Daily Papers

Non-ideal measurement computed tomography (NICT), which sacrifices optimal imaging standards for new advantages in CT imaging, is expanding the clinical application scope of CT images. However, with the reduction of imaging standards, the image quality has also been reduced, extremely limiting the clinical acceptability. Although numerous studies have demonstrated the feasibility of deep learning for the NICT enhancement in specific scenarios, their high data cost and limited generalizability have become large obstacles. The recent research on the foundation model has brought new opportunities for building a universal NICT enhancement model - bridging the image quality degradation with minimal data cost. However, owing to the challenges in the collection of large pre-training datasets and the compatibility of data variation, no success has been reported. In this paper, we propose a multi-scale integrated Transformer AMPlifier (TAMP), the first imaging foundation model for universal NICT enhancement. It has been pre-trained on a large-scale physical-driven simulation dataset with 3.6 million NICT-ICT image pairs, and is able to directly generalize to the NICT enhancement tasks with various non-ideal settings and body regions. Via the adaptation with few data, it can further achieve professional performance in real-world specific scenarios. Our extensive experiments have demonstrated that the proposed TAMP has significant potential for promoting the exploration and application of NICT and serving a wider range of medical scenarios.

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.

Computed tomography (CT) serves as an effective tool for lung cancer screening, diagnosis, treatment, and prognosis, providing a rich source of features to quantify temporal and spatial tumor changes. Nonetheless, the diversity of CT scanners and customized acquisition protocols can introduce significant inconsistencies in texture features, even when assessing the same patient. This variability poses a fundamental challenge for subsequent research that relies on consistent image features. Existing CT image standardization models predominantly utilize GAN-based supervised or semi-supervised learning, but their performance remains limited. We present DiffusionCT, an innovative score-based DDPM model that operates in the latent space to transform disparate non-standard distributions into a standardized form. The architecture comprises a U-Net-based encoder-decoder, augmented by a DDPM model integrated at the bottleneck position. First, the encoder-decoder is trained independently, without embedding DDPM, to capture the latent representation of the input data. Second, the latent DDPM model is trained while keeping the encoder-decoder parameters fixed. Finally, the decoder uses the transformed latent representation to generate a standardized CT image, providing a more consistent basis for downstream analysis. Empirical tests on patient CT images indicate notable improvements in image standardization using DiffusionCT. Additionally, the model significantly reduces image noise in SPAD images, further validating the effectiveness of DiffusionCT for advanced imaging tasks.

Diffusion models have recently emerged as powerful priors for solving inverse problems. While computed tomography (CT) is theoretically a linear inverse problem, it poses many practical challenges. These include correlated noise, artifact structures, reliance on system geometry, and misaligned value ranges, which make the direct application of diffusion models more difficult than in domains like natural image generation. To systematically evaluate how diffusion models perform in this context and compare them with established reconstruction methods, we introduce DM4CT, a comprehensive benchmark for CT reconstruction. DM4CT includes datasets from both medical and industrial domains with sparse-view and noisy configurations. To explore the challenges of deploying diffusion models in practice, we additionally acquire a high-resolution CT dataset at a high-energy synchrotron facility and evaluate all methods under real experimental conditions. We benchmark ten recent diffusion-based methods alongside seven strong baselines, including model-based, unsupervised, and supervised approaches. Our analysis provides detailed insights into the behavior, strengths, and limitations of diffusion models for CT reconstruction. The real-world dataset is publicly available at zenodo.org/records/15420527, and the codebase is open-sourced at github.com/DM4CT/DM4CT.

Widely adopted evaluation metrics for sparse-view CT reconstruction--such as Structural Similarity Index Measure and Peak Signal-to-Noise Ratio--prioritize pixel-wise fidelity but often fail to capture the completeness of critical anatomical structures, particularly small or thin regions that are easily missed. To address this limitation, we propose a suite of novel anatomy-aware evaluation metrics designed to assess structural completeness across anatomical structures, including large organs, small organs, intestines, and vessels. Building on these metrics, we introduce CARE, a Completeness-Aware Reconstruction Enhancement framework that incorporates structural penalties during training to encourage anatomical preservation of significant structures. CARE is model-agnostic and can be seamlessly integrated into analytical, implicit, and generative methods. When applied to these methods, CARE substantially improves structural completeness in CT reconstructions, achieving up to +32% improvement for large organs, +22% for small organs, +40% for intestines, and +36% for vessels.

The rapid increase of computed tomography (CT) scans and their time-consuming manual analysis have created an urgent need for robust automated analysis techniques in clinical settings. These aim to assist radiologists and help them managing their growing workload. Existing methods typically generate entire reports directly from 3D CT images, without explicitly focusing on observed abnormalities. This unguided approach often results in repetitive content or incomplete reports, failing to prioritize anomaly-specific descriptions. We propose a new anomaly-guided report generation model, which first predicts abnormalities and then generates targeted descriptions for each. Evaluation on a public dataset demonstrates significant improvements in report quality and clinical relevance. We extend our work by conducting an ablation study to demonstrate its effectiveness.

Conventional Computed Tomography (CT) methods require large numbers of noise-free projections for accurate density reconstructions, limiting their applicability to the more complex class of Cone Beam Geometry CT (CBCT) reconstruction. Recently, deep learning methods have been proposed to overcome these limitations, with methods based on neural fields (NF) showing strong performance, by approximating the reconstructed density through a continuous-in-space coordinate based neural network. Our focus is on improving such methods, however, unlike previous work, which requires training an NF from scratch for each new set of projections, we instead propose to leverage anatomical consistencies over different scans by training a single conditional NF on a dataset of projections. We propose a novel conditioning method where local modulations are modeled per patient as a field over the input domain through a Neural Modulation Field (NMF). The resulting Conditional Cone Beam Neural Tomography (CondCBNT) shows improved performance for both high and low numbers of available projections on noise-free and noisy data.

Bone density prediction via CT scans to estimate T-scores is crucial, providing a more precise assessment of bone health compared to traditional methods like X-ray bone density tests, which lack spatial resolution and the ability to detect localized changes. However, CT-based prediction faces two major challenges: the high computational complexity of transformer-based architectures, which limits their deployment in portable and clinical settings, and the imbalanced, long-tailed distribution of real-world hospital data that skews predictions. To address these issues, we introduce MedConv, a convolutional model for bone density prediction that outperforms transformer models with lower computational demands. We also adapt Bal-CE loss and post-hoc logit adjustment to improve class balance. Extensive experiments on our AustinSpine dataset shows that our approach achieves up to 21% improvement in accuracy and 20% in ROC AUC over previous state-of-the-art methods.

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (>0.87/0.90) and gamma pass rates for photon (>98.1%/99.0%) and proton (>99.0%/97.3%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy.

This paper presents a comprehensive evaluation of GPT-4V's capabilities across diverse medical imaging tasks, including Radiology Report Generation, Medical Visual Question Answering (VQA), and Visual Grounding. While prior efforts have explored GPT-4V's performance in medical image analysis, to the best of our knowledge, our study represents the first quantitative evaluation on publicly available benchmarks. Our findings highlight GPT-4V's potential in generating descriptive reports for chest X-ray images, particularly when guided by well-structured prompts. Meanwhile, its performance on the MIMIC-CXR dataset benchmark reveals areas for improvement in certain evaluation metrics, such as CIDEr. In the domain of Medical VQA, GPT-4V demonstrates proficiency in distinguishing between question types but falls short of the VQA-RAD benchmark in terms of accuracy. Furthermore, our analysis finds the limitations of conventional evaluation metrics like the BLEU scores, advocating for the development of more semantically robust assessment methods. In the field of Visual Grounding, GPT-4V exhibits preliminary promise in recognizing bounding boxes, but its precision is lacking, especially in identifying specific medical organs and signs. Our evaluation underscores the significant potential of GPT-4V in the medical imaging domain, while also emphasizing the need for targeted refinements to fully unlock its capabilities.

Accurate classification of computed tomography (CT) images is essential for diagnosis and treatment planning, but existing methods often struggle with the subtle and spatially diverse nature of pathological features. Current approaches typically process images uniformly, limiting their ability to detect localized abnormalities that require focused analysis. We introduce UGPL, an uncertainty-guided progressive learning framework that performs a global-to-local analysis by first identifying regions of diagnostic ambiguity and then conducting detailed examination of these critical areas. Our approach employs evidential deep learning to quantify predictive uncertainty, guiding the extraction of informative patches through a non-maximum suppression mechanism that maintains spatial diversity. This progressive refinement strategy, combined with an adaptive fusion mechanism, enables UGPL to integrate both contextual information and fine-grained details. Experiments across three CT datasets demonstrate that UGPL consistently outperforms state-of-the-art methods, achieving improvements of 3.29%, 2.46%, and 8.08% in accuracy for kidney abnormality, lung cancer, and COVID-19 detection, respectively. Our analysis shows that the uncertainty-guided component provides substantial benefits, with performance dramatically increasing when the full progressive learning pipeline is implemented. Our code is available at: https://github.com/shravan-18/UGPL

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.

Multimodal large language models (MLLMs) have achieved significant success in the general field of image processing. Their emerging task generalization and freeform conversational capabilities can greatly facilitate medical diagnostic assistance, helping patients better understand their conditions and enhancing doctor-patient trust. Computed Tomography (CT) is a non-invasive imaging technique used to capture the internal mechanisms of a patient's condition and is widely utilized. However, in past research, the complex textural features of this imaging data have made accurate interpretation by algorithms challenging, impeding the performance of general LLMs in diagnostic assistance. To address this, we developed OrthoDoc, a MLLM designed for CT diagnostics. OrthoDoc is trained on 120,000 CT images and diagnostic reports and includes a Retrieval-Augmented Generation (RAG) module capable of effectively mitigating model hallucinations. This module is informed by extensive medical literature, textbooks, and explanatory data. Thus, OrthoDoc not only processes complex CT images but also stores, understands, and reasons over medical knowledge and language. In extensive experiments, OrthoDoc outperforms commercial models led by GPT-4, demonstrating superior diagnostic capabilities and accuracy. Specifically, OrthoDoc significantly surpasses existing models in the diagnosis of common orthopedic conditions such as fractures, arthritis, and tumors. Additionally, OrthoDoc exhibits robust generalization and stability when handling rare and complex cases.

This study presents the development of a spatially adaptive weighting strategy for Total Variation regularization, aimed at addressing under-determined linear inverse problems. The method leverages the rapid computation of an accurate approximation of the true image (or its gradient magnitude) through a neural network. Our approach operates without requiring prior knowledge of the noise intensity in the data and avoids the iterative recomputation of weights. Additionally, the paper includes a theoretical analysis of the proposed method, establishing its validity as a regularization approach. This framework integrates advanced neural network capabilities within a regularization context, thereby making the results of the networks interpretable. The results are promising as they enable high-quality reconstructions from limited-view tomographic measurements.

This paper proposes a new two-step procedure for sparse-view tomographic image reconstruction. It is called RISING, since it combines an early-stopped Rapid Iterative Solver with a subsequent Iteration Network-based Gaining step. So far, regularized iterative methods have widely been used for X-ray computed tomography image reconstruction from low-sampled data, since they converge to a sparse solution in a suitable domain, as upheld by the Compressed Sensing theory. Unfortunately, their use is practically limited by their high computational cost which imposes to perform only a few iterations in the available time for clinical exams. Data-driven methods, using neural networks to post-process a coarse and noisy image obtained from geometrical algorithms, have been recently studied and appreciated for both their computational speed and accurate reconstructions. However, there is no evidence, neither theoretically nor numerically, that neural networks based algorithms solve the mathematical inverse problem modeling the tomographic reconstruction process. In our two-step approach, the first phase executes very few iterations of a regularized model-based algorithm whereas the second step completes the missing iterations by means of a neural network. The resulting hybrid deep-variational framework preserves the convergence properties of the iterative method and, at the same time, it exploits the computational speed and flexibility of a data-driven approach. Experiments performed on a simulated and a real data set confirm the numerical and visual accuracy of the reconstructed RISING images in short computational times.

This paper focuses on the development of a space-variant regularization model for solving an under-determined linear inverse problem. The case study is a medical image reconstruction from few-view tomographic noisy data. The primary objective of the proposed optimization model is to achieve a good balance between denoising and the preservation of fine details and edges, overcoming the performance of the popular and largely used Total Variation (TV) regularization through the application of appropriate pixel-dependent weights. The proposed strategy leverages the role of gradient approximations for the computation of the space-variant TV weights. For this reason, a convolutional neural network is designed, to approximate both the ground truth image and its gradient using an elastic loss function in its training. Additionally, the paper provides a theoretical analysis of the proposed model, showing the uniqueness of its solution, and illustrates a Chambolle-Pock algorithm tailored to address the specific problem at hand. This comprehensive framework integrates innovative regularization techniques with advanced neural network capabilities, demonstrating promising results in achieving high-quality reconstructions from low-sampled tomographic data.

Purpose: Medical imaging has become increasingly important in diagnosing and treating oncological patients, particularly in radiotherapy. Recent advances in synthetic computed tomography (sCT) generation have increased interest in public challenges to provide data and evaluation metrics for comparing different approaches openly. This paper describes a dataset of brain and pelvis computed tomography (CT) images with rigidly registered CBCT and MRI images to facilitate the development and evaluation of sCT generation for radiotherapy planning. Acquisition and validation methods: The dataset consists of CT, CBCT, and MRI of 540 brains and 540 pelvic radiotherapy patients from three Dutch university medical centers. Subjects' ages ranged from 3 to 93 years, with a mean age of 60. Various scanner models and acquisition settings were used across patients from the three data-providing centers. Details are available in CSV files provided with the datasets. Data format and usage notes: The data is available on Zenodo (https://doi.org/10.5281/zenodo.7260705) under the SynthRAD2023 collection. The images for each subject are available in nifti format. Potential applications: This dataset will enable the evaluation and development of image synthesis algorithms for radiotherapy purposes on a realistic multi-center dataset with varying acquisition protocols. Synthetic CT generation has numerous applications in radiation therapy, including diagnosis, treatment planning, treatment monitoring, and surgical planning.

Many low-dose CT imaging methods rely on supervised learning, which requires a large number of paired noisy and clean images. However, obtaining paired images in clinical practice is challenging. To address this issue, zero-shot self-supervised methods train denoising networks using only the information within a single image, such as ZS-N2N. However, these methods often employ downsampling operations that degrade image resolution. Additionally, the training dataset is inherently constrained to the image itself. In this paper, we propose a zero-shot low-dose CT imaging method based on sinogram flicking, which operates within a single image but generates many copies via random conjugate ray matching. Specifically, two conjugate X-ray pencil beams measure the same path; their expected values should be identical, while their noise levels vary during measurements. By randomly swapping portions of the conjugate X-rays in the sinogram domain, we generate a large set of sinograms with consistent content but varying noise patterns. When displayed dynamically, these sinograms exhibit a flickering effect due to their identical structural content but differing noise patterns-hence the term sinogram flicking. We train the network on pairs of sinograms with the same content but different noise distributions using a lightweight model adapted from ZS-NSN. This process is repeated to obtain the final results. A simulation study demonstrates that our method outperforms state-of-the-art approaches such as ZS-N2N.

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.

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. Project website at: https://x2-gaussian.github.io/.

Objective: While recent advances in text-conditioned generative models have enabled the synthesis of realistic medical images, progress has been largely confined to 2D modalities such as chest X-rays. Extending text-to-image generation to volumetric Computed Tomography (CT) remains a significant challenge, due to its high dimensionality, anatomical complexity, and the absence of robust frameworks that align vision-language data in 3D medical imaging. Methods: We introduce a novel architecture for Text-to-CT generation that combines a latent diffusion model with a 3D contrastive vision-language pretraining scheme. Our approach leverages a dual-encoder CLIP-style model trained on paired CT volumes and radiology reports to establish a shared embedding space, which serves as the conditioning input for generation. CT volumes are compressed into a low-dimensional latent space via a pretrained volumetric VAE, enabling efficient 3D denoising diffusion without requiring external super-resolution stages. Results: We evaluate our method on the CT-RATE dataset and conduct a comprehensive assessment of image fidelity, clinical relevance, and semantic alignment. Our model achieves competitive performance across all tasks, significantly outperforming prior baselines for text-to-CT generation. Moreover, we demonstrate that CT scans synthesized by our framework can effectively augment real data, improving downstream diagnostic performance. Conclusion: Our results show that modality-specific vision-language alignment is a key component for high-quality 3D medical image generation. By integrating contrastive pretraining and volumetric diffusion, our method offers a scalable and controllable solution for synthesizing clinically meaningful CT volumes from text, paving the way for new applications in data augmentation, medical education, and automated clinical simulation.

Score-based generative modeling, informally referred to as diffusion models, continue to grow in popularity across several important domains and tasks. While they provide high-quality and diverse samples from empirical distributions, important questions remain on the reliability and trustworthiness of these sampling procedures for their responsible use in critical scenarios. Conformal prediction is a modern tool to construct finite-sample, distribution-free uncertainty guarantees for any black-box predictor. In this work, we focus on image-to-image regression tasks and we present a generalization of the Risk-Controlling Prediction Sets (RCPS) procedure, that we term K-RCPS, which allows to (i) provide entrywise calibrated intervals for future samples of any diffusion model, and (ii) control a certain notion of risk with respect to a ground truth image with minimal mean interval length. Differently from existing conformal risk control procedures, ours relies on a novel convex optimization approach that allows for multidimensional risk control while provably minimizing the mean interval length. We illustrate our approach on two real-world image denoising problems: on natural images of faces as well as on computed tomography (CT) scans of the abdomen, demonstrating state of the art performance.

Deep learning has become the state-of-the-art approach to medical tomographic imaging. A common approach is to feed the result of a simple inversion, for example the backprojection, to a multiscale convolutional neural network (CNN) which computes the final reconstruction. Despite good results on in-distribution test data, this often results in overfitting certain large-scale structures and poor generalization on out-of-distribution (OOD) samples. Moreover, the memory and computational complexity of multiscale CNNs scale unfavorably with image resolution, making them impractical for application at realistic clinical resolutions. In this paper, we introduce Glimpse, a local coordinate-based neural network for computed tomography which reconstructs a pixel value by processing only the measurements associated with the neighborhood of the pixel. Glimpse significantly outperforms successful CNNs on OOD samples, while achieving comparable or better performance on in-distribution test data and maintaining a memory footprint almost independent of image resolution; 5GB memory suffices to train on 1024x1024 images which is orders of magnitude less than CNNs. Glimpse is fully differentiable and can be used plug-and-play in arbitrary deep learning architectures, enabling feats such as correcting miscalibrated projection orientations. Our implementation and Google Colab demo can be accessed at https://github.com/swing-research/Glimpse.

Generative modeling has experienced substantial progress in recent years, particularly in text-to-image and text-to-video synthesis. However, the medical field has not yet fully exploited the potential of large-scale foundational models for synthetic data generation. In this paper, we introduce GenerateCT, the first method for text-conditional computed tomography (CT) generation, addressing the limitations in 3D medical imaging research and making our entire framework open-source. GenerateCT consists of a pre-trained large language model, a transformer-based text-conditional 3D chest CT generation architecture, and a text-conditional spatial super-resolution diffusion model. We also propose CT-ViT, which efficiently compresses CT volumes while preserving auto-regressiveness in-depth, enabling the generation of 3D CT volumes with variable numbers of axial slices. Our experiments demonstrate that GenerateCT can produce realistic, high-resolution, and high-fidelity 3D chest CT volumes consistent with medical language text prompts. We further investigate the potential of GenerateCT by training a model using generated CT volumes for multi-abnormality classification of chest CT volumes. Our contributions provide a valuable foundation for future research in text-conditional 3D medical image generation and have the potential to accelerate advancements in medical imaging research. Our code, pre-trained models, and generated data are available at https://github.com/ibrahimethemhamamci/GenerateCT.

Lung cancer is the deadliest type of cancer worldwide and late detection is the major factor for the low survival rate of patients. Low dose computed tomography has been suggested as a potential screening tool but manual screening is costly, time-consuming and prone to variability. This has fueled the development of automatic methods for the detection, segmentation and characterisation of pulmonary nodules but its application to clinical routine is challenging. In this study, a new database for the development and testing of pulmonary nodule computer-aided strategies is presented which intends to complement current databases by giving additional focus to radiologist variability and local clinical reality. State-of-the-art nodule detection, segmentation and characterization methods are tested and compared to manual annotations as well as collaborative strategies combining multiple radiologists and radiologists and computer-aided systems. It is shown that state-of-the-art methodologies can determine a patient's follow-up recommendation as accurately as a radiologist, though the nodule detection method used shows decreased performance in this database.

This paper investigates the application of unsupervised learning methods for computed tomography (CT) reconstruction. To motivate our work, we review several existing priors, namely the truncated Gaussian prior, the l_1 prior, the total variation prior, and the deep image prior (DIP). We find that DIP outperforms the other three priors in terms of representational capability and visual performance. However, the performance of DIP deteriorates when the number of iterations exceeds a certain threshold due to overfitting. To address this issue, we propose a novel method (MCDIP-ADMM) based on Multi-Code Deep Image Prior and plug-and-play Alternative Direction Method of Multipliers. Specifically, MCDIP utilizes multiple latent codes to generate a series of feature maps at an intermediate layer within a generator model. These maps are then composed with trainable weights, representing the complete image prior. Experimental results demonstrate the superior performance of the proposed MCDIP-ADMM compared to three existing competitors. In the case of parallel beam projection with Gaussian noise, MCDIP-ADMM achieves an average improvement of 4.3 dB over DIP, 1.7 dB over ADMM DIP-WTV, and 1.2 dB over PnP-DIP in terms of PSNR. Similarly, for fan-beam projection with Poisson noise, MCDIP-ADMM achieves an average improvement of 3.09 dB over DIP, 1.86 dB over ADMM DIP-WTV, and 0.84 dB over PnP-DIP in terms of PSNR.

Medical report generation has achieved remarkable advancements yet has still been faced with several challenges. First, the inherent imbalance in the distribution of normal and abnormal cases may lead models to exhibit a biased focus on normal samples, resulting in unreliable diagnoses. Second, the frequent occurrence of common template sentences in the reports may overwhelm the critical abnormal information. Moreover, existing works focus on 2D chest X-rays, leaving CT report generation underexplored due to the high-dimensional nature of CT images and the limited availability of CT-report pairs. Recently, LLM has shown a great ability to generate reliable answers with appropriate prompts, which shed light on addressing the aforementioned challenges. In this paper, we propose Dia-LLaMA, a framework to adapt the LLaMA2-7B for CT report generation by incorporating diagnostic information as guidance prompts. Considering the high dimension of CT, we leverage a pre-trained ViT3D with perceiver to extract the visual information. To tailor the LLM for report generation and emphasize abnormality, we extract additional diagnostic information by referring to a disease prototype memory bank, which is updated during training to capture common disease representations. Furthermore, we introduce disease-aware attention to enable the model to adjust attention for different diseases. Experiments on the chest CT dataset demonstrated that our proposed method outperformed previous methods and achieved state-of-the-art on both clinical efficacy performance and natural language generation metrics. The code will be made publically available.

Full quantum tomography of high-dimensional quantum systems is experimentally infeasible due to the exponential scaling of the number of required measurements on the number of qubits in the system. However, several ideas were proposed recently for predicting the limited number of features for these states, or estimating the expectation values of operators, without the need for full state reconstruction. These ideas go under the general name of shadow tomography. Here we provide an experimental demonstration of property estimation based on classical shadows proposed in [H.-Y. Huang, R. Kueng, J. Preskill. Nat. Phys. https://doi.org/10.1038/s41567-020-0932-7 (2020)] and study its performance in the quantum optical experiment with high-dimensional spatial states of photons. We show on experimental data how this procedure outperforms conventional state reconstruction in fidelity estimation from a limited number of measurements.

Automated interpretation of CT images-particularly localizing and describing abnormal findings across multi-plane and whole-body scans-remains a significant challenge in clinical radiology. This work aims to address this challenge through four key contributions: (i) On taxonomy, we collaborate with senior radiologists to propose a comprehensive hierarchical classification system, with 404 representative abnormal findings across all body regions; (ii) On data, we contribute a dataset containing over 14.5K CT images from multiple planes and all human body regions, and meticulously provide grounding annotations for over 19K abnormalities, each linked to the detailed description and cast into the taxonomy; (iii) On model development, we propose OminiAbnorm-CT, which can automatically ground and describe abnormal findings on multi-plane and whole-body CT images based on text queries, while also allowing flexible interaction through visual prompts; (iv) On benchmarks, we establish three representative evaluation tasks based on real clinical scenarios. Through extensive experiments, we show that OminiAbnorm-CT can significantly outperform existing methods on all the tasks and metrics.

With an estimated 160,000 deaths in 2018, lung cancer is the most common cause of cancer death in the United States. Lung cancer CT screening has been shown to reduce mortality by up to 40% and is now included in US screening guidelines. Reducing the high error rates in lung cancer screening is imperative because of the high clinical and financial costs caused by diagnosis mistakes. Despite the use of standards for radiological diagnosis, persistent inter-grader variability and incomplete characterization of comprehensive imaging findings remain as limitations of current methods. These limitations suggest opportunities for more sophisticated systems to improve performance and inter-reader consistency. In this report, we reproduce a state-of-the-art deep learning algorithm for lung cancer risk prediction. Our model predicts malignancy probability and risk bucket classification from lung CT studies. This allows for risk categorization of patients being screened and suggests the most appropriate surveillance and management. Combining our solution high accuracy, consistency and fully automated nature, our approach may enable highly efficient screening procedures and accelerate the adoption of lung cancer screening.

Chest X-rays (CXRs) are commonly utilized as a low-dose modality for lung screening. Nonetheless, the efficacy of CXRs is somewhat impeded, given that approximately 75% of the lung area overlaps with bone, which in turn hampers the detection and diagnosis of diseases. As a remedial measure, bone suppression techniques have been introduced. The current dual-energy subtraction imaging technique in the clinic requires costly equipment and subjects being exposed to high radiation. To circumvent these issues, deep learning-based image generation algorithms have been proposed. However, existing methods fall short in terms of producing high-quality images and capturing texture details, particularly with pulmonary vessels. To address these issues, this paper proposes a new bone suppression framework, termed BS-Diff, that comprises a conditional diffusion model equipped with a U-Net architecture and a simple enhancement module to incorporate an autoencoder. Our proposed network cannot only generate soft tissue images with a high bone suppression rate but also possesses the capability to capture fine image details. Additionally, we compiled the largest dataset since 2010, including data from 120 patients with high-definition, high-resolution paired CXRs and soft tissue images collected by our affiliated hospital. Extensive experiments, comparative analyses, ablation studies, and clinical evaluations indicate that the proposed BS-Diff outperforms several bone-suppression models across multiple metrics. Our code can be accessed at https://github.com/Benny0323/BS-Diff.

Motion artefacts in magnetic resonance brain images can have a strong impact on diagnostic confidence. The assessment of MR image quality is fundamental before proceeding with the clinical diagnosis. Motion artefacts can alter the delineation of structures such as the brain, lesions or tumours and may require a repeat scan. Otherwise, an inaccurate (e.g. correct pathology but wrong severity) or incorrect diagnosis (e.g. wrong pathology) may occur. "Image quality assessment" as a fast, automated step right after scanning can assist in deciding if the acquired images are diagnostically sufficient. An automated image quality assessment based on the structural similarity index (SSIM) regression through a residual neural network is proposed in this work. Additionally, a classification into different groups - by subdividing with SSIM ranges - is evaluated. Importantly, this method predicts SSIM values of an input image in the absence of a reference ground truth image. The networks were able to detect motion artefacts, and the best performance for the regression and classification task has always been achieved with ResNet-18 with contrast augmentation. The mean and standard deviation of residuals' distribution were mu=-0.0009 and sigma=0.0139, respectively. Whilst for the classification task in 3, 5 and 10 classes, the best accuracies were 97, 95 and 89\%, respectively. The results show that the proposed method could be a tool for supporting neuro-radiologists and radiographers in evaluating image quality quickly.

In the radiation therapy of nasopharyngeal carcinoma (NPC), clinicians typically delineate the gross tumor volume (GTV) using non-contrast planning computed tomography to ensure accurate radiation dose delivery. However, the low contrast between tumors and adjacent normal tissues necessitates that radiation oncologists manually delineate the tumors, often relying on diagnostic MRI for guidance. % In this study, we propose a novel approach to directly segment NPC gross tumors on non-contrast planning CT images, circumventing potential registration errors when aligning MRI or MRI-derived tumor masks to planning CT. To address the low contrast issues between tumors and adjacent normal structures in planning CT, we introduce a 3D Semantic Asymmetry Tumor segmentation (SATs) method. Specifically, we posit that a healthy nasopharyngeal region is characteristically bilaterally symmetric, whereas the emergence of nasopharyngeal carcinoma disrupts this symmetry. Then, we propose a Siamese contrastive learning segmentation framework that minimizes the voxel-wise distance between original and flipped areas without tumor and encourages a larger distance between original and flipped areas with tumor. Thus, our approach enhances the sensitivity of features to semantic asymmetries. % Extensive experiments demonstrate that the proposed SATs achieves the leading NPC GTV segmentation performance in both internal and external testing, e.g., with at least 2\% absolute Dice score improvement and 12\% average distance error reduction when compared to other state-of-the-art methods in the external testing.

We present MInDI-3D (Medical Inversion by Direct Iteration in 3D), the first 3D conditional diffusion-based model for real-world sparse-view Cone Beam Computed Tomography (CBCT) artefact removal, aiming to reduce imaging radiation exposure. A key contribution is extending the "InDI" concept from 2D to a full 3D volumetric approach for medical images, implementing an iterative denoising process that refines the CBCT volume directly from sparse-view input. A further contribution is the generation of a large pseudo-CBCT dataset (16,182) from chest CT volumes of the CT-RATE public dataset to robustly train MInDI-3D. We performed a comprehensive evaluation, including quantitative metrics, scalability analysis, generalisation tests, and a clinical assessment by 11 clinicians. Our results show MInDI-3D's effectiveness, achieving a 12.96 (6.10) dB PSNR gain over uncorrected scans with only 50 projections on the CT-RATE pseudo-CBCT (independent real-world) test set and enabling an 8x reduction in imaging radiation exposure. We demonstrate its scalability by showing that performance improves with more training data. Importantly, MInDI-3D matches the performance of a 3D U-Net on real-world scans from 16 cancer patients across distortion and task-based metrics. It also generalises to new CBCT scanner geometries. Clinicians rated our model as sufficient for patient positioning across all anatomical sites and found it preserved lung tumour boundaries well.

Computed Tomography (CT) scan, which produces 3D volumetric medical data that can be viewed as hundreds of cross-sectional images (a.k.a. slices), provides detailed anatomical information for diagnosis. For radiologists, creating CT radiology reports is time-consuming and error-prone. A visual question answering (VQA) system that can answer radiologists' questions about some anatomical regions on the CT scan and even automatically generate a radiology report is urgently needed. However, existing VQA systems cannot adequately handle the CT radiology question answering (CTQA) task for: (1) anatomic complexity makes CT images difficult to understand; (2) spatial relationship across hundreds slices is difficult to capture. To address these issues, this paper proposes CT-Agent, a multimodal agentic framework for CTQA. CT-Agent adopts anatomically independent tools to break down the anatomic complexity; furthermore, it efficiently captures the across-slice spatial relationship with a global-local token compression strategy. Experimental results on two 3D chest CT datasets, CT-RATE and RadGenome-ChestCT, verify the superior performance of CT-Agent.

Prostate cancer is one of the most common and lethal cancers among men, making its early detection critically important. Although ultrasound imaging offers greater accessibility and cost-effectiveness compared to MRI, traditional transrectal ultrasound methods suffer from low sensitivity, especially in detecting anteriorly located tumors. Ultrasound computed tomography provides quantitative tissue characterization, but its clinical implementation faces significant challenges, particularly under anatomically constrained limited-angle acquisition conditions specific to prostate imaging. To address these unmet needs, we introduce OpenPros, the first large-scale benchmark dataset explicitly developed for limited-view prostate USCT. Our dataset includes over 280,000 paired samples of realistic 2D speed-of-sound (SOS) phantoms and corresponding ultrasound full-waveform data, generated from anatomically accurate 3D digital prostate models derived from real clinical MRI/CT scans and ex vivo ultrasound measurements, annotated by medical experts. Simulations are conducted under clinically realistic configurations using advanced finite-difference time-domain and Runge-Kutta acoustic wave solvers, both provided as open-source components. Through comprehensive baseline experiments, we demonstrate that state-of-the-art deep learning methods surpass traditional physics-based approaches in both inference efficiency and reconstruction accuracy. Nevertheless, current deep learning models still fall short of delivering clinically acceptable high-resolution images with sufficient accuracy. By publicly releasing OpenPros, we aim to encourage the development of advanced machine learning algorithms capable of bridging this performance gap and producing clinically usable, high-resolution, and highly accurate prostate ultrasound images. The dataset is publicly accessible at https://open-pros.github.io/.

Computed Tomography (CT) is one of the most widely used and diagnostically information-dense imaging modalities, covering critical organs such as the heart, lungs, liver, and colon. Clinical interpretation relies on both slice-driven local features (e.g., sub-centimeter nodules, lesion boundaries) and volume-driven spatial representations (e.g., tumor infiltration, inter-organ anatomical relations). However, existing Large Vision-Language Models (LVLMs) remain fragmented in CT slice versus volumetric understanding: slice-driven LVLMs show strong generalization but lack cross-slice spatial consistency, while volume-driven LVLMs explicitly capture volumetric semantics but suffer from coarse granularity and poor compatibility with slice inputs. The absence of a unified modeling paradigm constitutes a major bottleneck for the clinical translation of medical LVLMs. We present OmniCT, a powerful unified slice-volume LVLM for CT scenarios, which makes three contributions: (i) Spatial Consistency Enhancement (SCE): volumetric slice composition combined with tri-axial positional embedding that introduces volumetric consistency, and an MoE hybrid projection enables efficient slice-volume adaptation; (ii) Organ-level Semantic Enhancement (OSE): segmentation and ROI localization explicitly align anatomical regions, emphasizing lesion- and organ-level semantics; (iii) MedEval-CT: the largest slice-volume CT dataset and hybrid benchmark integrates comprehensive metrics for unified evaluation. OmniCT consistently outperforms existing methods with a substantial margin across diverse clinical tasks and satisfies both micro-level detail sensitivity and macro-level spatial reasoning. More importantly, it establishes a new paradigm for cross-modal medical imaging understanding. Our project is available at https://github.com/ZJU4HealthCare/OmniCT.

Prompt-based methods, which encode medical priors through descriptive text, have been only minimally explored for CT Image Quality Assessment (IQA). While such prompts can embed prior knowledge about diagnostic quality, they often introduce bias by reflecting idealized definitions that may not hold under real-world degradations such as noise, motion artifacts, or scanner variability. To address this, we propose the Context-Aware Prompt-guided Image Quality Assessment (CAP-IQA) framework, which integrates text-level priors with instance-level context prompts and applies causal debiasing to separate idealized knowledge from factual, image-specific degradations. Our framework combines a CNN-based visual encoder with a domain-specific text encoder to assess diagnostic visibility, anatomical clarity, and noise perception in abdominal CT images. The model leverages radiology-style prompts and context-aware fusion to align semantic and perceptual representations. On the 2023 LDCTIQA challenge benchmark, CAP-IQA achieves an overall correlation score of 2.8590 (sum of PLCC, SROCC, and KROCC), surpassing the top-ranked leaderboard team (2.7427) by 4.24%. Moreover, our comprehensive ablation experiments confirm that prompt-guided fusion and the simplified encoder-only design jointly enhance feature alignment and interpretability. Furthermore, evaluation on an in-house dataset of 91,514 pediatric CT images demonstrates the true generalizability of CAP-IQA in assessing perceptual fidelity in a different patient population.

Determining whether two sets of images belong to the same or different distributions or domains is a crucial task in modern medical image analysis and deep learning; for example, to evaluate the output quality of image generative models. Currently, metrics used for this task either rely on the (potentially biased) choice of some downstream task, such as segmentation, or adopt task-independent perceptual metrics (e.g., Fréchet Inception Distance/FID) from natural imaging, which we show insufficiently capture anatomical features. To this end, we introduce a new perceptual metric tailored for medical images, FRD (Fréchet Radiomic Distance), which utilizes standardized, clinically meaningful, and interpretable image features. We show that FRD is superior to other image distribution metrics for a range of medical imaging applications, including out-of-domain (OOD) detection, the evaluation of image-to-image translation (by correlating more with downstream task performance as well as anatomical consistency and realism), and the evaluation of unconditional image generation. Moreover, FRD offers additional benefits such as stability and computational efficiency at low sample sizes, sensitivity to image corruptions and adversarial attacks, feature interpretability, and correlation with radiologist-perceived image quality. Additionally, we address key gaps in the literature by presenting an extensive framework for the multifaceted evaluation of image similarity metrics in medical imaging -- including the first large-scale comparative study of generative models for medical image translation -- and release an accessible codebase to facilitate future research. Our results are supported by thorough experiments spanning a variety of datasets, modalities, and downstream tasks, highlighting the broad potential of FRD for medical image analysis.

Deep learning methods for unsupervised registration often rely on objectives that assume a uniform noise level across the spatial domain (e.g. mean-squared error loss), but noise distributions are often heteroscedastic and input-dependent in real-world medical images. Thus, this assumption often leads to degradation in registration performance, mainly due to the undesired influence of noise-induced outliers. To mitigate this, we propose a framework for heteroscedastic image uncertainty estimation that can adaptively reduce the influence of regions with high uncertainty during unsupervised registration. The framework consists of a collaborative training strategy for the displacement and variance estimators, and a novel image fidelity weighting scheme utilizing signal-to-noise ratios. Our approach prevents the model from being driven away by spurious gradients caused by the simplified homoscedastic assumption, leading to more accurate displacement estimation. To illustrate its versatility and effectiveness, we tested our framework on two representative registration architectures across three medical image datasets. Our method consistently outperforms baselines and produces sensible uncertainty estimates. The code is publicly available at https://voldemort108x.github.io/hetero_uncertainty/.

To investigate whether the pleurae, airways and vessels surrounding a nodule on non-contrast computed tomography (CT) can discriminate benign and malignant pulmonary nodules. The LIDC-IDRI dataset, one of the largest publicly available CT database, was exploited for study. A total of 1556 nodules from 694 patients were involved in statistical analysis, where nodules with average scorings <3 and >3 were respectively denoted as benign and malignant. Besides, 339 nodules from 113 patients with diagnosis ground-truth were independently evaluated. Computer algorithms were developed to segment pulmonary structures and quantify the distances to pleural surface, airways and vessels, as well as the counting number and normalized volume of airways and vessels near a nodule. Odds ratio (OR) and Chi-square (\chi^2) testing were performed to demonstrate the correlation between features of surrounding structures and nodule malignancy. A non-parametric receiver operating characteristic (ROC) analysis was conducted in logistic regression to evaluate discrimination ability of each structure. For benign and malignant groups, the average distances from nodules to pleural surface, airways and vessels are respectively (6.56, 5.19), (37.08, 26.43) and (1.42, 1.07) mm. The correlation between nodules and the counting number of airways and vessels that contact or project towards nodules are respectively (OR=22.96, \chi^2=105.04) and (OR=7.06, \chi^2=290.11). The correlation between nodules and the volume of airways and vessels are (OR=9.19, \chi^2=159.02) and (OR=2.29, \chi^2=55.89). The areas-under-curves (AUCs) for pleurae, airways and vessels are respectively 0.5202, 0.6943 and 0.6529. Our results show that malignant nodules are often surrounded by more pulmonary structures compared with benign ones, suggesting that features of these structures could be viewed as lung cancer biomarkers.

Many modern iterative solvers for large-scale tomographic reconstruction incur two major computational costs per iteration: expensive forward/adjoint projections to update the data fidelity term and costly proximal computations for the regulariser, often done via inner iterations. This paper studies for the first time the application of methods that couple randomised skipping of the proximal with variance-reduced subset-based optimisation of data-fit term, to simultaneously reduce both costs in challenging tomographic reconstruction tasks. We provide a series of experiments using both synthetic and real data, demonstrating striking speed-ups of the order 5x--20x compared to the non-skipped counterparts which have been so far the standard approach for efficiently solving these problems. Our work lays the groundwork for broader adoption of these methods in inverse problems.

Computed Tomography (CT) is one of the most popular modalities for medical imaging. By far, CT images have contributed to the largest publicly available datasets for volumetric medical segmentation tasks, covering full-body anatomical structures. Large amounts of full-body CT images provide the opportunity to pre-train powerful models, e.g., STU-Net pre-trained in a supervised fashion, to segment numerous anatomical structures. However, it remains unclear in which conditions these pre-trained models can be transferred to various downstream medical segmentation tasks, particularly segmenting the other modalities and diverse targets. To address this problem, a large-scale benchmark for comprehensive evaluation is crucial for finding these conditions. Thus, we collected 87 public datasets varying in modality, target, and sample size to evaluate the transfer ability of full-body CT pre-trained models. We then employed a representative model, STU-Net with multiple model scales, to conduct transfer learning across modalities and targets. Our experimental results show that (1) there may be a bottleneck effect concerning the dataset size in fine-tuning, with more improvement on both small- and large-scale datasets than medium-size ones. (2) Models pre-trained on full-body CT demonstrate effective modality transfer, adapting well to other modalities such as MRI. (3) Pre-training on the full-body CT not only supports strong performance in structure detection but also shows efficacy in lesion detection, showcasing adaptability across target tasks. We hope that this large-scale open evaluation of transfer learning can direct future research in volumetric medical image segmentation.

The rapid increase in the number of Computed Tomography (CT) scan examinations has created an urgent need for automated tools, such as organ segmentation, anomaly classification, and report generation, to assist radiologists with their growing workload. Multi-label classification of Three-Dimensional (3D) CT scans is a challenging task due to the volumetric nature of the data and the variety of anomalies to be detected. Existing deep learning methods based on Convolutional Neural Networks (CNNs) struggle to capture long-range dependencies effectively, while Vision Transformers require extensive pre-training, posing challenges for practical use. Additionally, these existing methods do not explicitly model the radiologist's navigational behavior while scrolling through CT scan slices, which requires both global context understanding and local detail awareness. In this study, we present CT-Scroll, a novel global-local attention model specifically designed to emulate the scrolling behavior of radiologists during the analysis of 3D CT scans. Our approach is evaluated on two public datasets, demonstrating its efficacy through comprehensive experiments and an ablation study that highlights the contribution of each model component.

Machine learning models for medical image analysis often suffer from poor performance on important subsets of a population that are not identified during training or testing. For example, overall performance of a cancer detection model may be high, but the model still consistently misses a rare but aggressive cancer subtype. We refer to this problem as hidden stratification, and observe that it results from incompletely describing the meaningful variation in a dataset. While hidden stratification can substantially reduce the clinical efficacy of machine learning models, its effects remain difficult to measure. In this work, we assess the utility of several possible techniques for measuring and describing hidden stratification effects, and characterize these effects on multiple medical imaging datasets. We find evidence that hidden stratification can occur in unidentified imaging subsets with low prevalence, low label quality, subtle distinguishing features, or spurious correlates, and that it can result in relative performance differences of over 20% on clinically important subsets. Finally, we explore the clinical implications of our findings, and suggest that evaluation of hidden stratification should be a critical component of any machine learning deployment in medical imaging.

We participated in the SynthRAD2025 challenge (Tasks 1 and 2) with a unified pipeline for synthetic CT (sCT) generation from MRI and CBCT, implemented using the KonfAI framework. Our model is a 2.5D U-Net++ with a ResNet-34 encoder, trained jointly across anatomical regions and fine-tuned per region. The loss function combined pixel-wise L1 loss with IMPACT-Synth, a perceptual loss derived from SAM and TotalSegmentator to enhance structural fidelity. Training was performed using AdamW (initial learning rate = 0.001, halved every 25k steps) on patch-based, normalized, body-masked inputs (320x320 for MRI, 256x256 for CBCT), with random flipping as the only augmentation. No post-processing was applied. Final predictions leveraged test-time augmentation and five-fold ensembling. The best model was selected based on validation MAE. Two registration strategies were evaluated: (i) Elastix with mutual information, consistent with the challenge pipeline, and (ii) IMPACT, a feature-based similarity metric leveraging pretrained segmentation networks. On the local test sets, IMPACT-based registration achieved more accurate and anatomically consistent alignments than mutual-information-based registration, resulting in improved sCT synthesis with lower MAE and more realistic anatomical structures. On the public validation set, however, models trained with Elastix-aligned data achieved higher scores, reflecting a registration bias favoring alignment strategies consistent with the evaluation pipeline. This highlights how registration errors can propagate into supervised learning, influencing both training and evaluation, and potentially inflating performance metrics at the expense of anatomical fidelity. By promoting anatomically consistent alignment, IMPACT helps mitigate this bias and supports the development of more robust and generalizable sCT synthesis models.

Limited-Angle Computed Tomography (LACT) is a non-destructive evaluation technique used in a variety of applications ranging from security to medicine. The limited angle coverage in LACT is often a dominant source of severe artifacts in the reconstructed images, making it a challenging inverse problem. We present DOLCE, a new deep model-based framework for LACT that uses a conditional diffusion model as an image prior. Diffusion models are a recent class of deep generative models that are relatively easy to train due to their implementation as image denoisers. DOLCE can form high-quality images from severely under-sampled data by integrating data-consistency updates with the sampling updates of a diffusion model, which is conditioned on the transformed limited-angle data. We show through extensive experimentation on several challenging real LACT datasets that, the same pre-trained DOLCE model achieves the SOTA performance on drastically different types of images. Additionally, we show that, unlike standard LACT reconstruction methods, DOLCE naturally enables the quantification of the reconstruction uncertainty by generating multiple samples consistent with the measured data.

Sparse-view computed tomography (CT) -- using a small number of projections for tomographic reconstruction -- enables much lower radiation dose to patients and accelerated data acquisition. The reconstructed images, however, suffer from strong artifacts, greatly limiting their diagnostic value. Current trends for sparse-view CT turn to the raw data for better information recovery. The resultant dual-domain methods, nonetheless, suffer from secondary artifacts, especially in ultra-sparse view scenarios, and their generalization to other scanners/protocols is greatly limited. A crucial question arises: have the image post-processing methods reached the limit? Our answer is not yet. In this paper, we stick to image post-processing methods due to great flexibility and propose global representation (GloRe) distillation framework for sparse-view CT, termed GloReDi. First, we propose to learn GloRe with Fourier convolution, so each element in GloRe has an image-wide receptive field. Second, unlike methods that only use the full-view images for supervision, we propose to distill GloRe from intermediate-view reconstructed images that are readily available but not explored in previous literature. The success of GloRe distillation is attributed to two key components: representation directional distillation to align the GloRe directions, and band-pass-specific contrastive distillation to gain clinically important details. Extensive experiments demonstrate the superiority of the proposed GloReDi over the state-of-the-art methods, including dual-domain ones. The source code is available at https://github.com/longzilicart/GloReDi.

Understanding radiologists' eye movement during Computed Tomography (CT) reading is crucial for developing effective interpretable computer-aided diagnosis systems. However, CT research in this area has been limited by the lack of publicly available eye-tracking datasets and the three-dimensional complexity of CT volumes. To address these challenges, we present the first publicly available eye gaze dataset on CT, called CT-ScanGaze. Then, we introduce CT-Searcher, a novel 3D scanpath predictor designed specifically to process CT volumes and generate radiologist-like 3D fixation sequences, overcoming the limitations of current scanpath predictors that only handle 2D inputs. Since deep learning models benefit from a pretraining step, we develop a pipeline that converts existing 2D gaze datasets into 3D gaze data to pretrain CT-Searcher. Through both qualitative and quantitative evaluations on CT-ScanGaze, we demonstrate the effectiveness of our approach and provide a comprehensive assessment framework for 3D scanpath prediction in medical imaging.

The development of larger models for medical image analysis has led to increased performance. However, it also affected our ability to explain and validate model decisions. Models can use non-relevant parts of images, also called spurious correlations or shortcuts, to obtain high performance on benchmark datasets but fail in real-world scenarios. In this work, we challenge the capacity of convolutional neural networks (CNN) to classify chest X-rays and eye fundus images while masking out clinically relevant parts of the image. We show that all models trained on the PadChest dataset, irrespective of the masking strategy, are able to obtain an Area Under the Curve (AUC) above random. Moreover, the models trained on full images obtain good performance on images without the region of interest (ROI), even superior to the one obtained on images only containing the ROI. We also reveal a possible spurious correlation in the Chaksu dataset while the performances are more aligned with the expectation of an unbiased model. We go beyond the performance analysis with the usage of the explainability method SHAP and the analysis of embeddings. We asked a radiology resident to interpret chest X-rays under different masking to complement our findings with clinical knowledge. Our code is available at https://github.com/TheoSourget/MMC_Masking and https://github.com/TheoSourget/MMC_Masking_EyeFundus

Purpose: In this study we investigate whether a Convolutional Neural Network (CNN) can generate clinically relevant parametric maps from CT perfusion data in a clinical setting of patients with acute ischemic stroke. Methods: Training of the CNN was done on a subset of 100 perfusion data, while 15 samples were used as validation. All the data used for the training/validation of the network and to generate ground truth (GT) maps, using a state-of-the-art deconvolution-algorithm, were previously pre-processed using a standard pipeline. Validation was carried out through manual segmentation of infarct core and penumbra on both CNN-derived maps and GT maps. Concordance among segmented lesions was assessed using the Dice and the Pearson correlation coefficients across lesion volumes. Results: Mean Dice scores from two different raters and the GT maps were > 0.70 (good-matching). Inter-rater concordance was also high and strong correlation was found between lesion volumes of CNN maps and GT maps (0.99, 0.98). Conclusion: Our CNN-based approach generated clinically relevant perfusion maps that are comparable to state-of-the-art perfusion analysis methods based on deconvolution of the data. Moreover, the proposed technique requires less information to estimate the ischemic core and thus might allow the development of novel perfusion protocols with lower radiation dose.

Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed. Eighty-One T2-weighted MRI scans from 28 patients with non-small cell lung cancers were analyzed. Cross-modality prior encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning model. This model augmented training data arising from 6 expert-segmented T2w MR patient scans with 377 pseudo MRI from non-small cell lung cancer CT patient scans with obtained from the Cancer Imaging Archive. A two-dimensional Unet implemented with batch normalization was trained to segment the tumors from T2w MRI. This method was benchmarked against (a) standard data augmentation and two state-of-the art cross-modality pseudo MR-based augmentation and (b) two segmentation networks. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdroff distance metrics, and volume ratio. The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of 0.75 and the lowest Hausdroff distance on the test dataset. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37). A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality priors to augment training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods.

Quantitative tools are increasingly appealing for decision support in healthcare, driven by the growing capabilities of advanced AI systems. However, understanding the predictive uncertainties surrounding a tool's output is crucial for decision-makers to ensure reliable and transparent decisions. In this paper, we present a case study on pulmonary nodule detection for lung cancer screening, enhancing an advanced detection model with an uncertainty quantification technique called conformal risk control (CRC). We demonstrate that prediction sets with conformal guarantees are attractive measures of predictive uncertainty in the safety-critical healthcare domain, allowing end-users to achieve arbitrary validity by trading off false positives and providing formal statistical guarantees on model performance. Among ground-truth nodules annotated by at least three radiologists, our model achieves a sensitivity that is competitive with that generally achieved by individual radiologists, with a slight increase in false positives. Furthermore, we illustrate the risks of using off-the-shelve prediction models when faced with ontological uncertainty, such as when radiologists disagree on what constitutes the ground truth on pulmonary nodules.

The purpose of this study is to present and compare three denoising diffusion probabilistic models (DDPMs) that generate 3D T_1-weighted MRI human brain images. Three DDPMs were trained using 80,675 image volumes from 42,406 subjects spanning 38 publicly available brain MRI datasets. These images had approximately 1 mm isotropic resolution and were manually inspected by three human experts to exclude those with poor quality, field-of-view issues, and excessive pathology. The images were minimally preprocessed to preserve the visual variability of the data. Furthermore, to enable the DDPMs to produce images with natural orientation variations and inhomogeneity, the images were neither registered to a common coordinate system nor bias field corrected. Evaluations included segmentation, Frechet Inception Distance (FID), and qualitative inspection. Regarding results, all three DDPMs generated coherent MR brain volumes. The velocity and flow prediction models achieved lower FIDs than the sample prediction model. However, all three models had higher FIDs compared to real images across multiple cohorts. In a permutation experiment, the generated brain regional volume distributions differed statistically from real data. However, the velocity and flow prediction models had fewer statistically different volume distributions in the thalamus and putamen. In conclusion this work presents and releases the first 3D non-latent diffusion model for brain data without skullstripping or registration. Despite the negative results in statistical testing, the presented DDPMs are capable of generating high-resolution 3D T_1-weighted brain images. All model weights and corresponding inference code are publicly available at https://github.com/piksl-research/medforj .

In some medical imaging tasks and other settings where only small parts of the image are informative for the classification task, traditional CNNs can sometimes struggle to generalise. Manually annotated Regions of Interest (ROI) are sometimes used to isolate the most informative parts of the image. However, these are expensive to collect and may vary significantly across annotators. To overcome these issues, we propose a framework that employs saliency maps to obtain soft spatial attention masks that modulate the image features at different scales. We refer to our method as Adversarial Counterfactual Attention (ACAT). ACAT increases the baseline classification accuracy of lesions in brain CT scans from 71.39% to 72.55% and of COVID-19 related findings in lung CT scans from 67.71% to 70.84% and exceeds the performance of competing methods. We investigate the best way to generate the saliency maps employed in our architecture and propose a way to obtain them from adversarially generated counterfactual images. They are able to isolate the area of interest in brain and lung CT scans without using any manual annotations. In the task of localising the lesion location out of 6 possible regions, they obtain a score of 65.05% on brain CT scans, improving the score of 61.29% obtained with the best competing method.

Image registration is fundamental in medical imaging, enabling precise alignment of anatomical structures for diagnosis, treatment planning, image-guided treatment or longitudinal monitoring. This work introduces IMPACT (Image Metric with Pretrained model-Agnostic Comparison for Transmodality registration), a generic semantic similarity metric designed for seamless integration into diverse image registration frameworks (such as Elastix and Voxelmorph). It compares deep learning-based features extracted from medical images without requiring task-specific training, ensuring broad applicability across various modalities. By leveraging the features of the large-scale pretrained TotalSegmentator models and the ability to integrate Segment Anything Model (SAM) and other large-scale segmentation networks, this approach offers significant advantages. It provides robust, scalable, and efficient solutions for multimodal image registration. The IMPACT loss was evaluated on five challenging registration tasks involving thoracic CT/CBCT, and pelvic MR/CT datasets. Quantitative metrics, such as Target Registration Error and Dice Similarity Coefficient, demonstrated significant improvements in anatomical alignment compared to baseline methods. Qualitative analyses further confirmed the increased robustness of the proposed metric in the face of noise, artifacts, and modality variations. IMPACT's versatility and efficiency make it a valuable tool for advancing registration performance in clinical and research applications, addressing critical challenges in multimodal medical imaging.

Medical vision-language models often struggle with generating accurate quantitative measurements in radiology reports, leading to hallucinations that undermine clinical reliability. We introduce FactCheXcker, a modular framework that de-hallucinates radiology report measurements by leveraging an improved query-code-update paradigm. Specifically, FactCheXcker employs specialized modules and the code generation capabilities of large language models to solve measurement queries generated based on the original report. After extracting measurable findings, the results are incorporated into an updated report. We evaluate FactCheXcker on endotracheal tube placement, which accounts for an average of 78% of report measurements, using the MIMIC-CXR dataset and 11 medical report-generation models. Our results show that FactCheXcker significantly reduces hallucinations, improves measurement precision, and maintains the quality of the original reports. Specifically, FactCheXcker improves the performance of 10/11 models and achieves an average improvement of 135.0% in reducing measurement hallucinations measured by mean absolute error. Code is available at https://github.com/rajpurkarlab/FactCheXcker.

Counterfactual explanations enhance the interpretability of deep learning models in medical imaging, yet adapting them to 3D CT scans poses challenges due to volumetric complexity and resource demands. We extend the Latent Shift counterfactual generation method from 2D applications to explain 3D computed tomography (CT) scans classifiers. We address the challenges associated with 3D classifiers, such as limited training samples and high memory demands, by implementing a slice-based autoencoder and gradient blocking except for specific chunks of slices. This method leverages a 2D encoder trained on CT slices, which are subsequently combined to maintain 3D context. We demonstrate this technique on two models for clinical phenotype prediction and lung segmentation. Our approach is both memory-efficient and effective for generating interpretable counterfactuals in high-resolution 3D medical imaging.

Coronavirus disease 2019 (Covid-19) is highly contagious with limited treatment options. Early and accurate diagnosis of Covid-19 is crucial in reducing the spread of the disease and its accompanied mortality. Currently, detection by reverse transcriptase polymerase chain reaction (RT-PCR) is the gold standard of outpatient and inpatient detection of Covid-19. RT-PCR is a rapid method, however, its accuracy in detection is only ~70-75%. Another approved strategy is computed tomography (CT) imaging. CT imaging has a much higher sensitivity of ~80-98%, but similar accuracy of 70%. To enhance the accuracy of CT imaging detection, we developed an open-source set of algorithms called CovidCTNet that successfully differentiates Covid-19 from community-acquired pneumonia (CAP) and other lung diseases. CovidCTNet increases the accuracy of CT imaging detection to 90% compared to radiologists (70%). The model is designed to work with heterogeneous and small sample sizes independent of the CT imaging hardware. In order to facilitate the detection of Covid-19 globally and assist radiologists and physicians in the screening process, we are releasing all algorithms and parametric details in an open-source format. Open-source sharing of our CovidCTNet enables developers to rapidly improve and optimize services, while preserving user privacy and data ownership.

We introduce the Discrete Min-Max Violation (DMMV) as a general optimization problem which seeks an assignment of discrete values to variables that minimizes the largest constraint violation. This context-free mathematical formulation is applicable to a wide range of use cases that have worst-case performance requirements. After defining the DMMV problem mathematically, we explore its properties to establish a foundational understanding. To tackle DMMV instance sizes of practical relevance, we develop a GPU-accelerated heuristic that takes advantage of the mathematical properties of DMMV for speeding up the solution process. We demonstrate the versatile applicability of our heuristic by solving three optimization problems as use cases: (1) post-training quantization of language models, (2) discrete tomography, and (3) Finite Impulse Response (FIR) filter design. In quantization without outlier separation, our heuristic achieves 14% improvement on average over existing methods. In discrete tomography, it reduces reconstruction error by 16% under uniform noise and accelerates computations by a factor of 6 on GPU. For FIR filter design, it nearly achieves 50% ripple reduction compared to using the commercial integer optimization solver, Gurobi. Our comparative results point to the benefits of studying DMMV as a context-free optimization problem and the advantages that our proposed heuristic offers on three distinct problems. Our GPU-accelerated heuristic will be made open-source to further stimulate research on DMMV and its other applications. The code is available at https://anonymous.4open.science/r/AMVM-5F3E/

Generating synthetic Computed Tomography (CT) images from Cone Beam Computed Tomography (CBCT) is desirable for improving the image quality of CBCT. Existing synthetic CT (sCT) generation methods using Convolutional Neural Networks (CNN) and Transformers often face difficulties in effectively capturing both global and local features and contrasts for high-quality sCT generation. In this work, we propose a Global-Local Feature and Contrast learning (GLFC) framework for sCT generation. First, a Mamba-Enhanced UNet (MEUNet) is introduced by integrating Mamba blocks into the skip connections of a high-resolution UNet for effective global and local feature learning. Second, we propose a Multiple Contrast Loss (MCL) that calculates synthetic loss at different intensity windows to improve quality for both soft tissues and bone regions. Experiments on the SynthRAD2023 dataset demonstrate that GLFC improved the SSIM of sCT from 77.91% to 91.50% compared with the original CBCT, and significantly outperformed several existing methods for sCT generation. The code is available at https://github.com/HiLab-git/GLFC

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. To exploit this structured information, we propose the use of Space-aware Memory Queues for In-painting and Detecting anomalies from radiography images (abbreviated as SQUID). We show that SQUID can taxonomize the ingrained anatomical structures into recurrent patterns; and in the inference, it can identify anomalies (unseen/modified patterns) in the image. SQUID surpasses 13 state-of-the-art methods in unsupervised anomaly detection by at least 5 points on two chest X-ray benchmark datasets measured by the Area Under the Curve (AUC). Additionally, we have created a new dataset (DigitAnatomy), which synthesizes the spatial correlation and consistent shape in chest anatomy. We hope DigitAnatomy can prompt the development, evaluation, and interpretability of anomaly detection methods.

Developing generalist foundation model has recently attracted tremendous attention among researchers in the field of AI for Medicine (AI4Medicine). A pivotal insight in developing these models is their reliance on dataset scaling, which emphasizes the requirements on developing open-source medical image datasets that incorporate diverse supervision signals across various imaging modalities. In this paper, we introduce RadGenome-Chest CT, a comprehensive, large-scale, region-guided 3D chest CT interpretation dataset based on CT-RATE. Specifically, we leverage the latest powerful universal segmentation and large language models, to extend the original datasets (over 25,692 non-contrast 3D chest CT volume and reports from 20,000 patients) from the following aspects: (i) organ-level segmentation masks covering 197 categories, which provide intermediate reasoning visual clues for interpretation; (ii) 665 K multi-granularity grounded reports, where each sentence of the report is linked to the corresponding anatomical region of CT volume in the form of a segmentation mask; (iii) 1.3 M grounded VQA pairs, where questions and answers are all linked with reference segmentation masks, enabling models to associate visual evidence with textual explanations. All grounded reports and VQA pairs in the validation set have gone through manual verification to ensure dataset quality. We believe that RadGenome-Chest CT can significantly advance the development of multimodal medical foundation models, by training to generate texts based on given segmentation regions, which is unattainable with previous relevant datasets. We will release all segmentation masks, grounded reports, and VQA pairs to facilitate further research and development in this field.

Recent work has investigated the distributions of learned convolution filters through a large-scale study containing hundreds of heterogeneous image models. Surprisingly, on average, the distributions only show minor drifts in comparisons of various studied dimensions including the learned task, image domain, or dataset. However, among the studied image domains, medical imaging models appeared to show significant outliers through "spikey" distributions, and, therefore, learn clusters of highly specific filters different from other domains. Following this observation, we study the collected medical imaging models in more detail. We show that instead of fundamental differences, the outliers are due to specific processing in some architectures. Quite the contrary, for standardized architectures, we find that models trained on medical data do not significantly differ in their filter distributions from similar architectures trained on data from other domains. Our conclusions reinforce previous hypotheses stating that pre-training of imaging models can be done with any kind of diverse image data.

The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases. A tremendous number of X-ray imaging studies accompanied by radiological reports are accumulated and stored in many modern hospitals' Picture Archiving and Communication Systems (PACS). On the other side, it is still an open question how this type of hospital-size knowledge database containing invaluable imaging informatics (i.e., loosely labeled) can be used to facilitate the data-hungry deep learning paradigms in building truly large-scale high precision computer-aided diagnosis (CAD) systems. In this paper, we present a new chest X-ray database, namely "ChestX-ray8", which comprises 108,948 frontal-view X-ray images of 32,717 unique patients with the text-mined eight disease image labels (where each image can have multi-labels), from the associated radiological reports using natural language processing. Importantly, we demonstrate that these commonly occurring thoracic diseases can be detected and even spatially-located via a unified weakly-supervised multi-label image classification and disease localization framework, which is validated using our proposed dataset. Although the initial quantitative results are promising as reported, deep convolutional neural network based "reading chest X-rays" (i.e., recognizing and locating the common disease patterns trained with only image-level labels) remains a strenuous task for fully-automated high precision CAD systems. Data download link: https://nihcc.app.box.com/v/ChestXray-NIHCC

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.

Ultrasound computed tomography (USCT) is a radiation-free, high-resolution modality but remains limited for musculoskeletal imaging due to conventional ray-based reconstructions that neglect strong scattering. We propose a generative neural physics framework that couples generative networks with physics-informed neural simulation for fast, high-fidelity 3D USCT. By learning a compact surrogate of ultrasonic wave propagation from only dozens of cross-modality images, our method merges the accuracy of wave modeling with the efficiency and stability of deep learning. This enables accurate quantitative imaging of in vivo musculoskeletal tissues, producing spatial maps of acoustic properties beyond reflection-mode images. On synthetic and in vivo data (breast, arm, leg), we reconstruct 3D maps of tissue parameters in under ten minutes, with sensitivity to biomechanical properties in muscle and bone and resolution comparable to MRI. By overcoming computational bottlenecks in strongly scattering regimes, this approach advances USCT toward routine clinical assessment of musculoskeletal disease.

This paper investigates discrepancies in how neural networks learn from different imaging domains, which are commonly overlooked when adopting computer vision techniques from the domain of natural images to other specialized domains such as medical images. Recent works have found that the generalization error of a trained network typically increases with the intrinsic dimension (d_{data}) of its training set. Yet, the steepness of this relationship varies significantly between medical (radiological) and natural imaging domains, with no existing theoretical explanation. We address this gap in knowledge by establishing and empirically validating a generalization scaling law with respect to d_{data}, and propose that the substantial scaling discrepancy between the two considered domains may be at least partially attributed to the higher intrinsic ``label sharpness'' (K_F) of medical imaging datasets, a metric which we propose. Next, we demonstrate an additional benefit of measuring the label sharpness of a training set: it is negatively correlated with the trained model's adversarial robustness, which notably leads to models for medical images having a substantially higher vulnerability to adversarial attack. Finally, we extend our d_{data} formalism to the related metric of learned representation intrinsic dimension (d_{repr}), derive a generalization scaling law with respect to d_{repr}, and show that d_{data} serves as an upper bound for d_{repr}. Our theoretical results are supported by thorough experiments with six models and eleven natural and medical imaging datasets over a range of training set sizes. Our findings offer insights into the influence of intrinsic dataset properties on generalization, representation learning, and robustness in deep neural networks. Code link: https://github.com/mazurowski-lab/intrinsic-properties

Modern reconstruction techniques can effectively model complex 3D scenes from sparse 2D views. However, automatically assessing the quality of novel views and identifying artifacts is challenging due to the lack of ground truth images and the limitations of no-reference image metrics in predicting detailed artifact maps. The absence of such quality metrics hinders accurate predictions of the quality of generated views and limits the adoption of post-processing techniques, such as inpainting, to enhance reconstruction quality. In this work, we propose a new no-reference metric, Puzzle Similarity, which is designed to localize artifacts in novel views. Our approach utilizes image patch statistics from the input views to establish a scene-specific distribution that is later used to identify poorly reconstructed regions in the novel views. We test and evaluate our method in the context of 3D reconstruction; to this end, we collected a novel dataset of human quality assessment in unseen reconstructed views. Through this dataset, we demonstrate that our method can not only successfully localize artifacts in novel views, correlating with human assessment, but do so without direct references. Surprisingly, our metric outperforms both no-reference metrics and popular full-reference image metrics. We can leverage our new metric to enhance applications like automatic image restoration, guided acquisition, or 3D reconstruction from sparse inputs.

Over 85 million computed tomography (CT) scans are performed annually in the US, of which approximately one quarter focus on the abdomen. Given the current radiologist shortage, there is a large impetus to use artificial intelligence to alleviate the burden of interpreting these complex imaging studies. Prior state-of-the-art approaches for automated medical image interpretation leverage vision language models (VLMs). However, current medical VLMs are generally limited to 2D images and short reports, and do not leverage electronic health record (EHR) data for supervision. We introduce Merlin - a 3D VLM that we train using paired CT scans (6+ million images from 15,331 CTs), EHR diagnosis codes (1.8+ million codes), and radiology reports (6+ million tokens). We evaluate Merlin on 6 task types and 752 individual tasks. The non-adapted (off-the-shelf) tasks include zero-shot findings classification (31 findings), phenotype classification (692 phenotypes), and zero-shot cross-modal retrieval (image to findings and image to impressions), while model adapted tasks include 5-year disease prediction (6 diseases), radiology report generation, and 3D semantic segmentation (20 organs). We perform internal validation on a test set of 5,137 CTs, and external validation on 7,000 clinical CTs and on two public CT datasets (VerSe, TotalSegmentator). Beyond these clinically-relevant evaluations, we assess the efficacy of various network architectures and training strategies to depict that Merlin has favorable performance to existing task-specific baselines. We derive data scaling laws to empirically assess training data needs for requisite downstream task performance. Furthermore, unlike conventional VLMs that require hundreds of GPUs for training, we perform all training on a single GPU.

We propose an adaptive training scheme for unsupervised medical image registration. Existing methods rely on image reconstruction as the primary supervision signal. However, nuisance variables (e.g. noise and covisibility), violation of the Lambertian assumption in physical waves (e.g. ultrasound), and inconsistent image acquisition can all cause a loss of correspondence between medical images. As the unsupervised learning scheme relies on intensity constancy between images to establish correspondence for reconstruction, this introduces spurious error residuals that are not modeled by the typical training objective. To mitigate this, we propose an adaptive framework that re-weights the error residuals with a correspondence scoring map during training, preventing the parametric displacement estimator from drifting away due to noisy gradients, which leads to performance degradation. To illustrate the versatility and effectiveness of our method, we tested our framework on three representative registration architectures across three medical image datasets along with other baselines. Our adaptive framework consistently outperforms other methods both quantitatively and qualitatively. Paired t-tests show that our improvements are statistically significant. Code available at: https://voldemort108x.github.io/AdaCS/.

Shadow tomography for quantum states provides a sample efficient approach for predicting the properties of quantum systems when the properties are restricted to expectation values of 2-outcome POVMs. However, these shadow tomography procedures yield poor bounds if there are more than 2 outcomes per measurement. In this paper, we consider a general problem of learning properties from unknown quantum states: given an unknown d-dimensional quantum state rho and M unknown quantum measurements M_1,...,M_M with Kgeq 2 outcomes, estimating the probability distribution for applying M_i on rho to within total variation distance epsilon. Compared to the special case when K=2, we need to learn unknown distributions instead of values. We develop an online shadow tomography procedure that solves this problem with high success probability requiring O(Klog^2Mlog d/epsilon^4) copies of rho. We further prove an information-theoretic lower bound that at least Omega(min{d^2,K+log M}/epsilon^2) copies of rho are required to solve this problem with high success probability. Our shadow tomography procedure requires sample complexity with only logarithmic dependence on M and d and is sample-optimal for the dependence on K.

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

X-ray imaging is a rapid and cost-effective tool for visualizing internal human anatomy. While multi-view X-ray imaging provides complementary information that enhances diagnosis, intervention, and education, acquiring images from multiple angles increases radiation exposure and complicates clinical workflows. To address these challenges, we propose a novel view-conditioned diffusion model for synthesizing multi-view X-ray images from a single view. Unlike prior methods, which are limited in angular range, resolution, and image quality, our approach leverages the Diffusion Transformer to preserve fine details and employs a weak-to-strong training strategy for stable high-resolution image generation. Experimental results demonstrate that our method generates higher-resolution outputs with improved control over viewing angles. This capability has significant implications not only for clinical applications but also for medical education and data extension, enabling the creation of diverse, high-quality datasets for training and analysis. Our code is available at https://github.com/xiechun298/SV-DRR.

Four-dimensional cone-beam computed tomography (4D CBCT) provides respiration-resolved images and can be used for image-guided radiation therapy. However, the ability to reveal respiratory motion comes at the cost of image artifacts. As raw projection data are sorted into multiple respiratory phases, the cone-beam projections become much sparser and the reconstructed 4D CBCT images will be covered by severe streak artifacts. Although several deep learning-based methods have been proposed to address this issue, most algorithms employ 2D network models as backbones, neglecting the intrinsic structural priors within 4D CBCT images. In this paper, we first explore the origin and appearance of streak artifacts in 4D CBCT images. We find that streak artifacts exhibit a unique rotational motion along with the patient's respiration, distinguishable from diaphragm-driven respiratory motion in the spatiotemporal domain. Therefore, we propose a novel 4D neural network model, RSTAR4D-Net, designed to address Rotational STreak Artifact Reduction by integrating the spatial and temporal information within 4D CBCT images. Specifically, we overcome the computational and training difficulties of a 4D neural network. The specially designed model adopts an efficient implementation of 4D convolutions to reduce computational costs and thus can process the whole 4D image in one pass. Additionally, a Tetris training strategy pertinent to the separable 4D convolutions is proposed to effectively train the model using limited 4D training samples. Extensive experiments substantiate the effectiveness of our proposed method, and the RSTAR4D-Net shows superior performance compared to other methods. The source code and dynamic demos are available at https://github.com/ivy9092111111/RSTAR.

Posterior sampling has been shown to be a powerful Bayesian approach for solving imaging inverse problems. The recent plug-and-play unadjusted Langevin algorithm (PnP-ULA) has emerged as a promising method for Monte Carlo sampling and minimum mean squared error (MMSE) estimation by combining physical measurement models with deep-learning priors specified using image denoisers. However, the intricate relationship between the sampling distribution of PnP-ULA and the mismatched data-fidelity and denoiser has not been theoretically analyzed. We address this gap by proposing a posterior-L2 pseudometric and using it to quantify an explicit error bound for PnP-ULA under mismatched posterior distribution. We numerically validate our theory on several inverse problems such as sampling from Gaussian mixture models and image deblurring. Our results suggest that the sensitivity of the sampling distribution of PnP-ULA to a mismatch in the measurement model and the denoiser can be precisely characterized.

Medical imaging plays a pivotal role in modern healthcare, with computed tomography pulmonary angiography (CTPA) being a critical tool for diagnosing pulmonary embolism and other thoracic conditions. However, the complexity of interpreting CTPA scans and generating accurate radiology reports remains a significant challenge. This paper introduces Abn-BLIP (Abnormality-aligned Bootstrapping Language-Image Pretraining), an advanced diagnosis model designed to align abnormal findings to generate the accuracy and comprehensiveness of radiology reports. By leveraging learnable queries and cross-modal attention mechanisms, our model demonstrates superior performance in detecting abnormalities, reducing missed findings, and generating structured reports compared to existing methods. Our experiments show that Abn-BLIP outperforms state-of-the-art medical vision-language models and 3D report generation methods in both accuracy and clinical relevance. These results highlight the potential of integrating multimodal learning strategies for improving radiology reporting. The source code is available at https://github.com/zzs95/abn-blip.

A major challenge in computational research in 3D medical imaging is the lack of comprehensive datasets. Addressing this issue, our study introduces CT-RATE, the first 3D medical imaging dataset that pairs images with textual reports. CT-RATE consists of 25,692 non-contrast chest CT volumes, expanded to 50,188 through various reconstructions, from 21,304 unique patients, along with corresponding radiology text reports. Leveraging CT-RATE, we developed CT-CLIP, a CT-focused contrastive language-image pre-training framework. As a versatile, self-supervised model, CT-CLIP is designed for broad application and does not require task-specific training. Remarkably, CT-CLIP outperforms state-of-the-art, fully supervised methods in multi-abnormality detection across all key metrics, thus eliminating the need for manual annotation. We also demonstrate its utility in case retrieval, whether using imagery or textual queries, thereby advancing knowledge dissemination. The open-source release of CT-RATE and CT-CLIP marks a significant advancement in medical AI, enhancing 3D imaging analysis and fostering innovation in healthcare.

Digitally reconstructed radiographs (DRRs) are simulated 2D X-ray images generated from 3D CT volumes, widely used in preoperative settings but limited in intraoperative applications due to computational bottlenecks, especially for accurate but heavy physics-based Monte Carlo methods. While analytical DRR renderers offer greater efficiency, they overlook anisotropic X-ray image formation phenomena, such as Compton scattering. We present a novel approach that marries realistic physics-inspired X-ray simulation with efficient, differentiable DRR generation using 3D Gaussian splatting (3DGS). Our direction-disentangled 3DGS (DDGS) method separates the radiosity contribution into isotropic and direction-dependent components, approximating complex anisotropic interactions without intricate runtime simulations. Additionally, we adapt the 3DGS initialization to account for tomography data properties, enhancing accuracy and efficiency. Our method outperforms state-of-the-art techniques in image accuracy. Furthermore, our DDGS shows promise for intraoperative applications and inverse problems such as pose registration, delivering superior registration accuracy and runtime performance compared to analytical DRR methods.

Visual anomaly detection aims to identify anomalous regions in images through unsupervised learning paradigms, with increasing application demand and value in fields such as industrial inspection and medical lesion detection. Despite significant progress in recent years, there is a lack of comprehensive benchmarks to adequately evaluate the performance of various mainstream methods across different datasets under the practical multi-class setting. The absence of standardized experimental setups can lead to potential biases in training epochs, resolution, and metric results, resulting in erroneous conclusions. This paper addresses this issue by proposing a comprehensive visual anomaly detection benchmark, ADer, which is a modular framework that is highly extensible for new methods. The benchmark includes multiple datasets from industrial and medical domains, implementing fifteen state-of-the-art methods and nine comprehensive metrics. Additionally, we have proposed the GPU-assisted ADEval package to address the slow evaluation problem of metrics like time-consuming mAU-PRO on large-scale data, significantly reducing evaluation time by more than 1000-fold. Through extensive experimental results, we objectively reveal the strengths and weaknesses of different methods and provide insights into the challenges and future directions of multi-class visual anomaly detection. We hope that ADer will become a valuable resource for researchers and practitioners in the field, promoting the development of more robust and generalizable anomaly detection systems. Full codes are open-sourced at https://github.com/zhangzjn/ader.

The progress in generative models, particularly Generative Adversarial Networks (GANs), opened new possibilities for image generation but raised concerns about potential malicious uses, especially in sensitive areas like medical imaging. This study introduces MITS-GAN, a novel approach to prevent tampering in medical images, with a specific focus on CT scans. The approach disrupts the output of the attacker's CT-GAN architecture by introducing finely tuned perturbations that are imperceptible to the human eye. Specifically, the proposed approach involves the introduction of appropriate Gaussian noise to the input as a protective measure against various attacks. Our method aims to enhance tamper resistance, comparing favorably to existing techniques. Experimental results on a CT scan demonstrate MITS-GAN's superior performance, emphasizing its ability to generate tamper-resistant images with negligible artifacts. As image tampering in medical domains poses life-threatening risks, our proactive approach contributes to the responsible and ethical use of generative models. This work provides a foundation for future research in countering cyber threats in medical imaging. Models and codes are publicly available on https://iplab.dmi.unict.it/MITS-GAN-2024/.

Medical vision-language pre-training shows great potential in learning representative features from massive paired radiographs and reports. However, in computed tomography (CT) scans, the distribution of lesions which contain intricate structures is characterized by spatial sparsity. Besides, the complex and implicit relationships between different pathological descriptions in each sentence of the report and their corresponding sub-regions in radiographs pose additional challenges. In this paper, we propose a Similarity-Driven Cross-Granularity Pre-training (SimCroP) framework on chest CTs, which combines similarity-driven alignment and cross-granularity fusion to improve radiograph interpretation. We first leverage multi-modal masked modeling to optimize the encoder for understanding precise low-level semantics from radiographs. Then, similarity-driven alignment is designed to pre-train the encoder to adaptively select and align the correct patches corresponding to each sentence in reports. The cross-granularity fusion module integrates multimodal information across instance level and word-patch level, which helps the model better capture key pathology structures in sparse radiographs, resulting in improved performance for multi-scale downstream tasks. SimCroP is pre-trained on a large-scale paired CT-reports dataset and validated on image classification and segmentation tasks across five public datasets. Experimental results demonstrate that SimCroP outperforms both cutting-edge medical self-supervised learning methods and medical vision-language pre-training methods. Codes and models are available at https://github.com/ToniChopp/SimCroP.

Wrist Fracture is the most common type of fracture with a high incidence rate. Conventional radiography (i.e. X-ray imaging) is used for wrist fracture detection routinely, but occasionally fracture delineation poses issues and an additional confirmation by computed tomography (CT) is needed for diagnosis. Recent advances in the field of Deep Learning (DL), a subfield of Artificial Intelligence (AI), have shown that wrist fracture detection can be automated using Convolutional Neural Networks. However, previous studies did not pay close attention to the difficult cases which can only be confirmed via CT imaging. In this study, we have developed and analyzed a state-of-the-art DL-based pipeline for wrist (distal radius) fracture detection -- DeepWrist, and evaluated it against one general population test set, and one challenging test set comprising only cases requiring confirmation by CT. Our results reveal that a typical state-of-the-art approach, such as DeepWrist, while having a near-perfect performance on the general independent test set, has a substantially lower performance on the challenging test set -- average precision of 0.99 (0.99-0.99) vs 0.64 (0.46-0.83), respectively. Similarly, the area under the ROC curve was of 0.99 (0.98-0.99) vs 0.84 (0.72-0.93), respectively. Our findings highlight the importance of a meticulous analysis of DL-based models before clinical use, and unearth the need for more challenging settings for testing medical AI systems.

Recently, diffusion models have been used to solve various inverse problems in an unsupervised manner with appropriate modifications to the sampling process. However, the current solvers, which recursively apply a reverse diffusion step followed by a projection-based measurement consistency step, often produce suboptimal results. By studying the generative sampling path, here we show that current solvers throw the sample path off the data manifold, and hence the error accumulates. To address this, we propose an additional correction term inspired by the manifold constraint, which can be used synergistically with the previous solvers to make the iterations close to the manifold. The proposed manifold constraint is straightforward to implement within a few lines of code, yet boosts the performance by a surprisingly large margin. With extensive experiments, we show that our method is superior to the previous methods both theoretically and empirically, producing promising results in many applications such as image inpainting, colorization, and sparse-view computed tomography. Code available https://github.com/HJ-harry/MCG_diffusion

Medical imaging is essential in modern radiotherapy, supporting diagnosis, treatment planning, and monitoring. Synthetic imaging, particularly synthetic computed tomography (sCT), is gaining traction in radiotherapy. The SynthRAD2025 dataset and Grand Challenge promote advancements in sCT generation by providing a benchmarking platform for algorithms using cone-beam CT (CBCT) and magnetic resonance imaging (MRI). The dataset includes 2362 cases: 890 MRI-CT and 1472 CBCT-CT pairs from head-and-neck, thoracic, and abdominal cancer patients treated at five European university medical centers (UMC Groningen, UMC Utrecht, Radboud UMC, LMU University Hospital Munich, and University Hospital of Cologne). Data were acquired with diverse scanners and protocols. Pre-processing, including rigid and deformable image registration, ensures high-quality, modality-aligned images. Extensive quality assurance validates image consistency and usability. All imaging data is provided in MetaImage (.mha) format, ensuring compatibility with medical image processing tools. Metadata, including acquisition parameters and registration details, is available in structured CSV files. To maintain dataset integrity, SynthRAD2025 is divided into training (65%), validation (10%), and test (25%) sets. The dataset is accessible at https://doi.org/10.5281/zenodo.14918089 under the SynthRAD2025 collection. This dataset supports benchmarking and the development of synthetic imaging techniques for radiotherapy applications. Use cases include sCT generation for MRI-only and MR-guided photon/proton therapy, CBCT-based dose calculations, and adaptive radiotherapy workflows. By integrating diverse acquisition settings, SynthRAD2025 fosters robust, generalizable image synthesis algorithms, advancing personalized cancer care and adaptive radiotherapy.

Background: Recent advances in large language models highlight the need for high-quality multilingual medical datasets. While Japan leads globally in CT scanner deployment and utilization, the lack of large-scale Japanese radiology datasets has hindered the development of specialized language models for medical imaging analysis. Objective: To develop a comprehensive Japanese CT report dataset through machine translation and establish a specialized language model for structured finding classification. Additionally, to create a rigorously validated evaluation dataset through expert radiologist review. Methods: We translated the CT-RATE dataset (24,283 CT reports from 21,304 patients) into Japanese using GPT-4o mini. The training dataset consisted of 22,778 machine-translated reports, while the validation dataset included 150 radiologist-revised reports. We developed CT-BERT-JPN based on "tohoku-nlp/bert-base-japanese-v3" architecture for extracting 18 structured findings from Japanese radiology reports. Results: Translation metrics showed strong performance with BLEU scores of 0.731 and 0.690, and ROUGE scores ranging from 0.770 to 0.876 for Findings and from 0.748 to 0.857 for Impression sections. CT-BERT-JPN demonstrated superior performance compared to GPT-4o in 11 out of 18 conditions, including lymphadenopathy (+14.2%), interlobular septal thickening (+10.9%), and atelectasis (+7.4%). The model maintained F1 scores exceeding 0.95 in 14 out of 18 conditions and achieved perfect scores in four conditions. Conclusions: Our study establishes a robust Japanese CT report dataset and demonstrates the effectiveness of a specialized language model for structured finding classification. The hybrid approach of machine translation and expert validation enables the creation of large-scale medical datasets while maintaining high quality.

Robust and accurate detection and segmentation of heterogenous tumors appearing in different anatomical organs with supervised methods require large-scale labeled datasets covering all possible types of diseases. Due to the unavailability of such rich datasets and the high cost of annotations, unsupervised anomaly detection (UAD) methods have been developed aiming to detect the pathologies as deviation from the normality by utilizing the unlabeled healthy image data. However, developed UAD models are often trained with an incomplete distribution of healthy anatomies and have difficulties in preserving anatomical constraints. This work intends to, first, propose a robust inpainting model to learn the details of healthy anatomies and reconstruct high-resolution images by preserving anatomical constraints. Second, we propose an autoinpainting pipeline to automatically detect tumors, replace their appearance with the learned healthy anatomies, and based on that segment the tumoral volumes in a purely unsupervised fashion. Three imaging datasets, including PET, CT, and PET-CT scans of lung tumors and head and neck tumors, are studied as benchmarks for evaluation. Experimental results demonstrate the significant superiority of the proposed method over a wide range of state-of-the-art UAD methods. Moreover, the unsupervised method we propose produces comparable results to a robust supervised segmentation method when applied to multimodal images.

We introduce CheXGenBench, a rigorous and multifaceted evaluation framework for synthetic chest radiograph generation that simultaneously assesses fidelity, privacy risks, and clinical utility across state-of-the-art text-to-image generative models. Despite rapid advancements in generative AI for real-world imagery, medical domain evaluations have been hindered by methodological inconsistencies, outdated architectural comparisons, and disconnected assessment criteria that rarely address the practical clinical value of synthetic samples. CheXGenBench overcomes these limitations through standardised data partitioning and a unified evaluation protocol comprising over 20 quantitative metrics that systematically analyse generation quality, potential privacy vulnerabilities, and downstream clinical applicability across 11 leading text-to-image architectures. Our results reveal critical inefficiencies in the existing evaluation protocols, particularly in assessing generative fidelity, leading to inconsistent and uninformative comparisons. Our framework establishes a standardised benchmark for the medical AI community, enabling objective and reproducible comparisons while facilitating seamless integration of both existing and future generative models. Additionally, we release a high-quality, synthetic dataset, SynthCheX-75K, comprising 75K radiographs generated by the top-performing model (Sana 0.6B) in our benchmark to support further research in this critical domain. Through CheXGenBench, we establish a new state-of-the-art and release our framework, models, and SynthCheX-75K dataset at https://raman1121.github.io/CheXGenBench/

Recently, Computer-Aided Diagnosis (CAD) systems have emerged as indispensable tools in clinical diagnostic workflows, significantly alleviating the burden on radiologists. Nevertheless, despite their integration into clinical settings, CAD systems encounter limitations. Specifically, while CAD systems can achieve high performance in the detection of lung nodules, they face challenges in accurately predicting multiple cancer types. This limitation can be attributed to the scarcity of publicly available datasets annotated with expert-level cancer type information. This research aims to bridge this gap by providing publicly accessible datasets and reliable tools for medical diagnosis, facilitating a finer categorization of different types of lung diseases so as to offer precise treatment recommendations. To achieve this objective, we curated a diverse dataset of lung Computed Tomography (CT) images, comprising 330 annotated nodules (nodules are labeled as bounding boxes) from 95 distinct patients. The quality of the dataset was evaluated using a variety of classical classification and detection models, and these promising results demonstrate that the dataset has a feasible application and further facilitate intelligent auxiliary diagnosis.

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

In this study, we present seg2med, an advanced medical image synthesis framework that uses Denoising Diffusion Probabilistic Models (DDPM) to generate high-quality synthetic medical images conditioned on anatomical masks from TotalSegmentator. The framework synthesizes CT and MR images from segmentation masks derived from real patient data and XCAT digital phantoms, achieving a Structural Similarity Index Measure (SSIM) of 0.94 +/- 0.02 for CT and 0.89 +/- 0.04 for MR images compared to ground-truth images of real patients. It also achieves a Feature Similarity Index Measure (FSIM) of 0.78 +/- 0.04 for CT images from XCAT. The generative quality is further supported by a Fr\'echet Inception Distance (FID) of 3.62 for CT image generation. Additionally, seg2med can generate paired CT and MR images with consistent anatomical structures and convert images between CT and MR modalities, achieving SSIM values of 0.91 +/- 0.03 for MR-to-CT and 0.77 +/- 0.04 for CT-to-MR conversion. Despite the limitations of incomplete anatomical details in segmentation masks, the framework shows strong performance in cross-modality synthesis and multimodal imaging. seg2med also demonstrates high anatomical fidelity in CT synthesis, achieving a mean Dice coefficient greater than 0.90 for 11 abdominal organs and greater than 0.80 for 34 organs out of 59 in 58 test cases. The highest Dice of 0.96 +/- 0.01 was recorded for the right scapula. Leveraging the TotalSegmentator toolkit, seg2med enables segmentation mask generation across diverse datasets, supporting applications in clinical imaging, data augmentation, multimodal synthesis, and diagnostic algorithm development.

Ensuring the quality and integrity of medical images is crucial for maintaining diagnostic accuracy in deep learning-based Computer-Aided Diagnosis and Computer-Aided Detection (CAD) systems. Covariate shifts are subtle variations in the data distribution caused by different imaging devices or settings and can severely degrade model performance, similar to the effects of adversarial attacks. Therefore, it is vital to have a lightweight and fast method to assess the quality of these images prior to using CAD models. AdverX-Ray addresses this need by serving as an image-quality assessment layer, designed to detect covariate shifts effectively. This Adversarial Variational Autoencoder prioritizes the discriminator's role, using the suboptimal outputs of the generator as negative samples to fine-tune the discriminator's ability to identify high-frequency artifacts. Images generated by adversarial networks often exhibit severe high-frequency artifacts, guiding the discriminator to focus excessively on these components. This makes the discriminator ideal for this approach. Trained on patches from X-ray images of specific machine models, AdverX-Ray can evaluate whether a scan matches the training distribution, or if a scan from the same machine is captured under different settings. Extensive comparisons with various OOD detection methods show that AdverX-Ray significantly outperforms existing techniques, achieving a 96.2% average AUROC using only 64 random patches from an X-ray. Its lightweight and fast architecture makes it suitable for real-time applications, enhancing the reliability of medical imaging systems. The code and pretrained models are publicly available.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

Vision-language models can connect the text description of an object to its specific location in an image through visual grounding. This has potential applications in enhanced radiology reporting. However, these models require large annotated image-text datasets, which are lacking for PET/CT. We developed an automated pipeline to generate weak labels linking PET/CT report descriptions to their image locations and used it to train a 3D vision-language visual grounding model. Our pipeline finds positive findings in PET/CT reports by identifying mentions of SUVmax and axial slice numbers. From 25,578 PET/CT exams, we extracted 11,356 sentence-label pairs. Using this data, we trained ConTEXTual Net 3D, which integrates text embeddings from a large language model with a 3D nnU-Net via token-level cross-attention. The model's performance was compared against LLMSeg, a 2.5D version of ConTEXTual Net, and two nuclear medicine physicians. The weak-labeling pipeline accurately identified lesion locations in 98% of cases (246/251), with 7.5% requiring boundary adjustments. ConTEXTual Net 3D achieved an F1 score of 0.80, outperforming LLMSeg (F1=0.22) and the 2.5D model (F1=0.53), though it underperformed both physicians (F1=0.94 and 0.91). The model achieved better performance on FDG (F1=0.78) and DCFPyL (F1=0.75) exams, while performance dropped on DOTATE (F1=0.58) and Fluciclovine (F1=0.66). The model performed consistently across lesion sizes but showed reduced accuracy on lesions with low uptake. Our novel weak labeling pipeline accurately produced an annotated dataset of PET/CT image-text pairs, facilitating the development of 3D visual grounding models. ConTEXTual Net 3D significantly outperformed other models but fell short of the performance of nuclear medicine physicians. Our study suggests that even larger datasets may be needed to close this performance gap.

Synthetic medical data generation has opened up new possibilities in the healthcare domain, offering a powerful tool for simulating clinical scenarios, enhancing diagnostic and treatment quality, gaining granular medical knowledge, and accelerating the development of unbiased algorithms. In this context, we present a novel approach called ViewXGen, designed to overcome the limitations of existing methods that rely on general domain pipelines using only radiology reports to generate frontal-view chest X-rays. Our approach takes into consideration the diverse view positions found in the dataset, enabling the generation of chest X-rays with specific views, which marks a significant advancement in the field. To achieve this, we introduce a set of specially designed tokens for each view position, tailoring the generation process to the user's preferences. Furthermore, we leverage multi-view chest X-rays as input, incorporating valuable information from different views within the same study. This integration rectifies potential errors and contributes to faithfully capturing abnormal findings in chest X-ray generation. To validate the effectiveness of our approach, we conducted statistical analyses, evaluating its performance in a clinical efficacy metric on the MIMIC-CXR dataset. Also, human evaluation demonstrates the remarkable capabilities of ViewXGen, particularly in producing realistic view-specific X-rays that closely resemble the original images.

We investigate a variational method for ill-posed problems, named graphLa+Psi, which embeds a graph Laplacian operator in the regularization term. The novelty of this method lies in constructing the graph Laplacian based on a preliminary approximation of the solution, which is obtained using any existing reconstruction method Psi from the literature. As a result, the regularization term is both dependent on and adaptive to the observed data and noise. We demonstrate that graphLa+Psi is a regularization method and rigorously establish both its convergence and stability properties. We present selected numerical experiments in 2D computerized tomography, wherein we integrate the graphLa+Psi method with various reconstruction techniques Psi, including Filter Back Projection (graphLa+FBP), standard Tikhonov (graphLa+Tik), Total Variation (graphLa+TV), and a trained deep neural network (graphLa+Net). The graphLa+Psi approach significantly enhances the quality of the approximated solutions for each method Psi. Notably, graphLa+Net is outperforming, offering a robust and stable application of deep neural networks in solving inverse problems.

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.

Since the introduction of TotalSegmentator CT, there is demand for a similar robust automated MRI segmentation tool that can be applied across all MRI sequences and anatomic structures. In this retrospective study, a nnU-Net model (TotalSegmentator) was trained on MRI and CT examinations to segment 80 anatomic structures relevant for use cases such as organ volumetry, disease characterization, surgical planning and opportunistic screening. Examinations were randomly sampled from routine clinical studies to represent real-world examples. Dice scores were calculated between the predicted segmentations and expert radiologist reference standard segmentations to evaluate model performance on an internal test set, two external test sets and against two publicly available models, and TotalSegmentator CT. The model was applied to an internal dataset containing abdominal MRIs to investigate age-dependent volume changes. A total of 1143 examinations (616 MRIs, 527 CTs) (median age 61 years, IQR 50-72) were split into training (n=1088, CT and MRI) and an internal test set (n=55; only MRI), two external test sets (AMOS, n=20; CHAOS, n=20; only MRI), and an internal aging-study dataset of 8672 abdominal MRIs (median age 59 years, IQR 45-70) were included. The model showed a Dice Score of 0.839 on the internal test set and outperformed two other models (Dice Score, 0.862 versus 0.759; and 0.838 versus 0.560; p<.001 for both). The proposed open-source, easy-to-use model allows for automatic, robust segmentation of 80 structures, extending the capabilities of TotalSegmentator to MRIs of any sequence. The ready-to-use online tool is available at https://totalsegmentator.com, the model at https://github.com/wasserth/TotalSegmentator, and the dataset at https://zenodo.org/records/14710732.

Background: Thyroid ultrasound is commonly performed using a combination of static images and cine clips (video recordings). However, the exact utility and impact of cine images remains unknown. This study aimed to evaluate the impact of cine imaging on accuracy and consistency of thyroid nodule assessment, using the American College of Radiology Thyroid Reporting and Data System (ACR TI-RADS). Methods: 50 benign and 50 malignant thyroid nodules with cytopathology results were included. A reader study with 4 specialty-trained radiologists was then conducted over 3 rounds, assessing only static images in the first two rounds and both static and cine images in the third round. TI-RADS scores and the consequent management recommendations were then evaluated by comparing them to the malignancy status of the nodules. Results: Mean sensitivity for malignancy detection was 0.65 for static images and 0.67 with both static and cine images (p>0.5). Specificity was 0.20 for static images and 0.22 with both static and cine images (p>0.5). Management recommendations were similar with and without cine images. Intrareader agreement on feature assignments remained consistent across all rounds, though TI-RADS point totals were slightly higher with cine images. Conclusion: The inclusion of cine imaging for thyroid nodule assessment on ultrasound did not significantly change diagnostic performance. Current practice guidelines, which do not mandate cine imaging, are sufficient for accurate diagnosis.

Background: Reporting and Data Systems (RADS) standardize radiology risk communication but automated RADS assignment from narrative reports is challenging because of guideline complexity, output-format constraints, and limited benchmarking across RADS frameworks and model sizes. Purpose: To create RXL-RADSet, a radiologist-verified synthetic multi-RADS benchmark, and compare validity and accuracy of open-weight small language models (SLMs) with a proprietary model for RADS assignment. Materials and Methods: RXL-RADSet contains 1,600 synthetic radiology reports across 10 RADS (BI-RADS, CAD-RADS, GB-RADS, LI-RADS, Lung-RADS, NI-RADS, O-RADS, PI-RADS, TI-RADS, VI-RADS) and multiple modalities. Reports were generated by LLMs using scenario plans and simulated radiologist styles and underwent two-stage radiologist verification. We evaluated 41 quantized SLMs (12 families, 0.135-32B parameters) and GPT-5.2 under a fixed guided prompt. Primary endpoints were validity and accuracy; a secondary analysis compared guided versus zero-shot prompting. Results: Under guided prompting GPT-5.2 achieved 99.8% validity and 81.1% accuracy (1,600 predictions). Pooled SLMs (65,600 predictions) achieved 96.8% validity and 61.1% accuracy; top SLMs in the 20-32B range reached ~99% validity and mid-to-high 70% accuracy. Performance scaled with model size (inflection between <1B and >=10B) and declined with RADS complexity primarily due to classification difficulty rather than invalid outputs. Guided prompting improved validity (99.2% vs 96.7%) and accuracy (78.5% vs 69.6%) compared with zero-shot. Conclusion: RXL-RADSet provides a radiologist-verified multi-RADS benchmark; large SLMs (20-32B) can approach proprietary-model performance under guided prompting, but gaps remain for higher-complexity schemes.

Industry standards require medical device manufacturers to perform implant-induced artefact testing in phantoms at a pre-clinical stage to define the extent of artefacts that can be expected during MRI. Once a device is commercially available, studies on volunteers, cadavers or patients are performed to investigate implant-induced artefacts and artefact reduction methods more in-depth. This study describes the design and evaluation of a realistic head phantom for pre-clinical implant-induced artefact testing in a relevant environment. A case study is performed where a state-of-the-art piezoelectric bone conduction implant is used in the 1.5 T and 3 T MRI environments. Images were acquired using clinical and novel metal artefact reducing (MARS) sequences at both field strengths. Artefact width and length were measured in a healthy volunteer and compared with artefact sizes obtained in the phantom. Artefact sizes are reported that are similar in shape between the phantom and a volunteer, yet with dimensions differing up to 20% between both. When the implant magnet is removed, the artefact size can be reduced below a diameter of 5 cm, whilst the presence of an implant magnet and splint creates higher artefacts up to 20 cm in diameter. Pulse sequences have been altered to reduce the scan time up to 7 minutes, while preserving the image quality. These results show that the anthropomorphic phantom can be used at a preclinical stage to provide clinically relevant images, illustrating the impact of the artefact on important brain structures.

This paper presents a proof-of-concept approach for learned synergistic reconstruction of medical images using multi-branch generative models. Leveraging variational autoencoders (VAEs) and generative adversarial networks (GANs), our models learn from pairs of images simultaneously, enabling effective denoising and reconstruction. Synergistic image reconstruction is achieved by incorporating the trained models in a regularizer that evaluates the distance between the images and the model, in a similar fashion to multichannel dictionary learning (DiL). We demonstrate the efficacy of our approach on both Modified National Institute of Standards and Technology (MNIST) and positron emission tomography (PET)/computed tomography (CT) datasets, showcasing improved image quality and information sharing between modalities. Despite challenges such as patch decomposition and model limitations, our results underscore the potential of generative models for enhancing medical imaging reconstruction.

Medical imaging is critical for diagnostics, but clinical adoption of advanced AI-driven imaging faces challenges due to patient variability, image artifacts, and limited model generalization. While deep learning has transformed image analysis, 3D medical imaging still suffers from data scarcity and inconsistencies due to acquisition protocols, scanner differences, and patient motion. Traditional augmentation uses a single pipeline for all transformations, disregarding the unique traits of each augmentation and struggling with large data volumes. To address these challenges, we propose a Multi-encoder Augmentation-Aware Learning (MEAL) framework that leverages four distinct augmentation variants processed through dedicated encoders. Three fusion strategies such as concatenation (CC), fusion layer (FL), and adaptive controller block (BD) are integrated to build multi-encoder models that combine augmentation-specific features before decoding. MEAL-BD uniquely preserves augmentation-aware representations, enabling robust, protocol-invariant feature learning. As demonstrated in a Computed Tomography (CT)-to-T1-weighted Magnetic Resonance Imaging (MRI) translation study, MEAL-BD consistently achieved the best performance on both unseen- and predefined-test data. On both geometric transformations (like rotations and flips) and non-augmented inputs, MEAL-BD outperformed other competing methods, achieving higher mean peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) scores. These results establish MEAL as a reliable framework for preserving structural fidelity and generalizing across clinically relevant variability. By reframing augmentation as a source of diverse, generalizable features, MEAL supports robust, protocol-invariant learning, advancing clinically reliable medical imaging solutions.

Spine-related diseases have high morbidity and cause a huge burden of social cost. Spine imaging is an essential tool for noninvasively visualizing and assessing spinal pathology. Segmenting vertebrae in computed tomography (CT) images is the basis of quantitative medical image analysis for clinical diagnosis and surgery planning of spine diseases. Current publicly available annotated datasets on spinal vertebrae are small in size. Due to the lack of a large-scale annotated spine image dataset, the mainstream deep learning-based segmentation methods, which are data-driven, are heavily restricted. In this paper, we introduce a large-scale spine CT dataset, called CTSpine1K, curated from multiple sources for vertebra segmentation, which contains 1,005 CT volumes with over 11,100 labeled vertebrae belonging to different spinal conditions. Based on this dataset, we conduct several spinal vertebrae segmentation experiments to set the first benchmark. We believe that this large-scale dataset will facilitate further research in many spine-related image analysis tasks, including but not limited to vertebrae segmentation, labeling, 3D spine reconstruction from biplanar radiographs, image super-resolution, and enhancement.

Medical imaging plays a crucial role in modern healthcare by providing non-invasive visualisation of internal structures and abnormalities, enabling early disease detection, accurate diagnosis, and treatment planning. This study aims to explore the application of deep learning models, particularly focusing on the UNet architecture and its variants, in medical image segmentation. We seek to evaluate the performance of these models across various challenging medical image segmentation tasks, addressing issues such as image normalization, resizing, architecture choices, loss function design, and hyperparameter tuning. The findings reveal that the standard UNet, when extended with a deep network layer, is a proficient medical image segmentation model, while the Res-UNet and Attention Res-UNet architectures demonstrate smoother convergence and superior performance, particularly when handling fine image details. The study also addresses the challenge of high class imbalance through careful preprocessing and loss function definitions. We anticipate that the results of this study will provide useful insights for researchers seeking to apply these models to new medical imaging problems and offer guidance and best practices for their implementation.

With the growing volume of CT examinations, there is an increasing demand for automated tools such as organ segmentation, abnormality detection, and report generation to support radiologists in managing their clinical workload. Multi-label classification of 3D Chest CT scans remains a critical yet challenging problem due to the complex spatial relationships inherent in volumetric data and the wide variability of abnormalities. Existing methods based on 3D convolutional neural networks struggle to capture long-range dependencies, while Vision Transformers often require extensive pre-training on large-scale, domain-specific datasets to perform competitively. In this work of academic research, we propose a 2.5D alternative by introducing a new graph-based framework that represents 3D CT volumes as structured graphs, where axial slice triplets serve as nodes processed through spectral graph convolution, enabling the model to reason over inter-slice dependencies while maintaining complexity compatible with clinical deployment. Our method, trained and evaluated on 3 datasets from independent institutions, achieves strong cross-dataset generalization, and shows competitive performance compared to state-of-the-art visual encoders. We further conduct comprehensive ablation studies to evaluate the impact of various aggregation strategies, edge-weighting schemes, and graph connectivity patterns. Additionally, we demonstrate the broader applicability of our approach through transfer experiments on automated radiology report generation and abdominal CT data.

Accurate delineation of anatomical structures in volumetric CT scans is crucial for diagnosis and treatment planning. While AI has advanced automated segmentation, current approaches typically target individual structures, creating a fragmented landscape of incompatible models with varying performance and disparate evaluation protocols. Foundational segmentation models address these limitations by providing a holistic anatomical view through a single model. Yet, robust clinical deployment demands comprehensive training data, which is lacking in existing whole-body approaches, both in terms of data heterogeneity and, more importantly, anatomical coverage. In this work, rather than pursuing incremental optimizations in model architecture, we present CADS, an open-source framework that prioritizes the systematic integration, standardization, and labeling of heterogeneous data sources for whole-body CT segmentation. At its core is a large-scale dataset of 22,022 CT volumes with complete annotations for 167 anatomical structures, representing a significant advancement in both scale and coverage, with 18 times more scans than existing collections and 60% more distinct anatomical targets. Building on this diverse dataset, we develop the CADS-model using established architectures for accessible and automated full-body CT segmentation. Through comprehensive evaluation across 18 public datasets and an independent real-world hospital cohort, we demonstrate advantages over SoTA approaches. Notably, thorough testing of the model's performance in segmentation tasks from radiation oncology validates its direct utility for clinical interventions. By making our large-scale dataset, our segmentation models, and our clinical software tool publicly available, we aim to advance robust AI solutions in radiology and make comprehensive anatomical analysis accessible to clinicians and researchers alike.

Solving the inverse problem is the key step in evaluating the capacity of a physical model to describe real phenomena. In medical image computing, it aligns with the classical theme of image-based model personalization. Traditionally, a solution to the problem is obtained by performing either sampling or variational inference based methods. Both approaches aim to identify a set of free physical model parameters that results in a simulation best matching an empirical observation. When applied to brain tumor modeling, one of the instances of image-based model personalization in medical image computing, the overarching drawback of the methods is the time complexity for finding such a set. In a clinical setting with limited time between imaging and diagnosis or even intervention, this time complexity may prove critical. As the history of quantitative science is the history of compression, we align in this paper with the historical tendency and propose a method compressing complex traditional strategies for solving an inverse problem into a simple database query task. We evaluated different ways of performing the database query task assessing the trade-off between accuracy and execution time. On the exemplary task of brain tumor growth modeling, we prove that the proposed method achieves one order speed-up compared to existing approaches for solving the inverse problem. The resulting compute time offers critical means for relying on more complex and, hence, realistic models, for integrating image preprocessing and inverse modeling even deeper, or for implementing the current model into a clinical workflow.

With over 85 million CT scans performed annually in the United States, creating tumor-related reports is a challenging and time-consuming task for radiologists. To address this need, we present RadGPT, an Anatomy-Aware Vision-Language AI Agent for generating detailed reports from CT scans. RadGPT first segments tumors, including benign cysts and malignant tumors, and their surrounding anatomical structures, then transforms this information into both structured reports and narrative reports. These reports provide tumor size, shape, location, attenuation, volume, and interactions with surrounding blood vessels and organs. Extensive evaluation on unseen hospitals shows that RadGPT can produce accurate reports, with high sensitivity/specificity for small tumor (<2 cm) detection: 80/73% for liver tumors, 92/78% for kidney tumors, and 77/77% for pancreatic tumors. For large tumors, sensitivity ranges from 89% to 97%. The results significantly surpass the state-of-the-art in abdominal CT report generation. RadGPT generated reports for 17 public datasets. Through radiologist review and refinement, we have ensured the reports' accuracy, and created the first publicly available image-text 3D medical dataset, comprising over 1.8 million text tokens and 2.7 million images from 9,262 CT scans, including 2,947 tumor scans/reports of 8,562 tumor instances. Our reports can: (1) localize tumors in eight liver sub-segments and three pancreatic sub-segments annotated per-voxel; (2) determine pancreatic tumor stage (T1-T4) in 260 reports; and (3) present individual analyses of multiple tumors--rare in human-made reports. Importantly, 948 of the reports are for early-stage tumors.

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

Long-tailed class distributions pose a significant challenge for multi-label chest X-ray (CXR) classification, where rare but clinically important findings are severely underrepresented. In this work, we present a systematic empirical evaluation of loss functions, CNN backbone architectures and post-training strategies on the CXR-LT 2026 benchmark, comprising approximately 143K images with 30 disease labels from PadChest. Our experiments demonstrate that LDAM with deferred re-weighting (LDAM-DRW) consistently outperforms standard BCE and asymmetric losses for rare class recognition. Amongst the architectures evaluated, ConvNeXt-Large achieves the best single-model performance with 0.5220 mAP and 0.3765 F1 on our development set, whilst classifier re-training and test-time augmentation further improve ranking metrics. On the official test leaderboard, our submission achieved 0.3950 mAP, ranking 5th amongst all 68 participating teams with total of 1528 submissions. We provide a candid analysis of the development-to-test performance gap and discuss practical insights for handling class imbalance in clinical imaging settings. Code is available at https://github.com/Nikhil-Rao20/Long_Tail.

The morphometry of a kidney tumor revealed by contrast-enhanced Computed Tomography (CT) imaging is an important factor in clinical decision making surrounding the lesion's diagnosis and treatment. Quantitative study of the relationship between kidney tumor morphology and clinical outcomes is difficult due to data scarcity and the laborious nature of manually quantifying imaging predictors. Automatic semantic segmentation of kidneys and kidney tumors is a promising tool towards automatically quantifying a wide array of morphometric features, but no sizeable annotated dataset is currently available to train models for this task. We present the KiTS19 challenge dataset: A collection of multi-phase CT imaging, segmentation masks, and comprehensive clinical outcomes for 300 patients who underwent nephrectomy for kidney tumors at our center between 2010 and 2018. 210 (70%) of these patients were selected at random as the training set for the 2019 MICCAI KiTS Kidney Tumor Segmentation Challenge and have been released publicly. With the presence of clinical context and surgical outcomes, this data can serve not only for benchmarking semantic segmentation models, but also for developing and studying biomarkers which make use of the imaging and semantic segmentation masks.

As lung cancer evolves, the presence of enlarged and potentially malignant lymph nodes must be assessed to properly estimate disease progression and select the best treatment strategy. Following the clinical guidelines, estimation of short-axis diameter and mediastinum station are paramount for correct diagnosis. A method for accurate and automatic segmentation is hence decisive for quantitatively describing lymph nodes. In this study, the use of 3D convolutional neural networks, either through slab-wise schemes or the leveraging of downsampled entire volumes, is investigated. Furthermore, the potential impact from simple ensemble strategies is considered. As lymph nodes have similar attenuation values to nearby anatomical structures, we suggest using the knowledge of other organs as prior information to guide the segmentation task. To assess the segmentation and instance detection performances, a 5-fold cross-validation strategy was followed over a dataset of 120 contrast-enhanced CT volumes. For the 1178 lymph nodes with a short-axis diameter geq10 mm, our best performing approach reached a patient-wise recall of 92%, a false positive per patient ratio of 5, and a segmentation overlap of 80.5%. The method performs similarly well across all stations. Fusing a slab-wise and a full volume approach within an ensemble scheme generated the best performances. The anatomical priors guiding strategy is promising, yet a larger set than four organs appears needed to generate an optimal benefit. A larger dataset is also mandatory, given the wide range of expressions a lymph node can exhibit (i.e., shape, location, and attenuation), and contrast uptake variations.

Incorporating prior information into inverse problems, e.g. via maximum-a-posteriori estimation, is an important technique for facilitating robust inverse problem solutions. In this paper, we devise two novel approaches for linear inverse problems that permit problem-specific statistical prior selections within the compound Gaussian (CG) class of distributions. The CG class subsumes many commonly used priors in signal and image reconstruction methods including those of sparsity-based approaches. The first method developed is an iterative algorithm, called generalized compound Gaussian least squares (G-CG-LS), that minimizes a regularized least squares objective function where the regularization enforces a CG prior. G-CG-LS is then unrolled, or unfolded, to furnish our second method, which is a novel deep regularized (DR) neural network, called DR-CG-Net, that learns the prior information. A detailed computational theory on convergence properties of G-CG-LS and thorough numerical experiments for DR-CG-Net are provided. Due to the comprehensive nature of the CG prior, these experiments show that DR-CG-Net outperforms competitive prior art methods in tomographic imaging and compressive sensing, especially in challenging low-training scenarios.

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.

Radiographs are used as the most important imaging tool for identifying spine anomalies in clinical practice. The evaluation of spinal bone lesions, however, is a challenging task for radiologists. This work aims at developing and evaluating a deep learning-based framework, named VinDr-SpineXR, for the classification and localization of abnormalities from spine X-rays. First, we build a large dataset, comprising 10,468 spine X-ray images from 5,000 studies, each of which is manually annotated by an experienced radiologist with bounding boxes around abnormal findings in 13 categories. Using this dataset, we then train a deep learning classifier to determine whether a spine scan is abnormal and a detector to localize 7 crucial findings amongst the total 13. The VinDr-SpineXR is evaluated on a test set of 2,078 images from 1,000 studies, which is kept separate from the training set. It demonstrates an area under the receiver operating characteristic curve (AUROC) of 88.61% (95% CI 87.19%, 90.02%) for the image-level classification task and a mean average precision (mAP@0.5) of 33.56% for the lesion-level localization task. These results serve as a proof of concept and set a baseline for future research in this direction. To encourage advances, the dataset, codes, and trained deep learning models are made publicly available.

Accurate segmentation of tumors in PET/CT images is important in computer-aided diagnosis and treatment of cancer. The key issue of such a segmentation problem lies in the effective integration of complementary information from PET and CT images. However, the quality of PET and CT images varies widely in clinical settings, which leads to uncertainty in the modality information extracted by networks. To take the uncertainty into account in multi-modal information fusion, this paper proposes a novel Multi-modal Evidential Fusion Network (MEFN) comprising a Cross-Modal Feature Learning (CFL) module and a Multi-modal Trusted Fusion (MTF) module. The CFL module reduces the domain gap upon modality conversion and highlights common tumor features, thereby alleviating the needs of the segmentation module to handle modality specificity. The MTF module utilizes mutual attention mechanisms and an uncertainty calibrator to fuse modality features based on modality uncertainty and then fuse the segmentation results under the guidance of Dempster-Shafer Theory. Besides, a new uncertainty perceptual loss is introduced to force the model focusing on uncertain features and hence improve its ability to extract trusted modality information. Extensive comparative experiments are conducted on two publicly available PET/CT datasets to evaluate the performance of our proposed method whose results demonstrate that our MEFN significantly outperforms state-of-the-art methods with improvements of 2.15% and 3.23% in DSC scores on the AutoPET dataset and the Hecktor dataset, respectively. More importantly, our model can provide radiologists with credible uncertainty of the segmentation results for their decision in accepting or rejecting the automatic segmentation results, which is particularly important for clinical applications. Our code will be available at https://github.com/QPaws/MEFN.

While recent advancing image super-resolution (SR) techniques are continually improving the perceptual quality of their outputs, they can usually fail in quantitative evaluations. This inconsistency leads to a growing distrust in existing image metrics for SR evaluations. Though image evaluation depends on both the metric and the reference ground truth (GT), researchers typically do not inspect the role of GTs, as they are generally accepted as `perfect' references. However, due to the data being collected in the early years and the ignorance of controlling other types of distortions, we point out that GTs in existing SR datasets can exhibit relatively poor quality, which leads to biased evaluations. Following this observation, in this paper, we are interested in the following questions: Are GT images in existing SR datasets 100% trustworthy for model evaluations? How does GT quality affect this evaluation? And how to make fair evaluations if there exist imperfect GTs? To answer these questions, this paper presents two main contributions. First, by systematically analyzing seven state-of-the-art SR models across three real-world SR datasets, we show that SR performances can be consistently affected across models by low-quality GTs, and models can perform quite differently when GT quality is controlled. Second, we propose a novel perceptual quality metric, Relative Quality Index (RQI), that measures the relative quality discrepancy of image pairs, thus issuing the biased evaluations caused by unreliable GTs. Our proposed model achieves significantly better consistency with human opinions. We expect our work to provide insights for the SR community on how future datasets, models, and metrics should be developed.

Radiology reporting generative AI holds significant potential to alleviate clinical workloads and streamline medical care. However, achieving high clinical accuracy is challenging, as radiological images often feature subtle lesions and intricate structures. Existing systems often fall short, largely due to their reliance on fixed size, patch-level image features and insufficient incorporation of pathological information. This can result in the neglect of such subtle patterns and inconsistent descriptions of crucial pathologies. To address these challenges, we propose an innovative approach that leverages pathology-aware regional prompts to explicitly integrate anatomical and pathological information of various scales, significantly enhancing the precision and clinical relevance of generated reports. We develop an anatomical region detector that extracts features from distinct anatomical areas, coupled with a novel multi-label lesion detector that identifies global pathologies. Our approach emulates the diagnostic process of radiologists, producing clinically accurate reports with comprehensive diagnostic capabilities. Experimental results show that our model outperforms previous state-of-the-art methods on most natural language generation and clinical efficacy metrics, with formal expert evaluations affirming its potential to enhance radiology practice.

Image enhancement improves visual quality and helps reveal details that are hard to see in the original image. In medical imaging, it can support clinical decision-making, but current models often over-edit. This can distort organs, create false findings, and miss small tumors because these models do not understand anatomy or contrast dynamics. We propose SMILE, an anatomy-aware diffusion model that learns how organs are shaped and how they take up contrast. It enhances only clinically relevant regions while leaving all other areas unchanged. SMILE introduces three key ideas: (1) structure-aware supervision that follows true organ boundaries and contrast patterns; (2) registration-free learning that works directly with unaligned multi-phase CT scans; (3) unified inference that provides fast and consistent enhancement across all contrast phases. Across six external datasets, SMILE outperforms existing methods in image quality (14.2% higher SSIM, 20.6% higher PSNR, 50% better FID) and in clinical usefulness by producing anatomically accurate and diagnostically meaningful images. SMILE also improves cancer detection from non-contrast CT, raising the F1 score by up to 10 percent.