leverages the latter diffusion steps and an adaptive sampling process. Unlike previous approaches, our single-stage framework achieves efficient and stable training without extra noise model training and offers adaptive and controllable results in the sampling process. Our thorough experiments on real and simulated data demonstrate that Di-Fusion achieves state-of-the-art performance in microstructure modeling, tractography tracking, and other downstream tasks. Code is available at https://github.com/FouierL/Di-Fusion.

Breast cancer is the most frequently diagnosed malignancy among women worldwide and a leading cause of cancer-related mortality. Dynamic contrast-enhanced magnetic resonance imaging plays a central role in tumor characterization and treatment monitoring, particularly in patients receiving neoadjuvant chemotherapy. However, existing artificial intelligence models for breast magnetic resonance imaging are typically developed and evaluated using heterogeneous datasets, study populations, and assessment protocols, making direct comparison difficult and limiting understanding of model robustness across institutions and clinically relevant patient subgroups. The MAMA-MIA Challenge was designed to address these challenges by providing a standardized benchmark for the joint evaluation of primary tumor segmentation and prediction of pathologic complete response using pre-treatment magnetic resonance imaging only. The training cohort comprised 1,506 patients from multiple institutions in the United States, while evaluation was conducted on an external test set of 574 patients from three independent European centers to assess cross-continental and cross-institutional generalization. A unified scoring framework combined predictive performance with subgroup consistency across age, menopausal status, and breast density. Twenty-six international teams participated in the final evaluation phase. Results demonstrate substantial performance variability under a common external evaluation framework and reveal trade-offs between overall accuracy and subgroup fairness. The challenge provides standardized datasets, evaluation protocols, and public resources to promote the development of robust and equitable artificial intelligence systems for breast cancer imaging.

Dynamic neuroimaging data, such as emission tomography measurements of radiotracer transport in blood or cerebrospinal fluid, often exhibit diffusion-like properties. These introduce distance-dependent temporal delays, scale-differences, and stretching effects that limit the effectiveness of conventional linear modeling and decomposition methods. To address this, we present the shift- and stretch-invariant non-negative matrix factorization framework. Our approach estimates both integer and non-integer temporal shifts as well as temporal stretching, all implemented in the frequency domain, where shifts correspond to phase modifications, and where stretching is handled via zero-padding or truncation. The model is implemented in PyTorch (https://github.com/anders-s-olsen/shiftstretchNMF). We demonstrate on synthetic data and brain emission tomography data that the model is able to account for stretching to provide more detailed characterization of brain tissue structure.

Accelerating Magnetic Resonance Imaging (MRI) by taking fewer measurements has the potential to reduce medical costs, minimize stress to patients and make MRI possible in applications where it is currently prohibitively slow or expensive. We introduce the fastMRI dataset, a large-scale collection of both raw MR measurements and clinical MR images, that can be used for training and evaluation of machine-learning approaches to MR image reconstruction. By introducing standardized evaluation criteria and a freely-accessible dataset, our goal is to help the community make rapid advances in the state of the art for MR image reconstruction. We also provide a self-contained introduction to MRI for machine learning researchers with no medical imaging background.

Diffusion models have quickly risen in popularity for their ability to model complex distributions and perform effective posterior sampling. Unfortunately, the iterative nature of these generative models makes them computationally expensive and unsuitable for real-time sequential inverse problems such as ultrasound imaging. Considering the strong temporal structure across sequences of frames, we propose a novel approach that models the transition dynamics to improve the efficiency of sequential diffusion posterior sampling in conditional image synthesis. Through modeling sequence data using a video vision transformer (ViViT) transition model based on previous diffusion outputs, we can initialize the reverse diffusion trajectory at a lower noise scale, greatly reducing the number of iterations required for convergence. We demonstrate the effectiveness of our approach on a real-world dataset of high frame rate cardiac ultrasound images and show that it achieves the same performance as a full diffusion trajectory while accelerating inference 25times, enabling real-time posterior sampling. Furthermore, we show that the addition of a transition model improves the PSNR up to 8\% in cases with severe motion. Our method opens up new possibilities for real-time applications of diffusion models in imaging and other domains requiring real-time inference.

Estimating the shape and motion state of the myocardium is essential in diagnosing cardiovascular diseases.However, cine magnetic resonance (CMR) imaging is dominated by 2D slices, whose large slice spacing challenges inter-slice shape reconstruction and motion acquisition.To address this problem, we propose a 4D reconstruction method that decouples motion and shape, which can predict the inter-/intra- shape and motion estimation from a given sparse point cloud sequence obtained from limited slices. Our framework comprises a neural motion model and an end-diastolic (ED) shape model. The implicit ED shape model can learn a continuous boundary and encourage the motion model to predict without the supervision of ground truth deformation, and the motion model enables canonical input of the shape model by deforming any point from any phase to the ED phase. Additionally, the constructed ED-space enables pre-training of the shape model, thereby guiding the motion model and addressing the issue of data scarcity. We propose the first 4D myocardial dataset as we know and verify our method on the proposed, public, and cross-modal datasets, showing superior reconstruction performance and enabling various clinical applications.

We, team AImsterdam, summarize our submission to the fastMRI challenge (Zbontar et al., 2018). Our approach builds on recent advances in invertible learning to infer models as presented in Putzky and Welling (2019). Both, our single-coil and our multi-coil model share the same basic architecture.

Magnetic Resonance Imaging with tagging (tMRI) has long been utilized for quantifying tissue motion and strain during deformation. However, a phenomenon known as tag fading, a gradual decrease in tag visibility over time, often complicates post-processing. The first contribution of this study is to model tag fading by considering the interplay between T_1 relaxation and the repeated application of radio frequency (RF) pulses during serial imaging sequences. This is a factor that has been overlooked in prior research on tMRI post-processing. Further, we have observed an emerging trend of utilizing raw tagged MRI within a deep learning-based (DL) registration framework for motion estimation. In this work, we evaluate and analyze the impact of commonly used image similarity objectives in training DL registrations on raw tMRI. This is then compared with the Harmonic Phase-based approach, a traditional approach which is claimed to be robust to tag fading. Our findings, derived from both simulated images and an actual phantom scan, reveal the limitations of various similarity losses in raw tMRI and emphasize caution in registration tasks where image intensity changes over time.

We address the problem of dynamic scene reconstruction from sparse-view videos. Prior work often requires dense multi-view captures with hundreds of calibrated cameras (e.g. Panoptic Studio). Such multi-view setups are prohibitively expensive to build and cannot capture diverse scenes in-the-wild. In contrast, we aim to reconstruct dynamic human behaviors, such as repairing a bike or dancing, from a small set of sparse-view cameras with complete scene coverage (e.g. four equidistant inward-facing static cameras). We find that dense multi-view reconstruction methods struggle to adapt to this sparse-view setup due to limited overlap between viewpoints. To address these limitations, we carefully align independent monocular reconstructions of each camera to produce time- and view-consistent dynamic scene reconstructions. Extensive experiments on PanopticStudio and Ego-Exo4D demonstrate that our method achieves higher quality reconstructions than prior art, particularly when rendering novel views. Code, data, and data-processing scripts are available on https://github.com/ImNotPrepared/MonoFusion.

Learning spatial-temporal correspondences in cardiac motion from images is important for understanding the underlying dynamics of cardiac anatomical structures. Many methods explicitly impose smoothness constraints such as the L_2 norm on the displacement vector field (DVF), while usually ignoring biomechanical feasibility in the transformation. Other geometric constraints either regularize specific regions of interest such as imposing incompressibility on the myocardium or introduce additional steps such as training a separate network-based regularizer on physically simulated datasets. In this work, we propose an explicit biomechanics-informed prior as regularization on the predicted DVF in modeling a more generic biomechanically plausible transformation within all cardiac structures without introducing additional training complexity. We validate our methods on two publicly available datasets in the context of 2D MRI data and perform extensive experiments to illustrate the effectiveness and robustness of our proposed methods compared to other competing regularization schemes. Our proposed methods better preserve biomechanical properties by visual assessment and show advantages in segmentation performance using quantitative evaluation metrics. The code is publicly available at https://github.com/Voldemort108X/bioinformed_reg.

Computed tomography and magnetic resonance imaging are two widely used clinical imaging modalities for non-invasive diagnosis. However, both of these modalities come with certain problems. CT uses harmful ionising radiation, and MRI suffers from slow acquisition speed. Both problems can be tackled by undersampling, such as sparse sampling. However, such undersampled data leads to lower resolution and introduces artefacts. Several techniques, including deep learning based methods, have been proposed to reconstruct such data. However, the undersampled reconstruction problem for these two modalities was always considered as two different problems and tackled separately by different research works. This paper proposes a unified solution for both sparse CT and undersampled radial MRI reconstruction, achieved by applying Fourier transform-based pre-processing on the radial MRI and then finally reconstructing both modalities using sinogram upsampling combined with filtered back-projection. The Primal-Dual network is a deep learning based method for reconstructing sparsely-sampled CT data. This paper introduces Primal-Dual UNet, which improves the Primal-Dual network in terms of accuracy and reconstruction speed. The proposed method resulted in an average SSIM of 0.932\textpm0.021 while performing sparse CT reconstruction for fan-beam geometry with a sparsity level of 16, achieving a statistically significant improvement over the previous model, which resulted in 0.919\textpm0.016. Furthermore, the proposed model resulted in 0.903\textpm0.019 and 0.957\textpm0.023 average SSIM while reconstructing undersampled brain and abdominal MRI data with an acceleration factor of 16, respectively - statistically significant improvements over the original model, which resulted in 0.867\textpm0.025 and 0.949\textpm0.025.

We provide a framework for solving inverse problems with diffusion models learned from linearly corrupted data. Our method, Ambient Diffusion Posterior Sampling (A-DPS), leverages a generative model pre-trained on one type of corruption (e.g. image inpainting) to perform posterior sampling conditioned on measurements from a potentially different forward process (e.g. image blurring). We test the efficacy of our approach on standard natural image datasets (CelebA, FFHQ, and AFHQ) and we show that A-DPS can sometimes outperform models trained on clean data for several image restoration tasks in both speed and performance. We further extend the Ambient Diffusion framework to train MRI models with access only to Fourier subsampled multi-coil MRI measurements at various acceleration factors (R=2, 4, 6, 8). We again observe that models trained on highly subsampled data are better priors for solving inverse problems in the high acceleration regime than models trained on fully sampled data. We open-source our code and the trained Ambient Diffusion MRI models: https://github.com/utcsilab/ambient-diffusion-mri .

Segmenting stroke lesions in Magnetic Resonance Imaging (MRI) is challenging due to diverse clinical imaging domains, with existing models struggling to generalise across different MRI acquisition parameters and sequences. In this work, we propose two novel physics-constrained approaches using synthetic quantitative MRI (qMRI) images to enhance the robustness and generalisability of segmentation models. We trained a qMRI estimation model to predict qMRI maps from MPRAGE images, which were used to simulate diverse MRI sequences for segmentation training. A second approach built upon prior work in synthetic data for stroke lesion segmentation, generating qMRI maps from a dataset of tissue labels. The proposed approaches improved over the baseline nnUNet on a variety of out-of-distribution datasets, with the second approach outperforming the prior synthetic data method.

Diffusion models have become a popular approach for image generation and reconstruction due to their numerous advantages. However, most diffusion-based inverse problem-solving methods only deal with 2D images, and even recently published 3D methods do not fully exploit the 3D distribution prior. To address this, we propose a novel approach using two perpendicular pre-trained 2D diffusion models to solve the 3D inverse problem. By modeling the 3D data distribution as a product of 2D distributions sliced in different directions, our method effectively addresses the curse of dimensionality. Our experimental results demonstrate that our method is highly effective for 3D medical image reconstruction tasks, including MRI Z-axis super-resolution, compressed sensing MRI, and sparse-view CT. Our method can generate high-quality voxel volumes suitable for medical applications.

Multimodal cardiovascular magnetic resonance (CMR) imaging provides comprehensive and non-invasive insights into cardiovascular disease (CVD) diagnosis and underlying mechanisms. Despite decades of advancements, its widespread clinical adoption remains constrained by prolonged scan times and heterogeneity across medical environments. This underscores the urgent need for a generalist reconstruction foundation model for ultra-fast CMR imaging, one capable of adapting across diverse imaging scenarios and serving as the essential substrate for all downstream analyses. To enable this goal, we curate MMCMR-427K, the largest and most comprehensive multimodal CMR k-space database to date, comprising 427,465 multi-coil k-space data paired with structured metadata across 13 international centers, 12 CMR modalities, 15 scanners, and 17 CVD categories in populations across three continents. Building on this unprecedented resource, we introduce CardioMM, a generalist reconstruction foundation model capable of dynamically adapting to heterogeneous fast CMR imaging scenarios. CardioMM unifies semantic contextual understanding with physics-informed data consistency to deliver robust reconstructions across varied scanners, protocols, and patient presentations. Comprehensive evaluations demonstrate that CardioMM achieves state-of-the-art performance in the internal centers and exhibits strong zero-shot generalization to unseen external settings. Even at imaging acceleration up to 24x, CardioMM reliably preserves key cardiac phenotypes, quantitative myocardial biomarkers, and diagnostic image quality, enabling a substantial increase in CMR examination throughput without compromising clinical integrity. Together, our open-access MMCMR-427K database and CardioMM framework establish a scalable pathway toward high-throughput, high-quality, and clinically accessible cardiovascular imaging.

Magnetic Resonance Imaging (MRI) is a critical medical imaging modality in clinical diagnosis and research, yet its complexity and heterogeneity pose challenges for automated analysis, particularly in scalable and generalizable machine learning applications. While foundation models have revolutionized natural language and vision tasks, their application to MRI remains limited due to data scarcity and narrow anatomical focus. In this work, we present Decipher-MR, a 3D MRI-specific vision-language foundation model trained on a large-scale dataset comprising 200,000 MRI series from over 22,000 studies spanning diverse anatomical regions, sequences, and pathologies. Decipher-MR integrates self-supervised vision learning with report-guided text supervision to build robust, generalizable representations, enabling effective adaptation across broad applications. To enable robust and diverse clinical tasks with minimal computational overhead, Decipher-MR supports a modular design that enables tuning of lightweight, task-specific decoders attached to a frozen pretrained encoder. Following this setting, we evaluate Decipher-MR across diverse benchmarks including disease classification, demographic prediction, anatomical localization, and cross-modal retrieval, demonstrating consistent performance gains over existing foundation models and task-specific approaches. Our results establish Decipher-MR as a scalable and versatile foundation for MRI-based AI, facilitating efficient development across clinical and research domains.

Brain MRI scans are often found in four modalities, consisting of T1-weighted with and without contrast enhancement (T1ce and T1w), T2-weighted imaging (T2w), and Flair. Leveraging complementary information from these different modalities enables models to learn richer, more discriminative features for understanding brain anatomy, which could be used in downstream tasks such as anomaly detection. However, in clinical practice, not all MRI modalities are always available due to various reasons. This makes missing modality generation a critical challenge in medical image analysis. In this paper, we propose SLaM-DiMM, a novel missing modality generation framework that harnesses the power of diffusion models to synthesize any of the four target MRI modalities from other available modalities. Our approach not only generates high-fidelity images but also ensures structural coherence across the depth of the volume through a dedicated coherence enhancement mechanism. Qualitative and quantitative evaluations on the BraTS-Lighthouse-2025 Challenge dataset demonstrate the effectiveness of the proposed approach in synthesizing anatomically plausible and structurally consistent results. Code is available at https://github.com/BheeshmSharma/SLaM-DiMM-MICCAI-BraTS-Challenge-2025.

Reconstructing medical images from partial measurements is an important inverse problem in Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). Existing solutions based on machine learning typically train a model to directly map measurements to medical images, leveraging a training dataset of paired images and measurements. These measurements are typically synthesized from images using a fixed physical model of the measurement process, which hinders the generalization capability of models to unknown measurement processes. To address this issue, we propose a fully unsupervised technique for inverse problem solving, leveraging the recently introduced score-based generative models. Specifically, we first train a score-based generative model on medical images to capture their prior distribution. Given measurements and a physical model of the measurement process at test time, we introduce a sampling method to reconstruct an image consistent with both the prior and the observed measurements. Our method does not assume a fixed measurement process during training, and can thus be flexibly adapted to different measurement processes at test time. Empirically, we observe comparable or better performance to supervised learning techniques in several medical imaging tasks in CT and MRI, while demonstrating significantly better generalization to unknown measurement processes.

Radiance of real-world scenes typically spans a much wider dynamic range than what standard cameras can capture. While conventional HDR methods merge alternating-exposure frames, these approaches are inherently constrained to 2D pixel-level alignment, often leading to ghosting artifacts and temporal inconsistency in dynamic scenes. To address these limitations, we present HDR-NSFF, a paradigm shift from 2D-based merging to 4D spatio-temporal modeling. Our framework reconstructs dynamic HDR radiance fields from alternating-exposure monocular videos by representing the scene as a continuous function of space and time, and is compatible with both neural radiance field and 4D Gaussian Splatting (4DGS) based dynamic representations. This unified end-to-end pipeline explicitly models HDR radiance, 3D scene flow, geometry, and tone-mapping, ensuring physical plausibility and global coherence. We further enhance robustness by (i) extending semantic-based optical flow with DINO features to achieve exposure-invariant motion estimation, and (ii) incorporating a generative prior as a regularizer to compensate for limited observation in monocular captures and saturation-induced information loss. To evaluate HDR space-time view synthesis, we present the first real-world HDR-GoPro dataset specifically designed for dynamic HDR scenes. Experiments demonstrate that HDR-NSFF recovers fine radiance details and coherent dynamics even under challenging exposure variations, thereby achieving state-of-the-art performance in novel space-time view synthesis. Project page: https://shin-dong-yeon.github.io/HDR-NSFF/

Tagged magnetic resonance imaging (tMRI) has been employed for decades to measure the motion of tissue undergoing deformation. However, registration-based motion estimation from tMRI is difficult due to the periodic patterns in these images, particularly when the motion is large. With a larger motion the registration approach gets trapped in a local optima, leading to motion estimation errors. We introduce a novel "momenta, shooting, and correction" framework for Lagrangian motion estimation in the presence of repetitive patterns and large motion. This framework, grounded in Lie algebra and Lie group principles, accumulates momenta in the tangent vector space and employs exponential mapping in the diffeomorphic space for rapid approximation towards true optima, circumventing local optima. A subsequent correction step ensures convergence to true optima. The results on a 2D synthetic dataset and a real 3D tMRI dataset demonstrate our method's efficiency in estimating accurate, dense, and diffeomorphic 2D/3D motion fields amidst large motion and repetitive patterns.

Multi-organ segmentation in medical imaging remains challenging due to large anatomical variability, complex inter-organ dependencies, and diverse organ scales and shapes. Conventional encoder-decoder architectures often struggle to capture both fine-grained local details and long-range context, which are crucial for accurate delineation - especially for small or deformable organs. To address these limitations, we propose MD-RWKV-UNet, a dynamic encoder network that enables scale-aware representation and spatially adaptive context modeling. At its core is the MD-RWKV block, a dual-path module that integrates deformable spatial shifts with the Receptance Weighted Key Value mechanism, allowing the receptive field to adapt dynamically to local structural cues. We further incorporate Selective Kernel Attention to enable adaptive selection of convolutional kernels with varying receptive fields, enhancing multi-scale interaction and improving robustness to organ size and shape variation. In parallel, a cross-stage dual-attention fusion strategy aggregates multi-level features across the encoder, preserving low-level structure while enhancing semantic consistency. Unlike methods that stack static convolutions or rely heavily on global attention, our approach provides a lightweight yet expressive solution for dynamic organ modeling. Experiments on Synapse and ACDC demonstrate state-of-the-art performance, particularly in boundary precision and small-organ segmentation.

Recent inverse problem solvers that leverage generative diffusion priors have garnered significant attention due to their exceptional quality. However, adaptation of the prior is necessary when there exists a discrepancy between the training and testing distributions. In this work, we propose deep diffusion image prior (DDIP), which generalizes the recent adaptation method of SCD by introducing a formal connection to the deep image prior. Under this framework, we propose an efficient adaptation method dubbed D3IP, specified for 3D measurements, which accelerates DDIP by orders of magnitude while achieving superior performance. D3IP enables seamless integration of 3D inverse solvers and thus leads to coherent 3D reconstruction. Moreover, we show that meta-learning techniques can also be applied to yield even better performance. We show that our method is capable of solving diverse 3D reconstructive tasks from the generative prior trained only with phantom images that are vastly different from the training set, opening up new opportunities of applying diffusion inverse solvers even when training with gold standard data is impossible. Code: https://github.com/HJ-harry/DDIP3D

Transforming two-dimensional (2D) images into three-dimensional (3D) volumes is a well-known yet challenging problem for the computer vision community. In the medical domain, a few previous studies attempted to convert two or more input radiographs into computed tomography (CT) volumes. Following their effort, we introduce a diffusion model-based technology that can rotate the anatomical content of any input radiograph in 3D space, potentially enabling the visualization of the entire anatomical content of the radiograph from any viewpoint in 3D. Similar to previous studies, we used CT volumes to create Digitally Reconstructed Radiographs (DRRs) as the training data for our model. However, we addressed two significant limitations encountered in previous studies: 1. We utilized conditional diffusion models with classifier-free guidance instead of Generative Adversarial Networks (GANs) to achieve higher mode coverage and improved output image quality, with the only trade-off being slower inference time, which is often less critical in medical applications; and 2. We demonstrated that the unreliable output of style transfer deep learning (DL) models, such as Cycle-GAN, to transfer the style of actual radiographs to DRRs could be replaced with a simple yet effective training transformation that randomly changes the pixel intensity histograms of the input and ground-truth imaging data during training. This transformation makes the diffusion model agnostic to any distribution variations of the input data pixel intensity, enabling the reliable training of a DL model on input DRRs and applying the exact same model to conventional radiographs (or DRRs) during inference.

Purpose: This study aims to explore training strategies to improve convolutional neural network-based image-to-image deformable registration for abdominal imaging. Methods: Different training strategies, loss functions, and transfer learning schemes were considered. Furthermore, an augmentation layer which generates artificial training image pairs on-the-fly was proposed, in addition to a loss layer that enables dynamic loss weighting. Results: Guiding registration using segmentations in the training step proved beneficial for deep-learning-based image registration. Finetuning the pretrained model from the brain MRI dataset to the abdominal CT dataset further improved performance on the latter application, removing the need for a large dataset to yield satisfactory performance. Dynamic loss weighting also marginally improved performance, all without impacting inference runtime. Conclusion: Using simple concepts, we improved the performance of a commonly used deep image registration architecture, VoxelMorph. In future work, our framework, DDMR, should be validated on different datasets to further assess its value.

Magnetic Resonance Imaging (MRI) is often acquired with anisotropic resolution to reduce scan time, producing stair-step artifacts along the through-plane direction. In through-plane MRI super-resolution, an efficiency-fidelity trade-off arises: feed-forward regressors are fast but oversmooth at large slice-thicknesses, while sampling-based methods improve fidelity at high inference cost. We propose DRIFT, a two-stage thickness-conditioned rectified flow framework for through-plane MRI super-resolution with continuous input slice-thickness. Stage 1 employs an Anatomical Projection Network (APN) to map low-resolution patches to a coarse high-resolution manifold, providing a deterministic anatomical initialization that shortens the residual transport of Stage 2 and stabilizes slice-wise refinement. Stage 2 refines details via rectified flow and introduces a Physics-Aware Difficulty (PAD) metric derived from slice-thickness induced through-plane bandwidth deficit to guide an Adaptive Integration Scheduler (AIS), allocating ODE steps by thickness. A Consistent Endpoint Trajectory Alignment (CETA) loss enforces thickness-consistent reconstructions. Experiments show that DRIFT outperforms super-resolution baselines while reducing inference cost. Code, models, and interactive demos are available at https://yoonseokchoi-ai.github.io/drift-eccv2026/.

Magnetic resonance imaging (MRI) is a common and life-saving medical imaging technique. However, acquiring high signal-to-noise ratio MRI scans requires long scan times, resulting in increased costs and patient discomfort, and decreased throughput. Thus, there is great interest in denoising MRI scans, especially for the subtype of diffusion MRI scans that are severely SNR-limited. While most prior MRI denoising methods are supervised in nature, acquiring supervised training datasets for the multitude of anatomies, MRI scanners, and scan parameters proves impractical. Here, we propose Denoising Diffusion Models for Denoising Diffusion MRI (DDM^2), a self-supervised denoising method for MRI denoising using diffusion denoising generative models. Our three-stage framework integrates statistic-based denoising theory into diffusion models and performs denoising through conditional generation. During inference, we represent input noisy measurements as a sample from an intermediate posterior distribution within the diffusion Markov chain. We conduct experiments on 4 real-world in-vivo diffusion MRI datasets and show that our DDM^2 demonstrates superior denoising performances ascertained with clinically-relevant visual qualitative and quantitative metrics.

Objective: To allow efficient learning using the Recurrent Inference Machine (RIM) for image reconstruction whereas not being strictly dependent on the training data distribution so that unseen modalities and pathologies are still accurately recovered. Methods: Theoretically, the RIM learns to solve the inverse problem of accelerated-MRI reconstruction whereas being robust to variable imaging conditions. The efficiency and generalization capabilities with different training datasets were studied, as well as recurrent network units with decreasing complexity: the Gated Recurrent Unit (GRU), the Minimal Gated Unit (MGU), and the Independently Recurrent Neural Network (IndRNN), to reduce inference times. Validation was performed against Compressed Sensing (CS) and further assessed based on data unseen during training. A pathology study was conducted by reconstructing simulated white matter lesions and prospectively undersampled data of a Multiple Sclerosis patient. Results: Training on a single modality of 3T T_1-weighted brain data appeared sufficient to also reconstruct 7T T_{2}^*-weighted brain and 3T T_2-weighted knee data. The IndRNN is an efficient recurrent unit, reducing inference time by 68\% compared to CS, whereas maintaining performance. The RIM was able to reconstruct lesions unseen during training more accurately than CS when trained on T_2-weighted knee data. Training on T_1-weighted brain data and on combined data slightly enhanced the signal compared to CS. Conclusion: The RIM is efficient when decreasing its complexity, which reduces the inference time, whereas still being able to reconstruct data and pathology that was unseen during training.

The demand for high-quality medical imaging in clinical practice and assisted diagnosis has made 3D image reconstruction in radiological imaging a key research focus. Artificial intelligence (AI) has emerged as a promising approach for improving reconstruction accuracy while reducing acquisition and processing time, thereby minimizing patient radiation exposure and discomfort and ultimately benefiting clinical diagnosis. This review surveys state-of-the-art AI-based 3D reconstruction algorithms in radiological imaging and organizes them into four representation families according to how the reconstructed target is parameterized: discrete grid representations, explicit basis expansion representations, explicit primitive representations, and implicit neural representations. In particular, the review clarifies the relationships among these representation forms and highlights radiance field methods as a specialized subtype of implicit neural representation. In addition, we summarize commonly used evaluation metrics and benchmark datasets for radiological image reconstruction. Finally, we discuss the current state of development, major challenges, and future research directions in this rapidly evolving field. Our project is available at: https://github.com/Bean-Young/AI4Radiology.

Monocular dynamic reconstruction is a challenging and long-standing vision problem due to the highly ill-posed nature of the task. Existing approaches are limited in that they either depend on templates, are effective only in quasi-static scenes, or fail to model 3D motion explicitly. In this work, we introduce a method capable of reconstructing generic dynamic scenes, featuring explicit, full-sequence-long 3D motion, from casually captured monocular videos. We tackle the under-constrained nature of the problem with two key insights: First, we exploit the low-dimensional structure of 3D motion by representing scene motion with a compact set of SE3 motion bases. Each point's motion is expressed as a linear combination of these bases, facilitating soft decomposition of the scene into multiple rigidly-moving groups. Second, we utilize a comprehensive set of data-driven priors, including monocular depth maps and long-range 2D tracks, and devise a method to effectively consolidate these noisy supervisory signals, resulting in a globally consistent representation of the dynamic scene. Experiments show that our method achieves state-of-the-art performance for both long-range 3D/2D motion estimation and novel view synthesis on dynamic scenes. Project Page: https://shape-of-motion.github.io/

We introduce a strategy for learning image registration without acquired imaging data, producing powerful networks agnostic to contrast introduced by magnetic resonance imaging (MRI). While classical registration methods accurately estimate the spatial correspondence between images, they solve an optimization problem for every new image pair. Learning-based techniques are fast at test time but limited to registering images with contrasts and geometric content similar to those seen during training. We propose to remove this dependency on training data by leveraging a generative strategy for diverse synthetic label maps and images that exposes networks to a wide range of variability, forcing them to learn more invariant features. This approach results in powerful networks that accurately generalize to a broad array of MRI contrasts. We present extensive experiments with a focus on 3D neuroimaging, showing that this strategy enables robust and accurate registration of arbitrary MRI contrasts even if the target contrast is not seen by the networks during training. We demonstrate registration accuracy surpassing the state of the art both within and across contrasts, using a single model. Critically, training on arbitrary shapes synthesized from noise distributions results in competitive performance, removing the dependency on acquired data of any kind. Additionally, since anatomical label maps are often available for the anatomy of interest, we show that synthesizing images from these dramatically boosts performance, while still avoiding the need for real intensity images. Our code is available at https://w3id.org/synthmorph.

Reconstruction of the soft tissues in robotic surgery from endoscopic stereo videos is important for many applications such as intra-operative navigation and image-guided robotic surgery automation. Previous works on this task mainly rely on SLAM-based approaches, which struggle to handle complex surgical scenes. Inspired by recent progress in neural rendering, we present a novel framework for deformable tissue reconstruction from binocular captures in robotic surgery under the single-viewpoint setting. Our framework adopts dynamic neural radiance fields to represent deformable surgical scenes in MLPs and optimize shapes and deformations in a learning-based manner. In addition to non-rigid deformations, tool occlusion and poor 3D clues from a single viewpoint are also particular challenges in soft tissue reconstruction. To overcome these difficulties, we present a series of strategies of tool mask-guided ray casting, stereo depth-cueing ray marching and stereo depth-supervised optimization. With experiments on DaVinci robotic surgery videos, our method significantly outperforms the current state-of-the-art reconstruction method for handling various complex non-rigid deformations. To our best knowledge, this is the first work leveraging neural rendering for surgical scene 3D reconstruction with remarkable potential demonstrated. Code is available at: https://github.com/med-air/EndoNeRF.

Deep learning underpins a wide range of applications in MRI, including reconstruction, artifact removal, and segmentation. However, progress has been driven largely by public datasets focused on brain and knee imaging, shaping how models are trained and evaluated. As a result, careful studies of the reliability of these models across diverse anatomical settings remain limited. In this work, we introduce MosaicMRI, a large and diverse collection of fully sampled raw musculoskeletal (MSK) MR measurements designed for training and evaluating machine-learning-based methods. MosaicMRI is the largest open-source raw MSK MRI dataset to date, comprising 2,671 volumes and 80,156 slices. The dataset offers substantial diversity in volume orientation (e.g., axial, sagittal), imaging contrasts (e.g., PD, T1, T2), anatomies (e.g., spine, knee, hip, ankle, and others), and numbers of acquisition coils. Using VarNet as a baseline for accelerated reconstruction task, we perform a comprehensive set of experiments to study scaling behavior with respect to both model capacity and dataset size. Interestingly, models trained on the combined anatomies significantly outperform anatomy-specific models in low-sample regimes, highlighting the benefits of anatomical diversity and the presence of exploitable cross-anatomical correlations. We further evaluate robustness and cross-anatomy generalization by training models on one anatomy (e.g., spine) and testing them on another (e.g., knee). Notably, we identify groups of body parts (e.g., foot and elbow) that generalize well with each other, and highlight that performance under domain shifts depends on both training set size, anatomy, and protocol-specific factors.

Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) are the predominant modalities utilized in the field of medical imaging. Although MRI capture the complexity of anatomical structures with greater detail than CT, it entails a higher financial costs and requires longer image acquisition times. In this study, we aim to train latent diffusion model for CT to MRI conversion, replacing the commonly-used U-Net or Transformer backbone with a State-Space Model (SSM) called Mamba that operates on latent patches. First, we noted critical oversights in the scan scheme of most Mamba-based vision methods, including inadequate attention to the spatial continuity of patch tokens and the lack of consideration for their varying importance to the target task. Secondly, extending from this insight, we introduce Diffusion Mamba (DiffMa), employing soft masked to integrate Cross-Sequence Attention into Mamba and conducting selective scan in a spiral manner. Lastly, extensive experiments demonstrate impressive performance by DiffMa in medical image generation tasks, with notable advantages in input scaling efficiency over existing benchmark models. The code and models are available at https://github.com/wongzbb/DiffMa-Diffusion-Mamba

We present E(3)-Pose, a novel fast pose estimation method that jointly and explicitly models rotation equivariance and object symmetry. Our work is motivated by the challenging problem of accounting for fetal head motion during a diagnostic MRI scan. We aim to enable automatic adaptive prescription of 2D diagnostic MRI slices with 6-DoF head pose estimation, supported by 3D MRI volumes rapidly acquired before each 2D slice. Existing methods struggle to generalize to clinical volumes, due to pose ambiguities induced by inherent anatomical symmetries, as well as low resolution, noise, and artifacts. In contrast, E(3)-Pose captures anatomical symmetries and rigid pose equivariance by construction, and yields robust estimates of the fetal head pose. Our experiments on publicly available and representative clinical fetal MRI datasets demonstrate the superior robustness and generalization of our method across domains. Crucially, E(3)-Pose achieves state-of-the-art accuracy on clinical MRI volumes, paving the way for clinical translation. Our implementation is available at github.com/ramyamut/E3-Pose.

Synthesizing high-fidelity videos from real-world multi-view input is challenging because of the complexities of real-world environments and highly dynamic motions. Previous works based on neural radiance fields have demonstrated high-quality reconstructions of dynamic scenes. However, training such models on real-world scenes is time-consuming, usually taking days or weeks. In this paper, we present a novel method named MixVoxels to better represent the dynamic scenes with fast training speed and competitive rendering qualities. The proposed MixVoxels represents the 4D dynamic scenes as a mixture of static and dynamic voxels and processes them with different networks. In this way, the computation of the required modalities for static voxels can be processed by a lightweight model, which essentially reduces the amount of computation, especially for many daily dynamic scenes dominated by the static background. To separate the two kinds of voxels, we propose a novel variation field to estimate the temporal variance of each voxel. For the dynamic voxels, we design an inner-product time query method to efficiently query multiple time steps, which is essential to recover the high-dynamic motions. As a result, with 15 minutes of training for dynamic scenes with inputs of 300-frame videos, MixVoxels achieves better PSNR than previous methods. Codes and trained models are available at https://github.com/fengres/mixvoxels

Most existing learning-based methods for solving imaging inverse problems can be roughly divided into two classes: iterative algorithms, such as plug-and-play and diffusion methods, that leverage pretrained denoisers, and unrolled architectures that are trained end-to-end for specific imaging problems. Iterative methods in the first class are computationally costly and often provide suboptimal reconstruction performance, whereas unrolled architectures are generally specific to a single inverse problem and require expensive training. In this work, we propose a novel non-iterative, lightweight architecture that incorporates knowledge about the forward operator (acquisition physics and noise parameters) without relying on unrolling. Our model is trained to solve a wide range of inverse problems beyond denoising, including deblurring, magnetic resonance imaging, computed tomography, inpainting, and super-resolution. The proposed model can be easily adapted to unseen inverse problems or datasets with a few fine-tuning steps (up to a few images) in a self-supervised way, without ground-truth references. Throughout a series of experiments, we demonstrate state-of-the-art performance from medical imaging to low-photon imaging and microscopy.

Accelerated magnetic resonance (MR) imaging attempts to reduce acquisition time by collecting data below the Nyquist rate. As an ill-posed inverse problem, many plausible solutions exist, yet the majority of deep learning approaches generate only a single solution. We instead focus on sampling from the posterior distribution, which provides more comprehensive information for downstream inference tasks. To do this, we design a novel conditional normalizing flow (CNF) that infers the signal component in the measurement operator's nullspace, which is later combined with measured data to form complete images. Using fastMRI brain and knee data, we demonstrate fast inference and accuracy that surpasses recent posterior sampling techniques for MRI. Code is available at https://github.com/jwen307/mri_cnf/

Limitations on bandwidth and power consumption impose strict bounds on data rates of diagnostic imaging systems. Consequently, the design of suitable (i.e. task- and data-aware) compression and reconstruction techniques has attracted considerable attention in recent years. Compressed sensing emerged as a popular framework for sparse signal reconstruction from a small set of compressed measurements. However, typical compressed sensing designs measure a (non)linearly weighted combination of all input signal elements, which poses practical challenges. These designs are also not necessarily task-optimal. In addition, real-time recovery is hampered by the iterative and time-consuming nature of sparse recovery algorithms. Recently, deep learning methods have shown promise for fast recovery from compressed measurements, but the design of adequate and practical sensing strategies remains a challenge. Here, we propose a deep learning solution termed Deep Probabilistic Sub-sampling (DPS), that learns a task-driven sub-sampling pattern, while jointly training a subsequent task model. Once learned, the task-based sub-sampling patterns are fixed and straightforwardly implementable, e.g. by non-uniform analog-to-digital conversion, sparse array design, or slow-time ultrasound pulsing schemes. The effectiveness of our framework is demonstrated in-silico for sparse signal recovery from partial Fourier measurements, and in-vivo for both anatomical image and tissue-motion (Doppler) reconstruction from sub-sampled medical ultrasound imaging data.

Krylov subspace, which is generated by multiplying a given vector by the matrix of a linear transformation and its successive powers, has been extensively studied in classical optimization literature to design algorithms that converge quickly for large linear inverse problems. For example, the conjugate gradient method (CG), one of the most popular Krylov subspace methods, is based on the idea of minimizing the residual error in the Krylov subspace. However, with the recent advancement of high-performance diffusion solvers for inverse problems, it is not clear how classical wisdom can be synergistically combined with modern diffusion models. In this study, we propose a novel and efficient diffusion sampling strategy that synergistically combines the diffusion sampling and Krylov subspace methods. Specifically, we prove that if the tangent space at a denoised sample by Tweedie's formula forms a Krylov subspace, then the CG initialized with the denoised data ensures the data consistency update to remain in the tangent space. This negates the need to compute the manifold-constrained gradient (MCG), leading to a more efficient diffusion sampling method. Our method is applicable regardless of the parametrization and setting (i.e., VE, VP). Notably, we achieve state-of-the-art reconstruction quality on challenging real-world medical inverse imaging problems, including multi-coil MRI reconstruction and 3D CT reconstruction. Moreover, our proposed method achieves more than 80 times faster inference time than the previous state-of-the-art method. Code is available at https://github.com/HJ-harry/DDS

Magnetic Resonance Imaging (MRI) is a crucial imaging modality for viewing internal body structures. This research work analyses the performance of popular GAN models for accurate and precise MRI reconstruction by enhancing image quality and improving diagnostic accuracy. Three GAN architectures considered in this study are Vanilla GAN, Deep Convolutional GAN (DCGAN), and Wasserstein GAN (WGAN). They were trained and evaluated using knee, brain, and cardiac MRI datasets to assess their generalizability across body regions. While the Vanilla GAN operates on the fundamentals of the adversarial network setup, DCGAN advances image synthesis by securing the convolutional layers, giving a superior appearance to the prevalent spatial features. Training instability is resolved in WGAN through the Wasserstein distance to minimize an unstable regime, therefore, ensuring stable convergence and high-quality images. The GAN models were trained and tested using 1000 MR images of an anonymized knee, 805 images of Heart, 90 images of Brain MRI dataset. The Structural Similarity Index (SSIM) for Vanilla GAN is 0.84, DCGAN is 0.97, and WGAN is 0.99. The Peak Signal to Noise Ratio (PSNR) for Vanilla GAN is 26, DCGAN is 49.3, and WGAN is 43.5. The results were further statistically validated. This study shows that DCGAN and WGAN-based frameworks are promising in MR image reconstruction because of good image quality and superior accuracy. With the first cross-organ benchmark of baseline GANs under a common preprocessing pipeline, this work provides a reproducible benchmark for future hybrid GANs and clinical MRI applications.

This paper describes a novel nonparametric model for modeling diffusion MRI signals in q-space. In q-space, diffusion MRI signal is measured for a sequence of magnetic strengths (b-values) and magnetic gradient directions (b-vectors). We propose a Poly-RBF model, which employs a bidirectional framework with polynomial bases to model the signal along the b-value direction and Gaussian radial bases across the b-vectors. The model can accommodate sparse data on b-values and moderately dense data on b-vectors. The utility of Poly-RBF is inspected for two applications: 1) prediction of the dMRI signal, and 2) harmonization of dMRI data collected under different acquisition protocols with different scanners. Our results indicate that the proposed Poly-RBF model can more accurately predict the unmeasured diffusion signal than its competitors such as the Gaussian process model in {\tt Eddy} of FSL. Applying it to harmonizing the diffusion signal can significantly improve the reproducibility of derived white matter microstructure measures.

Multimodal magnetic resonance imaging (MRI) constitutes the first line of investigation for clinicians in the care of brain tumors, providing crucial insights for surgery planning, treatment monitoring, and biomarker identification. Pre-training on large datasets have been shown to help models learn transferable representations and adapt with minimal labeled data. This behavior is especially valuable in medical imaging, where annotations are often scarce. However, applying this paradigm to multimodal medical data introduces a challenge: most existing approaches assume that all imaging modalities are available during both pre-training and fine-tuning. In practice, missing modalities often occur due to acquisition issues, specialist unavailability, or specific experimental designs on small in-house datasets. Consequently, a common approach involves training a separate model for each desired modality combination, making the process both resource-intensive and impractical for clinical use. Therefore, we introduce BM-MAE, a masked image modeling pre-training strategy tailored for multimodal MRI data. The same pre-trained model seamlessly adapts to any combination of available modalities, extracting rich representations that capture both intra- and inter-modal information. This allows fine-tuning on any subset of modalities without requiring architectural changes, while still benefiting from a model pre-trained on the full set of modalities. Extensive experiments show that the proposed pre-training strategy outperforms or remains competitive with baselines that require separate pre-training for each modality subset, while substantially surpassing training from scratch on several downstream tasks. Additionally, it can quickly and efficiently reconstruct missing modalities, highlighting its practical value. Code and trained models are available at: https://github.com/Lucas-rbnt/BM-MAE

Functional magnetic resonance imaging techniques benefit from echo-planar imaging's fast image acquisition but are susceptible to inhomogeneities in the main magnetic field, resulting in geometric distortion and signal loss artifacts in the images. Traditional methods leverage a field map or voxel displacement map for distortion correction. However, voxel displacement map estimation requires additional sequence acquisitions, and the accuracy of the estimation influences correction performance. This work implements a novel approach called GDCNet, which estimates a geometric distortion map by non-linear registration to T1-weighted anatomical images and applies it for distortion correction. GDCNet demonstrated fast distortion correction of functional images in retrospectively and prospectively acquired datasets. Among the compared models, the 2D self-supervised configuration resulted in a statistically significant improvement to normalized mutual information between distortion-corrected functional and T1-weighted images compared to the benchmark methods FUGUE and TOPUP. Furthermore, GDCNet models achieved processing speeds 14 times faster than TOPUP in the prospective dataset.

Longitudinal multimodal data, including electronic health records (EHR) and sequential chest X-rays (CXRs), is critical for modeling disease progression, yet remains underutilized due to two key challenges: (1) redundancy in consecutive CXR sequences, where static anatomical regions dominate over clinically-meaningful dynamics, and (2) temporal misalignment between sparse, irregular imaging and continuous EHR data. We introduce DiPro, a novel framework that addresses these challenges through region-aware disentanglement and multi-timescale alignment. First, we disentangle static (anatomy) and dynamic (pathology progression) features in sequential CXRs, prioritizing disease-relevant changes. Second, we hierarchically align these static and dynamic CXR features with asynchronous EHR data via local (pairwise interval-level) and global (full-sequence) synchronization to model coherent progression pathways. Extensive experiments on the MIMIC dataset demonstrate that DiPro could effectively extract temporal clinical dynamics and achieve state-of-the-art performance on both disease progression identification and general ICU prediction tasks.

In this paper, we present Consistent4D, a novel approach for generating 4D dynamic objects from uncalibrated monocular videos. Uniquely, we cast the 360-degree dynamic object reconstruction as a 4D generation problem, eliminating the need for tedious multi-view data collection and camera calibration. This is achieved by leveraging the object-level 3D-aware image diffusion model as the primary supervision signal for training Dynamic Neural Radiance Fields (DyNeRF). Specifically, we propose a Cascade DyNeRF to facilitate stable convergence and temporal continuity under the supervision signal which is discrete along the time axis. To achieve spatial and temporal consistency, we further introduce an Interpolation-driven Consistency Loss. It is optimized by minimizing the discrepancy between rendered frames from DyNeRF and interpolated frames from a pre-trained video interpolation model. Extensive experiments show that our Consistent4D can perform competitively to prior art alternatives, opening up new possibilities for 4D dynamic object generation from monocular videos, whilst also demonstrating advantage for conventional text-to-3D generation tasks. Our project page is https://consistent4d.github.io/.

In the pursuit to understand the intricacies of human brain's visual processing, reconstructing dynamic visual experiences from brain activities emerges as a challenging yet fascinating endeavor. While recent advancements have achieved success in reconstructing static images from non-invasive brain recordings, the domain of translating continuous brain activities into video format remains underexplored. In this work, we introduce NeuroCine, a novel dual-phase framework to targeting the inherent challenges of decoding fMRI data, such as noises, spatial redundancy and temporal lags. This framework proposes spatial masking and temporal interpolation-based augmentation for contrastive learning fMRI representations and a diffusion model enhanced by dependent prior noise for video generation. Tested on a publicly available fMRI dataset, our method shows promising results, outperforming the previous state-of-the-art models by a notable margin of {20.97%}, {31.00%} and {12.30%} respectively on decoding the brain activities of three subjects in the fMRI dataset, as measured by SSIM. Additionally, our attention analysis suggests that the model aligns with existing brain structures and functions, indicating its biological plausibility and interpretability.

We address the problem of synthesizing novel views from a monocular video depicting a complex dynamic scene. State-of-the-art methods based on temporally varying Neural Radiance Fields (aka dynamic NeRFs) have shown impressive results on this task. However, for long videos with complex object motions and uncontrolled camera trajectories, these methods can produce blurry or inaccurate renderings, hampering their use in real-world applications. Instead of encoding the entire dynamic scene within the weights of MLPs, we present a new approach that addresses these limitations by adopting a volumetric image-based rendering framework that synthesizes new viewpoints by aggregating features from nearby views in a scene-motion-aware manner. Our system retains the advantages of prior methods in its ability to model complex scenes and view-dependent effects, but also enables synthesizing photo-realistic novel views from long videos featuring complex scene dynamics with unconstrained camera trajectories. We demonstrate significant improvements over state-of-the-art methods on dynamic scene datasets, and also apply our approach to in-the-wild videos with challenging camera and object motion, where prior methods fail to produce high-quality renderings. Our project webpage is at dynibar.github.io.

We introduce a new type of foundational model for parsing human anatomy in medical images that works for different modalities. It supports supervised or unsupervised training and can perform matching, registration, classification, or segmentation with or without user interaction. We achieve this by training a neural network estimator that maps query locations to atlas coordinates via regression. Efficiency is improved by sparsely sampling the input, enabling response times of less than 1 ms without additional accelerator hardware. We demonstrate the utility of the algorithm in both CT and MRI modalities.

Surface analysis of the cortex is ubiquitous in human neuroimaging with MRI, e.g., for cortical registration, parcellation, or thickness estimation. The convoluted cortical geometry requires isotropic scans (e.g., 1mm MPRAGEs) and good gray-white matter contrast for 3D reconstruction. This precludes the analysis of most brain MRI scans acquired for clinical purposes. Analyzing such scans would enable neuroimaging studies with sample sizes that cannot be achieved with current research datasets, particularly for underrepresented populations and rare diseases. Here we present the first method for cortical reconstruction, registration, parcellation, and thickness estimation for clinical brain MRI scans of any resolution and pulse sequence. The methods has a learning component and a classical optimization module. The former uses domain randomization to train a CNN that predicts an implicit representation of the white matter and pial surfaces (a signed distance function) at 1mm isotropic resolution, independently of the pulse sequence and resolution of the input. The latter uses geometry processing to place the surfaces while accurately satisfying topological and geometric constraints, thus enabling subsequent parcellation and thickness estimation with existing methods. We present results on 5mm axial FLAIR scans from ADNI and on a highly heterogeneous clinical dataset with 5,000 scans. Code and data are publicly available at https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical

Subsampling is commonly used to mitigate costs associated with data acquisition, such as time or energy requirements, motivating the development of algorithms for estimating the fully-sampled signal of interest x from partially observed measurements y. In maximum-entropy sampling, one selects measurement locations that are expected to have the highest entropy, so as to minimize uncertainty about x. This approach relies on an accurate model of the posterior distribution over future measurements, given the measurements observed so far. Recently, diffusion models have been shown to produce high-quality posterior samples of high-dimensional signals using guided diffusion. In this work, we propose Active Diffusion Subsampling (ADS), a method for performing active subsampling using guided diffusion in which the model tracks a distribution of beliefs over the true state of x throughout the reverse diffusion process, progressively decreasing its uncertainty by choosing to acquire measurements with maximum expected entropy, and ultimately generating the posterior distribution p(x | y). ADS can be applied using pre-trained diffusion models for any subsampling rate, and does not require task-specific retraining - just the specification of a measurement model. Furthermore, the maximum entropy sampling policy employed by ADS is interpretable, enhancing transparency relative to existing methods using black-box policies. Experimentally, we show that ADS outperforms fixed sampling strategies, and study an application of ADS in Magnetic Resonance Imaging acceleration using the fastMRI dataset, finding that ADS performs competitively with supervised methods. Code available at https://active-diffusion-subsampling.github.io/.

Dynamic novel view synthesis aims to capture the temporal evolution of visual content within videos. Existing methods struggle to distinguishing between motion and structure, particularly in scenarios where camera poses are either unknown or constrained compared to object motion. Furthermore, with information solely from reference images, it is extremely challenging to hallucinate unseen regions that are occluded or partially observed in the given videos. To address these issues, we first finetune a pretrained RGB-D diffusion model on the video frames using a customization technique. Subsequently, we distill the knowledge from the finetuned model to a 4D representations encompassing both dynamic and static Neural Radiance Fields (NeRF) components. The proposed pipeline achieves geometric consistency while preserving the scene identity. We perform thorough experiments to evaluate the efficacy of the proposed method qualitatively and quantitatively. Our results demonstrate the robustness and utility of our approach in challenging cases, further advancing dynamic novel view synthesis.

Sparse-view 3D CT reconstruction aims to recover volumetric structures from a limited number of 2D X-ray projections. Existing feedforward methods are constrained by the scarcity of large-scale training datasets and the absence of direct and consistent 3D representations. In this paper, we propose an X-ray Large Reconstruction Model (X-LRM) for extremely sparse-view (<10 views) CT reconstruction. X-LRM consists of two key components: X-former and X-triplane. X-former can handle an arbitrary number of input views using an MLP-based image tokenizer and a Transformer-based encoder. The output tokens are then upsampled into our X-triplane representation, which models the 3D radiodensity as an implicit neural field. To support the training of X-LRM, we introduce Torso-16K, a large-scale dataset comprising over 16K volume-projection pairs of various torso organs. Extensive experiments demonstrate that X-LRM outperforms the state-of-the-art method by 1.5 dB and achieves 27times faster speed with better flexibility. Furthermore, the evaluation of lung segmentation tasks also suggests the practical value of our approach. Our code and dataset will be released at https://github.com/Richard-Guofeng-Zhang/X-LRM

Purpose: Magnetic resonance imaging (MRI) to visualize anatomical motion is becoming increasingly important when treating cancer patients with radiotherapy. Hybrid MRI-linear accelerator (MRI-linac) systems allow real-time motion management during irradiation. This paper presents a multi-institutional real-time MRI time series dataset from different MRI-linac vendors. The dataset is designed to support developing and evaluating real-time tumor localization (tracking) algorithms for MRI-guided radiotherapy within the TrackRAD2025 challenge (https://trackrad2025.grand-challenge.org/). Acquisition and validation methods: The dataset consists of sagittal 2D cine MRIs in 585 patients from six centers (3 Dutch, 1 German, 1 Australian, and 1 Chinese). Tumors in the thorax, abdomen, and pelvis acquired on two commercially available MRI-linacs (0.35 T and 1.5 T) were included. For 108 cases, irradiation targets or tracking surrogates were manually segmented on each temporal frame. The dataset was randomly split into a public training set of 527 cases (477 unlabeled and 50 labeled) and a private testing set of 58 cases (all labeled). Data Format and Usage Notes: The data is publicly available under the TrackRAD2025 collection: https://doi.org/10.57967/hf/4539. Both the images and segmentations for each patient are available in metadata format. Potential Applications: This novel clinical dataset will enable the development and evaluation of real-time tumor localization algorithms for MRI-guided radiotherapy. By enabling more accurate motion management and adaptive treatment strategies, this dataset has the potential to advance the field of radiotherapy significantly.

Mixture of Experts (MoE) models scale capacity but often suffer from representation collapse and gradient instability. We propose Dynamic Subspace Composition (DSC), a framework that approximates context-dependent weights via a state-dependent, sparse expansion of a shared basis bank. Formally, DSC models the weight update as a residual trajectory within a Star- Shaped Domain, employing a Magnitude-Gated Simplex Interpolation to ensure continuity at the identity. Unlike standard Mixture-of-LoRAs, which incurs O(M rd) parameter complexity by retrieving independent rank-r matrices, DSC constructs a compositional rank-K approximation from decoupled unit-norm basis vectors. This reduces parameter complexity to O(M d) and memory traffic to O(Kd), while Frame-Theoretic regularization and spectral constraints provide rigorous worst-case bounds on the dynamic update. The code is available at https://github. com/VladimerKhasia/DSC

Unsupervised learning of object-centric representations in dynamic visual scenes is challenging. Unlike most previous approaches that learn to decompose 2D images, we present DynaVol, a 3D scene generative model that unifies geometric structures and object-centric learning in a differentiable volume rendering framework. The key idea is to perform object-centric voxelization to capture the 3D nature of the scene, which infers the probability distribution over objects at individual spatial locations. These voxel features evolve over time through a canonical-space deformation function, forming the basis for global representation learning via slot attention. The voxel features and global features are complementary and are both leveraged by a compositional NeRF decoder for volume rendering. DynaVol remarkably outperforms existing approaches for unsupervised dynamic scene decomposition. Once trained, the explicitly meaningful voxel features enable additional capabilities that 2D scene decomposition methods cannot achieve: it is possible to freely edit the geometric shapes or manipulate the motion trajectories of the objects.

Reconstructing dynamic 4D scenes remains challenging due to the presence of moving objects that corrupt camera pose estimation. Existing optimization methods alleviate this issue with additional supervision, but they are mostly computationally expensive and impractical in real-time applications. To address these limitations, we propose MoRe, a feedforward 4D reconstruction network that efficiently recovers dynamic 3D scenes from monocular videos. Built upon a strong static reconstruction backbone, MoRe employs an attention-forcing strategy to disentangle dynamic motion from static structure. To further enhance robustness, we fine-tune the model on large-scale, diverse datasets encompassing both dynamic and static scenes. Moreover, our grouped causal attention captures temporal dependencies and adapts to varying token lengths across frames, ensuring temporally coherent geometry reconstruction. Extensive experiments on multiple benchmarks demonstrate that MoRe achieves high-quality dynamic reconstructions with exceptional efficiency.

Despite the ever-increasing interest in applying deep learning (DL) models to medical imaging, the typical scarcity and imbalance of medical datasets can severely impact the performance of DL models. The generation of synthetic data that might be freely shared without compromising patient privacy is a well-known technique for addressing these difficulties. Inpainting algorithms are a subset of DL generative models that can alter one or more regions of an input image while matching its surrounding context and, in certain cases, non-imaging input conditions. Although the majority of inpainting techniques for medical imaging data use generative adversarial networks (GANs), the performance of these algorithms is frequently suboptimal due to their limited output variety, a problem that is already well-known for GANs. Denoising diffusion probabilistic models (DDPMs) are a recently introduced family of generative networks that can generate results of comparable quality to GANs, but with diverse outputs. In this paper, we describe a DDPM to execute multiple inpainting tasks on 2D axial slices of brain MRI with various sequences, and present proof-of-concept examples of its performance in a variety of evaluation scenarios. Our model and a public online interface to try our tool are available at: https://github.com/Mayo-Radiology-Informatics-Lab/MBTI

In medical imaging, the diffusion models have shown great potential in synthetic image generation tasks. However, these models often struggle with the interpretable connections between the generated and existing images and could create illusions. To address these challenges, our research proposes a novel diffusion-based generative model based on deformation diffusion and recovery. This model, named Deformation-Recovery Diffusion Model (DRDM), diverges from traditional score/intensity and latent feature-based approaches, emphasizing morphological changes through deformation fields rather than direct image synthesis. This is achieved by introducing a topological-preserving deformation field generation method, which randomly samples and integrates a set of multi-scale Deformation Vector Fields (DVF). DRDM is trained to learn to recover unreasonable deformation components, thereby restoring each randomly deformed image to a realistic distribution. These innovations facilitate the generation of diverse and anatomically plausible deformations, enhancing data augmentation and synthesis for further analysis in downstream tasks, such as few-shot learning and image registration. Experimental results in cardiac MRI and pulmonary CT show DRDM is capable of creating diverse, large (over 10\% image size deformation scale), and high-quality (negative rate of the Jacobian matrix's determinant is lower than 1\%) deformation fields. The further experimental results in downstream tasks, 2D image segmentation and 3D image registration, indicate significant improvements resulting from DRDM, showcasing the potential of our model to advance image manipulation and synthesis in medical imaging and beyond. Project page: https://jianqingzheng.github.io/def_diff_rec/

Dense 3D reconstruction from RGB images traditionally assumes static camera pose estimates. This assumption has endured, even as recent works have increasingly focused on real-time methods for mobile devices. However, the assumption of a fixed pose for each image does not hold for online execution: poses from real-time SLAM are dynamic and may be updated following events such as bundle adjustment and loop closure. This has been addressed in the RGB-D setting, by de-integrating past views and re-integrating them with updated poses, but it remains largely untreated in the RGB-only setting. We formalize this problem to define the new task of dense online reconstruction from dynamically-posed images. To support further research, we introduce a dataset called LivePose containing the dynamic poses from a SLAM system running on ScanNet. We select three recent reconstruction systems and apply a framework based on de-integration to adapt each one to the dynamic-pose setting. In addition, we propose a novel, non-linear de-integration module that learns to remove stale scene content. We show that responding to pose updates is critical for high-quality reconstruction, and that our de-integration framework is an effective solution.

Multimodal MR image synthesis aims to generate missing modality images by effectively fusing and mapping from a subset of available MRI modalities. Most existing methods adopt an image-to-image translation paradigm, treating multiple modalities as input channels. However, these approaches often yield sub-optimal results due to the inherent difficulty in achieving precise feature- or semantic-level alignment across modalities. To address these challenges, we propose an Adaptive Group-wise Interaction Network (AGI-Net) that explicitly models both inter-modality and intra-modality relationships for multimodal MR image synthesis. Specifically, feature channels are first partitioned into predefined groups, after which an adaptive rolling mechanism is applied to conventional convolutional kernels to better capture feature and semantic correspondences between different modalities. In parallel, a cross-group attention module is introduced to enable effective feature fusion across groups, thereby enhancing the network's representational capacity. We validate the proposed AGI-Net on the publicly available IXI and BraTS2023 datasets. Experimental results demonstrate that AGI-Net achieves state-of-the-art performance in multimodal MR image synthesis tasks, confirming the effectiveness of its modality-aware interaction design. We release the relevant code at: https://github.com/zunzhumu/Adaptive-Group-wise-Interaction-Network-for-Multimodal-MRI-Synthesis.git.

Many natural dynamic processes -- such as in vivo cellular differentiation or disease progression -- can only be observed through the lens of static sample snapshots. While challenging, reconstructing their temporal evolution to decipher underlying dynamic properties is of major interest to scientific research. Existing approaches enable data transport along a temporal axis but are poorly scalable in high dimension and require restrictive assumptions to be met. To address these issues, we propose \textbf{Multi-Marginal temporal Schr\"odinger Bridge Matching} (MMtSBM) for video generation from unpaired data, extending the theoretical guarantees and empirical efficiency of Diffusion Schr\"odinger Bridge Matching (arXiv:archive/2303.16852) by deriving the Iterative Markovian Fitting algorithm to multiple marginals in a novel factorized fashion. Experiments show that MMtSBM retains theoretical properties on toy examples, achieves state-of-the-art performance on real world datasets such as transcriptomic trajectory inference in 100 dimensions, and for the first time recovers couplings and dynamics in very high dimensional image settings. Our work establishes multi-marginal Schr\"odinger bridges as a practical and principled approach for recovering hidden dynamics from static data.

High dynamic range (HDR) imaging aims to retrieve information from multiple low-dynamic range inputs to generate realistic output. The essence is to leverage the contextual information, including both dynamic and static semantics, for better image generation. Existing methods often focus on the spatial misalignment across input frames caused by the foreground and/or camera motion. However, there is no research on jointly leveraging the dynamic and static context in a simultaneous manner. To delve into this problem, we propose a novel alignment-free network with a Semantics Consistent Transformer (SCTNet) with both spatial and channel attention modules in the network. The spatial attention aims to deal with the intra-image correlation to model the dynamic motion, while the channel attention enables the inter-image intertwining to enhance the semantic consistency across frames. Aside from this, we introduce a novel realistic HDR dataset with more variations in foreground objects, environmental factors, and larger motions. Extensive comparisons on both conventional datasets and ours validate the effectiveness of our method, achieving the best trade-off on the performance and the computational cost.

High-resolution (HR) medical videos are vital for accurate diagnosis, yet are hard to acquire due to hardware limitations and physiological constraints. Clinically, the collected low-resolution (LR) medical videos present unique challenges for video super-resolution (VSR) models, including camera shake, noise, and abrupt frame transitions, which result in significant optical flow errors and alignment difficulties. Additionally, tissues and organs exhibit continuous and nuanced structures, but current VSR models are prone to introducing artifacts and distorted features that can mislead doctors. To this end, we propose MedVSR, a tailored framework for medical VSR. It first employs Cross State-Space Propagation (CSSP) to address the imprecise alignment by projecting distant frames as control matrices within state-space models, enabling the selective propagation of consistent and informative features to neighboring frames for effective alignment. Moreover, we design an Inner State-Space Reconstruction (ISSR) module that enhances tissue structures and reduces artifacts with joint long-range spatial feature learning and large-kernel short-range information aggregation. Experiments across four datasets in diverse medical scenarios, including endoscopy and cataract surgeries, show that MedVSR significantly outperforms existing VSR models in reconstruction performance and efficiency. Code released at https://github.com/CUHK-AIM-Group/MedVSR.

We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.

Respiratory motion complicates accurate irradiation of thoraco-abdominal tumors during radiotherapy, as treatment-system latency entails target-location uncertainties. This work addresses frame forecasting in chest and liver cine MRI to compensate for such delays. We investigate RNNs trained with online learning algorithms, enabling adaptation to changing respiratory patterns via on-the-fly parameter updates, and transformers, increasingly common in time-series forecasting for their ability to capture long-term dependencies. Experiments used 12 sagittal thoracic and upper-abdominal cine-MRI sequences from ETH Zürich and OvGU; the OvGU data exhibited higher motion variability, noise, and lower contrast. PCA decomposes the Lucas-Kanade optical-flow field into static deformation modes and low-dimensional, time-dependent weights. We compare various methods for forecasting these weights: linear filters, population and sequence-specific transformer encoders, and RNNs trained with real-time recurrent learning (RTRL), unbiased online recurrent optimization, decoupled neural interfaces, and sparse one-step approximation (SnAp-1). Predicted displacements were used to warp the reference frame and generate future images. Prediction accuracy decreased with the horizon h. Linear regression performed best at short horizons (1.3mm geometrical error at h=0.32s, ETH Zürich dataset), while RTRL and SnAp-1 outperformed the other algorithms at medium-to-long horizons, with geometrical errors below 1.4mm and 2.8mm on the sequences from ETH Zürich and OvGU, respectively. The sequence-specific transformer was competitive for low-to-medium horizons, but transformers remained overall limited by data scarcity and domain shift between datasets. Predicted frames visually resembled the ground truth, with notable errors occurring near the diaphragm at end-inspiration and regions affected by out-of-plane motion.