Daily Papers

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.

Interstitial lung diseases (ILD) present diagnostic challenges due to their varied manifestations and overlapping imaging features. To address this, we propose a machine learning approach that utilizes CLIP, a multimodal (image and text) self-supervised model, for ILD classification. We extensively integrate zero-shot CLIP throughout our workflow, starting from the initial extraction of image patches from volumetric CT scans and proceeding to ILD classification using "patch montages". Furthermore, we investigate how domain adaptive pretraining (DAPT) CLIP with task-specific images (CT "patch montages" extracted with ILD-specific prompts for CLIP) and/or text (lung-specific sections of radiology reports) affects downstream ILD classification performance. By leveraging CLIP-extracted "patch montages" and DAPT, we achieve strong zero-shot ILD classification results, including an AUROC of 0.893, without the need for any labeled training data. This work highlights the versatility and potential of multimodal models like CLIP for medical image classification tasks where labeled data is scarce.

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.

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.

Vision-and-language models (VLMs) have been increasingly explored in the medical domain, particularly following the success of CLIP in general domain. However, unlike the relatively straightforward pairing of 2D images and text, curating large-scale paired data in the medical field for volumetric modalities such as CT scans remains a challenging and time-intensive process. This difficulty often limits the performance on downstream tasks. To address these challenges, we propose a novel vision-language pre-training (VLP) framework, termed as VELVET-Med, specifically designed for limited volumetric data such as 3D CT and associated radiology reports. Instead of relying on large-scale data collection, our method focuses on the development of effective pre-training objectives and model architectures. The key contributions are: 1) We incorporate uni-modal self-supervised learning into VLP framework, which are often underexplored in the existing literature. 2) We propose a novel language encoder, termed as TriBERT, for learning multi-level textual semantics. 3) We devise the hierarchical contrastive learning to capture multi-level vision-language correspondence. Using only 38,875 scan-report pairs, our approach seeks to uncover rich spatial and semantic relationships embedded in volumetric medical images and corresponding clinical narratives, thereby enhancing the generalization ability of the learned encoders. The resulting encoders exhibit strong transferability, achieving state-of-the-art performance across a wide range of downstream tasks, including 3D segmentation, cross-modal retrieval, visual question answering, and report generation.

Accurate tumor size measurement is a cornerstone of evaluating cancer treatment response. The most widely adopted standard for this purpose is the Response Evaluation Criteria in Solid Tumors (RECIST) v1.1, which relies on measuring the longest tumor diameter in a single plane. However, volumetric measurements have been shown to provide a more reliable assessment of treatment effect. Their clinical adoption has been limited, though, due to the labor-intensive nature of manual volumetric annotation. In this paper, we present Lite ENSAM, a lightweight adaptation of the ENSAM architecture designed for efficient volumetric tumor segmentation from CT scans annotated with RECIST annotations. Lite ENSAM was submitted to the MICCAI FLARE 2025 Task 1: Pan-cancer Segmentation in CT Scans, Subtask 2, where it achieved a Dice Similarity Coefficient (DSC) of 60.7% and a Normalized Surface Dice (NSD) of 63.6% on the hidden test set, and an average total RAM time of 50.6 GBs and an average inference time of 14.4 s on CPU on the public validation dataset.

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.

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.

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.

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.

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.

Recently, deep convolutional neural networks have achieved great success for medical image segmentation. However, unlike segmentation of natural images, most medical images such as MRI and CT are volumetric data. In order to make full use of volumetric information, 3D CNNs are widely used. However, 3D CNNs suffer from higher inference time and computation cost, which hinders their further clinical applications. Additionally, with the increased number of parameters, the risk of overfitting is higher, especially for medical images where data and annotations are expensive to acquire. To issue this problem, many 2.5D segmentation methods have been proposed to make use of volumetric spatial information with less computation cost. Despite these works lead to improvements on a variety of segmentation tasks, to the best of our knowledge, there has not previously been a large-scale empirical comparison of these methods. In this paper, we aim to present a review of the latest developments of 2.5D methods for volumetric medical image segmentation. Additionally, to compare the performance and effectiveness of these methods, we provide an empirical study of these methods on three representative segmentation tasks involving different modalities and targets. Our experimental results highlight that 3D CNNs may not always be the best choice. Despite all these 2.5D methods can bring performance gains to 2D baseline, not all the methods hold the benefits on different datasets. We hope the results and conclusions of our study will prove useful for the community on exploring and developing efficient volumetric medical image segmentation methods.

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.

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.

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.

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.

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.

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.

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.

Medical image analysis is crucial in modern radiological diagnostics, especially given the exponential growth in medical imaging data. The demand for automated report generation systems has become increasingly urgent. While prior research has mainly focused on using machine learning and multimodal language models for 2D medical images, the generation of reports for 3D medical images has been less explored due to data scarcity and computational complexities. This paper introduces 3D-CT-GPT, a Visual Question Answering (VQA)-based medical visual language model specifically designed for generating radiology reports from 3D CT scans, particularly chest CTs. Extensive experiments on both public and private datasets demonstrate that 3D-CT-GPT significantly outperforms existing methods in terms of report accuracy and quality. Although current methods are few, including the partially open-source CT2Rep and the open-source M3D, we ensured fair comparison through appropriate data conversion and evaluation methodologies. Experimental results indicate that 3D-CT-GPT enhances diagnostic accuracy and report coherence, establishing itself as a robust solution for clinical radiology report generation. Future work will focus on expanding the dataset and further optimizing the model to enhance its performance and applicability.

Precise image segmentation provides clinical study with meaningful and well-structured information. Despite the remarkable progress achieved in medical image segmentation, there is still an absence of foundation segmentation model that can segment a wide range of anatomical categories with easy user interaction. In this paper, we propose a universal and interactive volumetric medical image segmentation model, named SegVol. By training on 90k unlabeled Computed Tomography (CT) volumes and 6k labeled CTs, this foundation model supports the segmentation of over 200 anatomical categories using semantic and spatial prompts. Extensive experiments verify that SegVol outperforms the state of the art by a large margin on multiple segmentation benchmarks. Notably, on three challenging lesion datasets, our method achieves around 20% higher Dice score than nnU-Net. The model and data are publicly available at: https://github.com/BAAI-DCAI/SegVol.

Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation. Automating report generation has emerged as a critical need to alleviate the workload of radiologists. While machine learning has facilitated report generation for 2D medical imaging, extending this to 3D has been unexplored due to computational complexity and data scarcity. We introduce the first method to generate radiology reports for 3D medical imaging, specifically targeting chest CT volumes. Given the absence of comparable methods, we establish a baseline using an advanced 3D vision encoder in medical imaging to demonstrate our method's effectiveness, which leverages a novel auto-regressive causal transformer. Furthermore, recognizing the benefits of leveraging information from previous visits, we augment CT2Rep with a cross-attention-based multi-modal fusion module and hierarchical memory, enabling the incorporation of longitudinal multimodal data. Access our code at https://github.com/ibrahimethemhamamci/CT2Rep

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.

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.

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.

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.

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.

Existing volumetric medical image segmentation models are typically task-specific, excelling at specific target but struggling to generalize across anatomical structures or modalities. This limitation restricts their broader clinical use. In this paper, we introduce SAM-Med3D for general-purpose segmentation on volumetric medical images. Given only a few 3D prompt points, SAM-Med3D can accurately segment diverse anatomical structures and lesions across various modalities. To achieve this, we gather and process a large-scale 3D medical image dataset, SA-Med3D-140K, from a blend of public sources and licensed private datasets. This dataset includes 22K 3D images and 143K corresponding 3D masks. Then SAM-Med3D, a promptable segmentation model characterized by the fully learnable 3D structure, is trained on this dataset using a two-stage procedure and exhibits impressive performance on both seen and unseen segmentation targets. We comprehensively evaluate SAM-Med3D on 16 datasets covering diverse medical scenarios, including different anatomical structures, modalities, targets, and zero-shot transferability to new/unseen tasks. The evaluation shows the efficiency and efficacy of SAM-Med3D, as well as its promising application to diverse downstream tasks as a pre-trained model. Our approach demonstrates that substantial medical resources can be utilized to develop a general-purpose medical AI for various potential applications. Our dataset, code, and models are available at https://github.com/uni-medical/SAM-Med3D.

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/.

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.

Volumetric video is a technology that digitally records dynamic events such as artistic performances, sporting events, and remote conversations. When acquired, such volumography can be viewed from any viewpoint and timestamp on flat screens, 3D displays, or VR headsets, enabling immersive viewing experiences and more flexible content creation in a variety of applications such as sports broadcasting, video conferencing, gaming, and movie productions. With the recent advances and fast-growing interest in neural scene representations for volumetric video, there is an urgent need for a unified open-source library to streamline the process of volumetric video capturing, reconstruction, and rendering for both researchers and non-professional users to develop various algorithms and applications of this emerging technology. In this paper, we present EasyVolcap, a Python & Pytorch library for accelerating neural volumetric video research with the goal of unifying the process of multi-view data processing, 4D scene reconstruction, and efficient dynamic volumetric video rendering. Our source code is available at https://github.com/zju3dv/EasyVolcap.

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.

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.

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.

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.

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.

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.

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.

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.

A brain tumour is a mass or cluster of abnormal cells in the brain, which has the possibility of becoming life-threatening because of its ability to invade neighbouring tissues and also form metastases. An accurate diagnosis is essential for successful treatment planning and magnetic resonance imaging is the principal imaging modality for diagnostic of brain tumours and their extent. Deep Learning methods in computer vision applications have shown significant improvement in recent years, most of which can be credited to the fact that a sizeable amount of data is available to train models on, and the improvements in the model architectures yielding better approximations in a supervised setting. Classifying tumours using such deep learning methods has made significant progress with the availability of open datasets with reliable annotations. Typically those methods are either 3D models, which use 3D volumetric MRIs or even 2D models considering each slice separately. However, by treating the slice spatial dimension separately, spatiotemporal models can be employed as spatiospatial models for this task. These models have the capabilities of learning specific spatial and temporal relationship, while reducing computational costs. This paper uses two spatiotemporal models, ResNet (2+1)D and ResNet Mixed Convolution, to classify different types of brain tumours. It was observed that both these models performed superior to the pure 3D convolutional model, ResNet18. Furthermore, it was also observed that pre-training the models on a different, even unrelated dataset before training them for the task of tumour classification improves the performance. Finally, Pre-trained ResNet Mixed Convolution was observed to be the best model in these experiments, achieving a macro F1-score of 0.93 and a test accuracy of 96.98\%, while at the same time being the model with the least computational cost.

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.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

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.

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.

Accurate analysis and modeling of renal functions require a precise segmentation of the renal blood vessels. Micro-CT scans provide image data at higher resolutions, making more small vessels near the renal cortex visible. Although deep-learning-based methods have shown state-of-the-art performance in automatic blood vessel segmentations, they require a large amount of labeled training data. However, voxel-wise labeling in micro-CT scans is extremely time-consuming given the huge volume sizes. To mitigate the problem, we simulate synthetic renal vascular trees physiologically while generating corresponding scans of the simulated trees by training a generative model on unlabeled scans. This enables the generative model to learn the mapping implicitly without the need for explicit functions to emulate the image acquisition process. We further propose an additional segmentation branch over the generative model trained on the generated scans. We demonstrate that the model can directly segment blood vessels on real scans and validate our method on both 3D micro-CT scans of rat kidneys and a proof-of-concept experiment on 2D retinal images. Code and 3D results are available at https://github.com/miccai2023anony/RenalVesselSeg

We introduce VoxTell, a vision-language model for text-prompted volumetric medical image segmentation. It maps free-form descriptions, from single words to full clinical sentences, to 3D masks. Trained on 62K+ CT, MRI, and PET volumes spanning over 1K anatomical and pathological classes, VoxTell uses multi-stage vision-language fusion across decoder layers to align textual and visual features at multiple scales. It achieves state-of-the-art zero-shot performance across modalities on unseen datasets, excelling on familiar concepts while generalizing to related unseen classes. Extensive experiments further demonstrate strong cross-modality transfer, robustness to linguistic variations and clinical language, as well as accurate instance-specific segmentation from real-world text. Code is available at: https://www.github.com/MIC-DKFZ/VoxTell

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.

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

Artificial intelligence (AI) can automatically delineate lesions on computed tomography (CT) and generate radiology report content, yet progress is limited by the scarcity of publicly available CT datasets with lesion-level annotations. To bridge this gap, we introduce CT-Bench, a first-of-its-kind benchmark dataset comprising two components: a Lesion Image and Metadata Set containing 20,335 lesions from 7,795 CT studies with bounding boxes, descriptions, and size information, and a multitask visual question answering benchmark with 2,850 QA pairs covering lesion localization, description, size estimation, and attribute categorization. Hard negative examples are included to reflect real-world diagnostic challenges. We evaluate multiple state-of-the-art multimodal models, including vision-language and medical CLIP variants, by comparing their performance to radiologist assessments, demonstrating the value of CT-Bench as a comprehensive benchmark for lesion analysis. Moreover, fine-tuning models on the Lesion Image and Metadata Set yields significant performance gains across both components, underscoring the clinical utility of CT-Bench.

Automated radiology report generation from 3D computed tomography (CT) volumes is challenging due to extreme sequence lengths, severe class imbalance, and the tendency of large language models (LLMs) to ignore visual tokens in favor of linguistic priors. We present Ker-VLJEPA-3B, a four-phase curriculum learning framework for free-text report generation from thoracic CT volumes. A phased training curriculum progressively adapts a Llama 3.2 3B decoder to ground its output in visual features from a frozen, self-supervised encoder. Our visual backbone (LeJEPA ViT-Large) is trained via self-supervised joint-embedding prediction on unlabeled CTs, without text supervision. Unlike contrastive models (CLIP, BiomedCLIP), this language-free backbone yields modality-pure representations. Vision-language alignment is deferred to the curriculum's bridge and generation phases. This modality-agnostic design can integrate any self-supervised encoder into an LLM without paired text during foundation training. Methodological innovations include: (1) zone-constrained cross-attention compressing slice embeddings into 32 spatially-grounded visual tokens; (2) PCA whitening of anisotropic LLM embeddings; (3) a positive-findings-only strategy eliminating posterior collapse; (4) warm bridge initialization transferring projection weights; and (5) selective cross-attention freezing with elastic weight consolidation to prevent catastrophic forgetting. Evaluated on the CT-RATE benchmark (2,984 validation volumes, 18 classes), Ker-VLJEPA-3B achieves a macro F1 of 0.429, surpassing the state-of-the-art (U-VLM, macro F1 = 0.414) by 3.6%, and reaching 0.448 (+8.2%) with threshold optimization. Ablation studies confirm 56.6% of generation quality derives from patient-specific visual content. Code and weights are available.

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.

Medical Visual Question Answering (Med-VQA) holds significant potential for clinical decision support, yet existing efforts primarily focus on 2D imaging with limited task diversity. This paper presents 3D-RAD, a large-scale dataset designed to advance 3D Med-VQA using radiology CT scans. The 3D-RAD dataset encompasses six diverse VQA tasks: anomaly detection, image observation, medical computation, existence detection, static temporal diagnosis, and longitudinal temporal diagnosis. It supports both open- and closed-ended questions while introducing complex reasoning challenges, including computational tasks and multi-stage temporal analysis, to enable comprehensive benchmarking. Extensive evaluations demonstrate that existing vision-language models (VLMs), especially medical VLMs exhibit limited generalization, particularly in multi-temporal tasks, underscoring the challenges of real-world 3D diagnostic reasoning. To drive future advancements, we release a high-quality training set 3D-RAD-T of 136,195 expert-aligned samples, showing that fine-tuning on this dataset could significantly enhance model performance. Our dataset and code, aiming to catalyze multimodal medical AI research and establish a robust foundation for 3D medical visual understanding, are publicly available at https://github.com/Tang-xiaoxiao/3D-RAD.

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.

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.

The integration of artificial intelligence in image-guided interventions holds transformative potential, promising to extract 3D geometric and quantitative information from conventional 2D imaging modalities during complex procedures. Achieving this requires the rapid and precise alignment of 2D intraoperative images (e.g., X-ray) with 3D preoperative volumes (e.g., CT, MRI). However, current 2D/3D registration methods fail across the broad spectrum of procedures dependent on X-ray guidance: traditional optimization techniques require custom parameter tuning for each subject, whereas neural networks trained on small datasets do not generalize to new patients or require labor-intensive manual annotations, increasing clinical burden and precluding application to new anatomical targets. To address these challenges, we present xvr, a fully automated framework for training patient-specific neural networks for 2D/3D registration. xvr uses physics-based simulation to generate abundant high-quality training data from a patient's own preoperative volumetric imaging, thereby overcoming the inherently limited ability of supervised models to generalize to new patients and procedures. Furthermore, xvr requires only 5 minutes of training per patient, making it suitable for emergency interventions as well as planned procedures. We perform the largest evaluation of a 2D/3D registration algorithm on real X-ray data to date and find that xvr robustly generalizes across a diverse dataset comprising multiple anatomical structures, imaging modalities, and hospitals. Across surgical tasks, xvr achieves submillimeter-accurate registration at intraoperative speeds, improving upon existing methods by an order of magnitude. xvr is released as open-source software freely available at https://github.com/eigenvivek/xvr.

X-ray images play a vital role in the intraoperative processes due to their high resolution and fast imaging speed and greatly promote the subsequent segmentation, registration and reconstruction. However, over-dosed X-rays superimpose potential risks to human health to some extent. Data-driven algorithms from volume scans to X-ray images are restricted by the scarcity of paired X-ray and volume data. Existing methods are mainly realized by modelling the whole X-ray imaging procedure. In this study, we propose a learning-based approach termed CT2X-GAN to synthesize the X-ray images in an end-to-end manner using the content and style disentanglement from three different image domains. Our method decouples the anatomical structure information from CT scans and style information from unpaired real X-ray images/ digital reconstructed radiography (DRR) images via a series of decoupling encoders. Additionally, we introduce a novel consistency regularization term to improve the stylistic resemblance between synthesized X-ray images and real X-ray images. Meanwhile, we also impose a supervised process by computing the similarity of computed real DRR and synthesized DRR images. We further develop a pose attention module to fully strengthen the comprehensive information in the decoupled content code from CT scans, facilitating high-quality multi-view image synthesis in the lower 2D space. Extensive experiments were conducted on the publicly available CTSpine1K dataset and achieved 97.8350, 0.0842 and 3.0938 in terms of FID, KID and defined user-scored X-ray similarity, respectively. In comparison with 3D-aware methods (pi-GAN, EG3D), CT2X-GAN is superior in improving the synthesis quality and realistic to the real X-ray images.

Model-based reconstruction employing the time separation technique (TST) was found to improve dynamic perfusion imaging of the liver using C-arm cone-beam computed tomography (CBCT). To apply TST using prior knowledge extracted from CT perfusion data, the liver should be accurately segmented from the CT scans. Reconstructions of primary and model-based CBCT data need to be segmented for proper visualisation and interpretation of perfusion maps. This research proposes Turbolift learning, which trains a modified version of the multi-scale Attention UNet on different liver segmentation tasks serially, following the order of the trainings CT, CBCT, CBCT TST - making the previous trainings act as pre-training stages for the subsequent ones - addressing the problem of limited number of datasets for training. For the final task of liver segmentation from CBCT TST, the proposed method achieved an overall Dice scores of 0.874pm0.031 and 0.905pm0.007 in 6-fold and 4-fold cross-validation experiments, respectively - securing statistically significant improvements over the model, which was trained only for that task. Experiments revealed that Turbolift not only improves the overall performance of the model but also makes it robust against artefacts originating from the embolisation materials and truncation artefacts. Additionally, in-depth analyses confirmed the order of the segmentation tasks. This paper shows the potential of segmenting the liver from CT, CBCT, and CBCT TST, learning from the available limited training data, which can possibly be used in the future for the visualisation and evaluation of the perfusion maps for the treatment evaluation of liver diseases.

The COVID-19 pandemic has spread globally for several months. Because its transmissibility and high pathogenicity seriously threaten people's lives, it is crucial to accurately and quickly detect COVID-19 infection. Many recent studies have shown that deep learning (DL) based solutions can help detect COVID-19 based on chest CT scans. However, most existing work focuses on 2D datasets, which may result in low quality models as the real CT scans are 3D images. Besides, the reported results span a broad spectrum on different datasets with a relatively unfair comparison. In this paper, we first use three state-of-the-art 3D models (ResNet3D101, DenseNet3D121, and MC3\_18) to establish the baseline performance on the three publicly available chest CT scan datasets. Then we propose a differentiable neural architecture search (DNAS) framework to automatically search for the 3D DL models for 3D chest CT scans classification with the Gumbel Softmax technique to improve the searching efficiency. We further exploit the Class Activation Mapping (CAM) technique on our models to provide the interpretability of the results. The experimental results show that our automatically searched models (CovidNet3D) outperform the baseline human-designed models on the three datasets with tens of times smaller model size and higher accuracy. Furthermore, the results also verify that CAM can be well applied in CovidNet3D for COVID-19 datasets to provide interpretability for medical diagnosis.

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.

Template-based segmentation, a widely used paradigm in medical imaging, propagates anatomical labels via deformable registration from a labeled atlas to a target image, and is often used to compute volumetric biomarkers for downstream decision-making. While conformal prediction (CP) provides finite-sample valid intervals for scalar metrics, existing segmentation-based uncertainty quantification (UQ) approaches either rely on learned model features, often unavailable in classic template-based pipelines, or treat the registration process as a black box, resulting in overly conservative intervals when applied directly in output space. We introduce ConVOLT, a CP framework that achieves efficient volumetric UQ by conditioning calibration on properties of the estimated deformation field from template-based segmentation. ConVOLT calibrates a learned volumetric scaling factor from deformation space features. We evaluate ConVOLT on template-based segmentation tasks involving global, regional, and label volumetry across multiple datasets and registration methods. ConVOLT achieves target coverage while producing substantially tighter intervals than output-space conformal baselines. Our work paves way to exploit the registration process for efficient UQ in medical imaging pipelines.

The recent release of RadGenome-Chest CT has significantly advanced CT-based report generation. However, existing methods primarily focus on global features, making it challenging to capture region-specific details, which may cause certain abnormalities to go unnoticed. To address this, we propose MedRegion-CT, a region-focused Multi-Modal Large Language Model (MLLM) framework, featuring three key innovations. First, we introduce Region Representative (R^2) Token Pooling, which utilizes a 2D-wise pretrained vision model to efficiently extract 3D CT features. This approach generates global tokens representing overall slice features and region tokens highlighting target areas, enabling the MLLM to process comprehensive information effectively. Second, a universal segmentation model generates pseudo-masks, which are then processed by a mask encoder to extract region-centric features. This allows the MLLM to focus on clinically relevant regions, using six predefined region masks. Third, we leverage segmentation results to extract patient-specific attributions, including organ size, diameter, and locations. These are converted into text prompts, enriching the MLLM's understanding of patient-specific contexts. To ensure rigorous evaluation, we conducted benchmark experiments on report generation using the RadGenome-Chest CT. MedRegion-CT achieved state-of-the-art performance, outperforming existing methods in natural language generation quality and clinical relevance while maintaining interpretability. The code for our framework is publicly available.

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.

Currently, evaluating vision-language models (VLMs) in medical imaging tasks oversimplifies clinical reality by relying on pre-selected 2D images that demand significant manual labor to curate. This setup misses the core challenge of realworld diagnostics: a true clinical agent must actively navigate full 3D volumes across multiple sequences or modalities to gather evidence and ultimately support a final decision. To address this, we propose MEDOPENCLAW, an auditable runtime designed to let VLMs operate dynamically within standard medical tools or viewers (e.g., 3D Slicer). On top of this runtime, we introduce MEDFLOWBENCH, a full-study medical imaging benchmark covering multi-sequence brain MRI and lung CT/PET. It systematically evaluates medical agentic capabilities across viewer-only, tool-use, and open-method tracks. Initial results reveal a critical insight: while state-of-the-art LLMs/VLMs (e.g., Gemini 3.1 Pro and GPT-5.4) can successfully navigate the viewer to solve basic study-level tasks, their performance paradoxically degrades when given access to professional support tools due to a lack of precise spatial grounding. By bridging the gap between static-image perception and interactive clinical workflows, MEDOPENCLAW and MEDFLOWBENCH establish a reproducible foundation for developing auditable, full-study medical imaging agents.

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.

Large medical imaging datasets can be cheaply and quickly annotated with low-confidence, weak labels (e.g., radiological scores). Access to high-confidence labels, such as histology-based diagnoses, is rare and costly. Pretraining strategies, like contrastive learning (CL) methods, can leverage unlabeled or weakly-annotated datasets. These methods typically require large batch sizes, which poses a difficulty in the case of large 3D images at full resolution, due to limited GPU memory. Nevertheless, volumetric positional information about the spatial context of each 2D slice can be very important for some medical applications. In this work, we propose an efficient weakly-supervised positional (WSP) contrastive learning strategy where we integrate both the spatial context of each 2D slice and a weak label via a generic kernel-based loss function. We illustrate our method on cirrhosis prediction using a large volume of weakly-labeled images, namely radiological low-confidence annotations, and small strongly-labeled (i.e., high-confidence) datasets. The proposed model improves the classification AUC by 5% with respect to a baseline model on our internal dataset, and by 26% on the public LIHC dataset from the Cancer Genome Atlas. The code is available at: https://github.com/Guerbet-AI/wsp-contrastive.

Accurate medical image segmentation is crucial for precise anatomical delineation. Deep learning models like U-Net have shown great success but depend heavily on large datasets and struggle with domain shifts, complex structures, and limited training samples. Recent studies have explored diffusion models for segmentation by iteratively refining masks. However, these methods still retain the conventional image-to-mask mapping, making them highly sensitive to input data, which hampers stability and generalization. In contrast, we introduce DiffAtlas, a novel generative framework that models both images and masks through diffusion during training, effectively ``GenAI-fying'' atlas-based segmentation. During testing, the model is guided to generate a specific target image-mask pair, from which the corresponding mask is obtained. DiffAtlas retains the robustness of the atlas paradigm while overcoming its scalability and domain-specific limitations. Extensive experiments on CT and MRI across same-domain, cross-modality, varying-domain, and different data-scale settings using the MMWHS and TotalSegmentator datasets demonstrate that our approach outperforms existing methods, particularly in limited-data and zero-shot modality segmentation. Code is available at https://github.com/M3DV/DiffAtlas.

Traditional volume visualization (VolVis) methods, like direct volume rendering, suffer from rigid transfer function designs and high computational costs. Although novel view synthesis approaches enhance rendering efficiency, they require additional learning effort for non-experts and lack support for semantic-level interaction. To bridge this gap, we propose NLI4VolVis, an interactive system that enables users to explore, query, and edit volumetric scenes using natural language. NLI4VolVis integrates multi-view semantic segmentation and vision-language models to extract and understand semantic components in a scene. We introduce a multi-agent large language model architecture equipped with extensive function-calling tools to interpret user intents and execute visualization tasks. The agents leverage external tools and declarative VolVis commands to interact with the VolVis engine powered by 3D editable Gaussians, enabling open-vocabulary object querying, real-time scene editing, best-view selection, and 2D stylization. We validate our system through case studies and a user study, highlighting its improved accessibility and usability in volumetric data exploration. We strongly recommend readers check our case studies, demo video, and source code at https://nli4volvis.github.io/.

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.

Recent progress in medical vision-language models (VLMs) has achieved strong performance on image-level text-centric tasks such as report generation and visual question answering (VQA). However, achieving fine-grained visual grounding and volumetric spatial reasoning in 3D medical VLMs remains challenging, particularly when aiming to unify these capabilities within a single, generalizable framework. To address this challenge, we proposed MedVL-SAM2, a unified 3D medical multimodal model that concurrently supports report generation, VQA, and multi-paradigm segmentation, including semantic, referring, and interactive segmentation. MedVL-SAM2 integrates image-level reasoning and pixel-level perception through a cohesive architecture tailored for 3D medical imaging, and incorporates a SAM2-based volumetric segmentation module to enable precise multi-granular spatial reasoning. The model is trained in a multi-stage pipeline: it is first pre-trained on a large-scale corpus of 3D CT image-text pairs to align volumetric visual features with radiology-language embeddings. It is then jointly optimized with both language-understanding and segmentation objectives using a comprehensive 3D CT segmentation dataset. This joint training enables flexible interaction via language, point, or box prompts, thereby unifying high-level visual reasoning with spatially precise localization. Our unified architecture delivers state-of-the-art performance across report generation, VQA, and multiple 3D segmentation tasks. Extensive analyses further show that the model provides reliable 3D visual grounding, controllable interactive segmentation, and robust cross-modal reasoning, demonstrating that high-level semantic reasoning and precise 3D localization can be jointly achieved within a unified 3D medical VLM.

Vision-Language Models (VLMs) have shown promise in various 2D visual tasks, yet their readiness for 3D clinical diagnosis remains unclear due to stringent demands for recognition precision, reasoning ability, and domain knowledge. To systematically evaluate these dimensions, we present DeepTumorVQA, a diagnostic visual question answering (VQA) benchmark targeting abdominal tumors in CT scans. It comprises 9,262 CT volumes (3.7M slices) from 17 public datasets, with 395K expert-level questions spanning four categories: Recognition, Measurement, Visual Reasoning, and Medical Reasoning. DeepTumorVQA introduces unique challenges, including small tumor detection and clinical reasoning across 3D anatomy. Benchmarking four advanced VLMs (RadFM, M3D, Merlin, CT-CHAT), we find current models perform adequately on measurement tasks but struggle with lesion recognition and reasoning, and are still not meeting clinical needs. Two key insights emerge: (1) large-scale multimodal pretraining plays a crucial role in DeepTumorVQA testing performance, making RadFM stand out among all VLMs. (2) Our dataset exposes critical differences in VLM components, where proper image preprocessing and design of vision modules significantly affect 3D perception. To facilitate medical multimodal research, we have released DeepTumorVQA as a rigorous benchmark: https://github.com/Schuture/DeepTumorVQA.

Photon-counting CT (PCCT) provides superior image quality with higher spatial resolution and lower noise compared to conventional energy-integrating CT (EICT), but its limited clinical availability restricts large-scale research and clinical deployment. To bridge this gap, we propose SUMI, a simulated degradation-to-enhancement method that learns to reverse realistic acquisition artifacts in low-quality EICT by leveraging high-quality PCCT as reference. Our central insight is to explicitly model realistic acquisition degradations, transforming PCCT into clinically plausible lower-quality counterparts and learning to invert this process. The simulated degradations were validated for clinical realism by board-certified radiologists, enabling faithful supervision without requiring paired acquisitions at scale. As outcomes of this technical contribution, we: (1) train a latent diffusion model on 1,046 PCCTs, using an autoencoder first pre-trained on both these PCCTs and 405,379 EICTs from 145 hospitals to extract general CT latent features that we release for reuse in other generative medical imaging tasks; (2) construct a large-scale dataset of over 17,316 publicly available EICTs enhanced to PCCT-like quality, with radiologist-validated voxel-wise annotations of airway trees, arteries, veins, lungs, and lobes; and (3) demonstrate substantial improvements: across external data, SUMI outperforms state-of-the-art image translation methods by 15% in SSIM and 20% in PSNR, improves radiologist-rated clinical utility in reader studies, and enhances downstream top-ranking lesion detection performance, increasing sensitivity by up to 15% and F1 score by up to 10%. Our results suggest that emerging imaging advances can be systematically distilled into routine EICT using limited high-quality scans as reference.

Existing foundation models (FMs) in the medical domain often require extensive fine-tuning or rely on training resource-intensive decoders, while many existing encoders are pretrained with objectives biased toward specific tasks. This illustrates a need for a strong, task-agnostic foundation model that requires minimal fine-tuning beyond feature extraction. In this work, we introduce a suite of task-agnostic pretraining of CT foundation models (TAP-CT): a simple yet effective adaptation of Vision Transformers (ViTs) and DINOv2 for volumetric data, enabling scalable self-supervised pretraining directly on 3D CT volumes. Our approach incorporates targeted modifications to patch embeddings, positional encodings, and volumetric augmentations, making the architecture depth-aware while preserving the simplicity of the underlying architectures. We show that large-scale 3D pretraining on an extensive in-house CT dataset (105K volumes) yields stable, robust frozen representations that generalize strongly across downstream tasks. To promote transparency and reproducibility, and to establish a powerful, low-resource baseline for future research in medical imaging, we will release all pretrained models, experimental configurations, and downstream benchmark code at https://huggingface.co/fomofo/tap-ct-b-3d.

In this study, we aim to build up a model that can Segment Anything in radiology scans, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three folds: (i) for dataset construction, we construct the first multi-modal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build up the largest and most comprehensive segmentation dataset for training, by collecting over 22K 3D medical image scans from72 segmentation datasets, across 497 classes, with careful standardization on both image scans and label space; (ii) for architecture design, we propose to inject medical knowledge into a text encoder via contrastive learning, and then formulate a universal segmentation model, that can be prompted by feeding in medical terminologies in text form; (iii) As a result, we have trained SAT-Nano (110M parameters) and SAT-Pro (447M parameters), demonstrating superior or comparable performance to 72 specialist models, i.e., nnU-Nets, U-Mamba or SwinUNETR, trained on each dataset/subsets. We validate SAT as a foundational segmentation model, with better generalization on external (cross-center) datasets, and can be further improved on specific tasks after fine-tuning adaptation. Comparing with state-of-the-art interactive segmentation model MedSAM, SAT demonstrate superior performance, scalability and robustness. We further compare SAT with BiomedParse, and observe SAT is significantly superior in both internal and external evaluation. Through extensive ablation study, we validate the benefit of domain knowledge on universal segmentation, especially on tail categories. As a use case, we demonstrate that SAT can act as a powerful out-of-the-box agent for large language models, enabling visual grounding in versatile application scenarios. All the data, codes, and models in this work have been released.

Medical image registration is a critical task that estimates the spatial correspondence between pairs of images. However, current traditional and deep-learning-based methods rely on similarity measures to generate a deforming field, which often results in disproportionate volume changes in dissimilar regions, especially in tumor regions. These changes can significantly alter the tumor size and underlying anatomy, which limits the practical use of image registration in clinical diagnosis. To address this issue, we have formulated image registration with tumors as a constraint problem that preserves tumor volumes while maximizing image similarity in other normal regions. Our proposed strategy involves a two-stage process. In the first stage, we use similarity-based registration to identify potential tumor regions by their volume change, generating a soft tumor mask accordingly. In the second stage, we propose a volume-preserving registration with a novel adaptive volume-preserving loss that penalizes the change in size adaptively based on the masks calculated from the previous stage. Our approach balances image similarity and volume preservation in different regions, i.e., normal and tumor regions, by using soft tumor masks to adjust the imposition of volume-preserving loss on each one. This ensures that the tumor volume is preserved during the registration process. We have evaluated our strategy on various datasets and network architectures, demonstrating that our method successfully preserves the tumor volume while achieving comparable registration results with state-of-the-art methods. Our codes is available at: https://dddraxxx.github.io/Volume-Preserving-Registration/.

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.

Recent advances in 3D X-ray Computed Tomographic (CT) sensors have stimulated research efforts to unveil the extremely complex micro-scale processes that control the activity of soil microorganisms. Voxel-based description (up to hundreds millions voxels) of the pore space can be extracted, from grey level 3D CT scanner images, by means of simple image processing tools. Classical methods for numerical simulation of biological dynamics using mesh of voxels, such as Lattice Boltzmann Model (LBM), are too much time consuming. Thus, the use of more compact and reliable geometrical representations of pore space can drastically decrease the computational cost of the simulations. Several recent works propose basic analytic volume primitives (e.g. spheres, generalized cylinders, ellipsoids) to define a piece-wise approximation of pore space for numerical simulation of draining, diffusion and microbial decomposition. Such approaches work well but the drawback is that it generates approximation errors. In the present work, we study another alternative where pore space is described by means of geometrically relevant connected subsets of voxels (regions) computed from the curvilinear skeleton. Indeed, many works use the curvilinear skeleton (3D medial axis) for analyzing and partitioning 3D shapes within various domains (medicine, material sciences, petroleum engineering, etc.) but only a few ones in soil sciences. Within the context of soil sciences, most studies dealing with 3D medial axis focus on the determination of pore throats. Here, we segment pore space using curvilinear skeleton in order to achieve numerical simulation of microbial decomposition (including diffusion processes). We validate simulation outputs by comparison with other methods using different pore space geometrical representations (balls, voxels).

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.

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.

Recent advances in neural reconstruction using posed image sequences have made remarkable progress. However, due to the lack of depth information, existing volumetric-based techniques simply duplicate 2D image features of the object surface along the entire camera ray. We contend this duplication introduces noise in empty and occluded spaces, posing challenges for producing high-quality 3D geometry. Drawing inspiration from traditional multi-view stereo methods, we propose an end-to-end 3D neural reconstruction framework CVRecon, designed to exploit the rich geometric embedding in the cost volumes to facilitate 3D geometric feature learning. Furthermore, we present Ray-contextual Compensated Cost Volume (RCCV), a novel 3D geometric feature representation that encodes view-dependent information with improved integrity and robustness. Through comprehensive experiments, we demonstrate that our approach significantly improves the reconstruction quality in various metrics and recovers clear fine details of the 3D geometries. Our extensive ablation studies provide insights into the development of effective 3D geometric feature learning schemes. Project page: https://cvrecon.ziyue.cool/

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.

Language-image pre-training has demonstrated strong performance in 2D medical imaging, but its success in 3D modalities such as CT and MRI remains limited due to the high computational demands of volumetric data, which pose a significant barrier to training on large-scale, uncurated clinical studies. In this study, we introduce Hierarchical attention for Language-Image Pre-training (HLIP), a scalable pre-training framework for 3D medical imaging. HLIP adopts a lightweight hierarchical attention mechanism inspired by the natural hierarchy of radiology data: slice, scan, and study. This mechanism exhibits strong generalizability, e.g., +4.3% macro AUC on the Rad-ChestCT benchmark when pre-trained on CT-RATE. Moreover, the computational efficiency of HLIP enables direct training on uncurated datasets. Trained on 220K patients with 3.13 million scans for brain MRI and 240K patients with 1.44 million scans for head CT, HLIP achieves state-of-the-art performance, e.g., +32.4% balanced ACC on the proposed publicly available brain MRI benchmark Pub-Brain-5; +1.4% and +6.9% macro AUC on head CT benchmarks RSNA and CQ500, respectively. These results demonstrate that, with HLIP, directly pre-training on uncurated clinical datasets is a scalable and effective direction for language-image pre-training in 3D medical imaging. The code is available at https://github.com/Zch0414/hlip

Foundation models (FMs) have shown transformative potential in radiology by performing diverse, complex tasks across imaging modalities. Here, we developed CT-FM, a large-scale 3D image-based pre-trained model designed explicitly for various radiological tasks. CT-FM was pre-trained using 148,000 computed tomography (CT) scans from the Imaging Data Commons through label-agnostic contrastive learning. We evaluated CT-FM across four categories of tasks, namely, whole-body and tumor segmentation, head CT triage, medical image retrieval, and semantic understanding, showing superior performance against state-of-the-art models. Beyond quantitative success, CT-FM demonstrated the ability to cluster regions anatomically and identify similar anatomical and structural concepts across scans. Furthermore, it remained robust across test-retest settings and indicated reasonable salient regions attached to its embeddings. This study demonstrates the value of large-scale medical imaging foundation models and by open-sourcing the model weights, code, and data, aims to support more adaptable, reliable, and interpretable AI solutions in radiology.

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.

Due to the three-dimensional nature of CT- or MR-scans, generative modeling of medical images is a particularly challenging task. Existing approaches mostly apply patch-wise, slice-wise, or cascaded generation techniques to fit the high-dimensional data into the limited GPU memory. However, these approaches may introduce artifacts and potentially restrict the model's applicability for certain downstream tasks. This work presents WDM, a wavelet-based medical image synthesis framework that applies a diffusion model on wavelet decomposed images. The presented approach is a simple yet effective way of scaling diffusion models to high resolutions and can be trained on a single 40 GB GPU. Experimental results on BraTS and LIDC-IDRI unconditional image generation at a resolution of 128 times 128 times 128 show state-of-the-art image fidelity (FID) and sample diversity (MS-SSIM) scores compared to GANs, Diffusion Models, and Latent Diffusion Models. Our proposed method is the only one capable of generating high-quality images at a resolution of 256 times 256 times 256.

The volumetric representation of human interactions is one of the fundamental domains in the development of immersive media productions and telecommunication applications. Particularly in the context of the rapid advancement of Extended Reality (XR) applications, this volumetric data has proven to be an essential technology for future XR elaboration. In this work, we present a new multimodal database to help advance the development of immersive technologies. Our proposed database provides ethically compliant and diverse volumetric data, in particular 27 participants displaying posed facial expressions and subtle body movements while speaking, plus 11 participants wearing head-mounted displays (HMDs). The recording system consists of a volumetric capture (VoCap) studio, including 31 synchronized modules with 62 RGB cameras and 31 depth cameras. In addition to textured meshes, point clouds, and multi-view RGB-D data, we use one Lytro Illum camera for providing light field (LF) data simultaneously. Finally, we also provide an evaluation of our dataset employment with regard to the tasks of facial expression classification, HMDs removal, and point cloud reconstruction. The dataset can be helpful in the evaluation and performance testing of various XR algorithms, including but not limited to facial expression recognition and reconstruction, facial reenactment, and volumetric video. HEADSET and its all associated raw data and license agreement will be publicly available for research purposes.

Developing advanced medical imaging retrieval systems is challenging due to the varying definitions of `similar images' across different medical contexts. This challenge is compounded by the lack of large-scale, high-quality medical imaging retrieval datasets and benchmarks. In this paper, we propose a novel methodology that leverages dense radiology reports to define image-wise similarity ordering at multiple granularities in a scalable and fully automatic manner. Using this approach, we construct two comprehensive medical imaging retrieval datasets: MIMIC-IR for Chest X-rays and CTRATE-IR for CT scans, providing detailed image-image ranking annotations conditioned on diverse anatomical structures. Furthermore, we develop two retrieval systems, RadIR-CXR and model-ChestCT, which demonstrate superior performance in traditional image-image and image-report retrieval tasks. These systems also enable flexible, effective image retrieval conditioned on specific anatomical structures described in text, achieving state-of-the-art results on 77 out of 78 metrics.

Deep learning presents novel opportunities for the auto-segmentation of gross tumor volume (GTV) in head and neck cancer (HNC), yet fully automatic methods usually necessitate significant manual refinement. This study investigates the Segment Anything Model (SAM), recognized for requiring minimal human prompting and its zero-shot generalization ability across natural images. We specifically examine MedSAM, a version of SAM fine-tuned with large-scale public medical images. Despite its progress, the integration of multi-modality images (CT, PET, MRI) for effective GTV delineation remains a challenge. Focusing on SAM's application in HNC GTV segmentation, we assess its performance in both zero-shot and fine-tuned scenarios using single (CT-only) and fused multi-modality images. Our study demonstrates that fine-tuning SAM significantly enhances its segmentation accuracy, building upon the already effective zero-shot results achieved with bounding box prompts. These findings open a promising avenue for semi-automatic HNC GTV segmentation.

Vision-Language Foundation Models (VLMs), trained on large-scale multimodal datasets, have driven significant advances in Artificial Intelligence (AI) by enabling rich cross-modal reasoning. Despite their success in general domains, applying these models to medical imaging remains challenging due to the limited availability of diverse imaging modalities and multilingual clinical data. Most existing medical VLMs are trained on a subset of imaging modalities and focus primarily on high-resource languages, thus limiting their generalizability and clinical utility. To address these limitations, we introduce a novel Vietnamese-language multimodal medical dataset consisting of 2,757 whole-body PET/CT volumes from independent patients and their corresponding full-length clinical reports. This dataset is designed to fill two pressing gaps in medical AI development: (1) the lack of PET/CT imaging data in existing VLMs training corpora, which hinders the development of models capable of handling functional imaging tasks; and (2) the underrepresentation of low-resource languages, particularly the Vietnamese language, in medical vision-language research. To the best of our knowledge, this is the first dataset to provide comprehensive PET/CT-report pairs in Vietnamese. We further introduce a training framework to enhance VLMs' learning, including data augmentation and expert-validated test sets. We conduct comprehensive experiments benchmarking state-of-the-art VLMs on downstream tasks. The experimental results show that incorporating our dataset significantly improves the performance of existing VLMs. We believe this dataset and benchmark will serve as a pivotal step in advancing the development of more robust VLMs for medical imaging, especially for low-resource languages and clinical use in Vietnamese healthcare. The source code is available at https://github.com/AIoT-Lab-BKAI/ViPET-ReportGen.

In this study, we develop a novel methodology for annotating the brain vasculature using dynamic 4D-CTA head scans. By using multiple time points from dynamic CTA acquisitions, we subtract bone and soft tissue to enhance the visualization of arteries and veins, reducing the effort required to obtain manual annotations of brain vessels. We then train deep learning models on our ground truth annotations by using the same segmentation for multiple phases from the dynamic 4D-CTA collection, effectively enlarging our dataset by 4 to 5 times and inducing robustness to contrast phases. In total, our dataset comprises 110 training images from 25 patients and 165 test images from 14 patients. In comparison with two similarly-sized datasets for CTA-based brain vessel segmentation, a nnUNet model trained on our dataset can achieve significantly better segmentations across all vascular regions, with an average mDC of 0.846 for arteries and 0.957 for veins in the TopBrain dataset. Furthermore, metrics such as average directed Hausdorff distance (adHD) and topology sensitivity (tSens) reflected similar trends: using our dataset resulted in low error margins (adHD of 0.304 mm for arteries and 0.078 for veins) and high sensitivity (tSens of 0.877 for arteries and 0.974 for veins), indicating excellent accuracy in capturing vessel morphology. Our code and model weights are available online at https://github.com/alceballosa/robust-vessel-segmentation

Deep learning has demonstrated remarkable success in medical image segmentation and computer-aided diagnosis. In particular, numerous advanced methods have achieved state-of-the-art performance in brain tumor segmentation from MRI scans. While recent studies in other medical imaging domains have revealed that integrating textual reports with visual data can enhance segmentation accuracy, the field of brain tumor analysis lacks a comprehensive dataset that combines radiological images with corresponding textual annotations. This limitation has hindered the exploration of multimodal approaches that leverage both imaging and textual data. To bridge this critical gap, we introduce the TextBraTS dataset, the first publicly available volume-level multimodal dataset that contains paired MRI volumes and rich textual annotations, derived from the widely adopted BraTS2020 benchmark. Building upon this novel dataset, we propose a novel baseline framework and sequential cross-attention method for text-guided volumetric medical image segmentation. Through extensive experiments with various text-image fusion strategies and templated text formulations, our approach demonstrates significant improvements in brain tumor segmentation accuracy, offering valuable insights into effective multimodal integration techniques. Our dataset, implementation code, and pre-trained models are publicly available at https://github.com/Jupitern52/TextBraTS.

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. Here we introduce BrainFM, a modality-agnostic, multi-task vision foundation model for human brain imaging. With the proposed "mild-to-severe" intra-subject generation and "real-synth" mix-up training strategy, BrainFM is resilient to the appearance of acquired images (e.g., modality, contrast, deformation, resolution, artifacts), and can be directly applied to five fundamental brain imaging tasks, including image synthesis for CT and T1w/T2w/FLAIR MRI, anatomy segmentation, scalp-to-cortical distance, bias field estimation, and registration. We evaluate the efficacy of BrainFM on eleven public datasets, and demonstrate its robustness and effectiveness across all tasks and input modalities. Code is available at https://github.com/jhuldr/BrainFM.

Current volumetric biomedical foundation models struggle to generalize as public 3D datasets are small and do not cover the broad diversity of medical procedures, conditions, anatomical regions, and imaging protocols. We address this by creating a representation learning method that instead anticipates strong domain shifts at training time itself. We first propose a data engine that synthesizes highly variable training samples that would enable generalization to new biomedical contexts. To then train a single 3D network for any voxel-level task, we develop a contrastive learning method that pretrains the network to be stable against nuisance imaging variation simulated by the data engine, a key inductive bias for generalization. This network's features can be used as robust representations of input images for downstream tasks and its weights provide a strong, dataset-agnostic initialization for finetuning on new datasets. As a result, we set new standards across both multimodality registration and few-shot segmentation, a first for any 3D biomedical vision model, all without (pre-)training on any existing dataset of real images.

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.

Clinical monitoring of metastatic disease to the brain can be a laborious and time-consuming process, especially in cases involving multiple metastases when the assessment is performed manually. The Response Assessment in Neuro-Oncology Brain Metastases (RANO-BM) guideline, which utilizes the unidimensional longest diameter, is commonly used in clinical and research settings to evaluate response to therapy in patients with brain metastases. However, accurate volumetric assessment of the lesion and surrounding peri-lesional edema holds significant importance in clinical decision-making and can greatly enhance outcome prediction. The unique challenge in performing segmentations of brain metastases lies in their common occurrence as small lesions. Detection and segmentation of lesions that are smaller than 10 mm in size has not demonstrated high accuracy in prior publications. The brain metastases challenge sets itself apart from previously conducted MICCAI challenges on glioma segmentation due to the significant variability in lesion size. Unlike gliomas, which tend to be larger on presentation scans, brain metastases exhibit a wide range of sizes and tend to include small lesions. We hope that the BraTS-METS dataset and challenge will advance the field of automated brain metastasis detection and segmentation.

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.

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.

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms towards labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the the results of this evaluation and further investigate the performance-variation at vertebra-level, scan-level, and at different fields-of-view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The content and code concerning VerSe can be accessed at: https://github.com/anjany/verse.

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

Image segmentation plays an essential role in medicine for both diagnostic and interventional tasks. Segmentation approaches are either manual, semi-automated or fully-automated. Manual segmentation offers full control over the quality of the results, but is tedious, time consuming and prone to operator bias. Fully automated methods require no human effort, but often deliver sub-optimal results without providing users with the means to make corrections. Semi-automated approaches keep users in control of the results by providing means for interaction, but the main challenge is to offer a good trade-off between precision and required interaction. In this paper we present a deep learning (DL) based semi-automated segmentation approach that aims to be a "smart" interactive tool for region of interest delineation in medical images. We demonstrate its use for segmenting multiple organs on computed tomography (CT) of the abdomen. Our approach solves some of the most pressing clinical challenges: (i) it requires only one to a few user clicks to deliver excellent 2D segmentations in a fast and reliable fashion; (ii) it can generalize to previously unseen structures and "corner cases"; (iii) it delivers results that can be corrected quickly in a smart and intuitive way up to an arbitrary degree of precision chosen by the user and (iv) ensures high accuracy. We present our approach and compare it to other techniques and previous work to show the advantages brought by our method.

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.

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.

Purpose: To evaluate the performance of an automated deep learning method in detecting ascites and subsequently quantifying its volume in patients with liver cirrhosis and ovarian cancer. Materials and Methods: This retrospective study included contrast-enhanced and non-contrast abdominal-pelvic CT scans of patients with cirrhotic ascites and patients with ovarian cancer from two institutions, National Institutes of Health (NIH) and University of Wisconsin (UofW). The model, trained on The Cancer Genome Atlas Ovarian Cancer dataset (mean age, 60 years +/- 11 [s.d.]; 143 female), was tested on two internal (NIH-LC and NIH-OV) and one external dataset (UofW-LC). Its performance was measured by the Dice coefficient, standard deviations, and 95% confidence intervals, focusing on ascites volume in the peritoneal cavity. Results: On NIH-LC (25 patients; mean age, 59 years +/- 14 [s.d.]; 14 male) and NIH-OV (166 patients; mean age, 65 years +/- 9 [s.d.]; all female), the model achieved Dice scores of 0.855 +/- 0.061 (CI: 0.831-0.878) and 0.826 +/- 0.153 (CI: 0.764-0.887), with median volume estimation errors of 19.6% (IQR: 13.2-29.0) and 5.3% (IQR: 2.4-9.7) respectively. On UofW-LC (124 patients; mean age, 46 years +/- 12 [s.d.]; 73 female), the model had a Dice score of 0.830 +/- 0.107 (CI: 0.798-0.863) and median volume estimation error of 9.7% (IQR: 4.5-15.1). The model showed strong agreement with expert assessments, with r^2 values of 0.79, 0.98, and 0.97 across the test sets. Conclusion: The proposed deep learning method performed well in segmenting and quantifying the volume of ascites in concordance with expert radiologist assessments.

Vision-language models (VLM) have markedly advanced AI-driven interpretation and reporting of complex medical imaging, such as computed tomography (CT). Yet, existing methods largely relegate clinicians to passive observers of final outputs, offering no interpretable reasoning trace for them to inspect, validate, or refine. To address this, we introduce RadAgent, a tool-using AI agent that generates CT reports through a stepwise and interpretable process. Each resulting report is accompanied by a fully inspectable trace of intermediate decisions and tool interactions, allowing clinicians to examine how the reported findings are derived. In our experiments, we observe that RadAgent improves Chest CT report generation over its 3D VLM counterpart, CT-Chat, across three dimensions. Clinical accuracy improves by 6.0 points (36.4% relative) in macro-F1 and 5.4 points (19.6% relative) in micro-F1. Robustness under adversarial conditions improves by 24.7 points (41.9% relative). Furthermore, RadAgent achieves 37.0% in faithfulness, a new capability entirely absent in its 3D VLM counterpart. By structuring the interpretation of chest CT as an explicit, tool-augmented and iterative reasoning trace, RadAgent brings us closer toward transparent and reliable AI for radiology.

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.

Generating 3D images of complex objects conditionally from a few 2D views is a difficult synthesis problem, compounded by issues such as domain gap and geometric misalignment. For instance, a unified framework such as Generative Adversarial Networks cannot achieve this unless they explicitly define both a domain-invariant and geometric-invariant joint latent distribution, whereas Neural Radiance Fields are generally unable to handle both issues as they optimize at the pixel level. By contrast, we propose a simple and novel 2D to 3D synthesis approach based on conditional diffusion with vector-quantized codes. Operating in an information-rich code space enables high-resolution 3D synthesis via full-coverage attention across the views. Specifically, we generate the 3D codes (e.g. for CT images) conditional on previously generated 3D codes and the entire codebook of two 2D views (e.g. 2D X-rays). Qualitative and quantitative results demonstrate state-of-the-art performance over specialized methods across varied evaluation criteria, including fidelity metrics such as density, coverage, and distortion metrics for two complex volumetric imagery datasets from in real-world scenarios.

We present ReXGroundingCT, the first publicly available dataset to link free-text radiology findings with pixel-level segmentations in 3D chest CT scans that is manually annotated. While prior datasets have relied on structured labels or predefined categories, ReXGroundingCT captures the full expressiveness of clinical language represented in free text and grounds it to spatially localized 3D segmentation annotations in volumetric imaging. This addresses a critical gap in medical AI: the ability to connect complex, descriptive text, such as "3 mm nodule in the left lower lobe", to its precise anatomical location in three-dimensional space, a capability essential for grounded radiology report generation systems. The dataset comprises 3,142 non-contrast chest CT scans paired with standardized radiology reports from the CT-RATE dataset. Using a systematic three-stage pipeline, GPT-4 was used to extract positive lung and pleural findings, which were then manually segmented by expert annotators. A total of 8,028 findings across 16,301 entities were annotated, with quality control performed by board-certified radiologists. Approximately 79% of findings are focal abnormalities, while 21% are non-focal. The training set includes up to three representative segmentations per finding, while the validation and test sets contain exhaustive labels for each finding entity. ReXGroundingCT establishes a new benchmark for developing and evaluating sentence-level grounding and free-text medical segmentation models in chest CT. The dataset can be accessed at https://huggingface.co/datasets/rajpurkarlab/ReXGroundingCT.

The anatomical structure segmentation of the spine and adjacent structures from computed tomography (CT) images is a key step for spinal disease diagnosis and treatment. However, the segmentation of CT images is impeded by low contrast and complex vertebral boundaries. Although advanced models such as the Segment Anything Model (SAM) have shown promise in various segmentation tasks, their performance in spinal CT imaging is limited by high annotation requirements and poor domain adaptability. To address these limitations, we propose SpinalSAM-R1, a multimodal vision-language interactive system that integrates a fine-tuned SAM with DeepSeek-R1, for spine CT image segmentation. Specifically, our SpinalSAM-R1 introduces an anatomy-guided attention mechanism to improve spine segmentation performance, and a semantics-driven interaction protocol powered by DeepSeek-R1, enabling natural language-guided refinement. The SpinalSAM-R1 is fine-tuned using Low-Rank Adaptation (LoRA) for efficient adaptation. We validate our SpinalSAM-R1 on the spine anatomical structure with CT images. Experimental results suggest that our method achieves superior segmentation performance. Meanwhile, we develop a PyQt5-based interactive software, which supports point, box, and text-based prompts. The system supports 11 clinical operations with 94.3\% parsing accuracy and sub-800 ms response times. The software is released on https://github.com/6jm233333/spinalsam-r1.

Current vision-language models (VLMs) in medicine are primarily designed for categorical question answering (e.g., "Is this normal or abnormal?") or qualitative descriptive tasks. However, clinical decision-making often relies on quantitative assessments, such as measuring the size of a tumor or the angle of a joint, from which physicians draw their own diagnostic conclusions. This quantitative reasoning capability remains underexplored and poorly supported in existing VLMs. In this work, we introduce MedVision, a large-scale dataset and benchmark specifically designed to evaluate and improve VLMs on quantitative medical image analysis. MedVision spans 22 public datasets covering diverse anatomies and modalities, with 30.8 million image-annotation pairs. We focus on three representative quantitative tasks: (1) detection of anatomical structures and abnormalities, (2) tumor/lesion (T/L) size estimation, and (3) angle/distance (A/D) measurement. Our benchmarks show that current off-the-shelf VLMs perform poorly on these tasks. However, with supervised fine-tuning on MedVision, we significantly enhance their performance across detection, T/L estimation, and A/D measurement, demonstrating reduced error rates and improved precision. This work provides a foundation for developing VLMs with robust quantitative reasoning capabilities in medical imaging. Code and data are available at https://medvision-vlm.github.io.

AI models for lung cancer screening are limited by data scarcity, impacting generalizability and clinical applicability. Generative models address this issue but are constrained by training data variability. We introduce SYN-LUNGS, a framework for generating high-quality 3D CT images with detailed annotations. SYN-LUNGS integrates XCAT3 phantoms for digital twin generation, X-Lesions for nodule simulation (varying size, location, and appearance), and DukeSim for CT image formation with vendor and parameter variability. The dataset includes 3,072 nodule images from 1,044 simulated CT scans, with 512 lesions and 174 digital twins. Models trained on clinical + simulated data outperform clinical only models, achieving 10% improvement in detection, 2-9% in segmentation and classification, and enhanced synthesis. By incorporating anatomy-informed simulations, SYN-LUNGS provides a scalable approach for AI model development, particularly in rare disease representation and improving model reliability.

Generating accurate 3D reconstructions from endoscopic video is a promising avenue for longitudinal radiation-free analysis of sinus anatomy and surgical outcomes. Several methods for monocular reconstruction have been proposed, yielding visually pleasant 3D anatomical structures by retrieving relative camera poses with structure-from-motion-type algorithms and fusion of monocular depth estimates. However, due to the complex properties of the underlying algorithms and endoscopic scenes, the reconstruction pipeline may perform poorly or fail unexpectedly. Further, acquiring medical data conveys additional challenges, presenting difficulties in quantitatively benchmarking these models, understanding failure cases, and identifying critical components that contribute to their precision. In this work, we perform a quantitative analysis of a self-supervised approach for sinus reconstruction using endoscopic sequences paired with optical tracking and high-resolution computed tomography acquired from nine ex-vivo specimens. Our results show that the generated reconstructions are in high agreement with the anatomy, yielding an average point-to-mesh error of 0.91 mm between reconstructions and CT segmentations. However, in a point-to-point matching scenario, relevant for endoscope tracking and navigation, we found average target registration errors of 6.58 mm. We identified that pose and depth estimation inaccuracies contribute equally to this error and that locally consistent sequences with shorter trajectories generate more accurate reconstructions. These results suggest that achieving global consistency between relative camera poses and estimated depths with the anatomy is essential. In doing so, we can ensure proper synergy between all components of the pipeline for improved reconstructions that will facilitate clinical application of this innovative technology.

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.

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.

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.

Medical image analysis is a fundamental component. As deep learning progresses, the focus has shifted from single-task applications, such as classification and segmentation, to more complex multimodal tasks, including medical visual question answering and report generation. Traditional shallow and task-specific models are increasingly limited in addressing the complexity and scalability required in clinical practice. The emergence of large language models (LLMs) has driven the development of medical Large Vision-Language Models (LVLMs), offering a unified solution for diverse vision-language tasks. In this study, we investigate various architectural designs for medical LVLMs based on the widely adopted LLaVA framework, which follows an encoder-connector-LLM paradigm. We construct two distinct models targeting 2D and 3D modalities, respectively. These models are designed to support both general-purpose medical tasks and domain-specific fine-tuning, thereby serving as effective foundation models. To facilitate reproducibility and further research, we develop a modular and extensible codebase, MedM-VL, and release two LVLM variants: MedM-VL-2D for 2D medical image analysis and MedM-VL-CT-Chest for 3D CT-based applications. The code and models are available at: https://github.com/MSIIP/MedM-VL

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/.

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.

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.

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (UniT) model to detect (tumor existence and location) and diagnose (tumor characteristics) eight major cancer-prevalent organs in CT scans. UniT is a query-based Mask Transformer model with the output of multi-organ and multi-tumor semantic segmentation. We decouple the object queries into organ queries, detection queries and diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. UniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, UniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-organ segmentation methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. Such a unified multi-cancer image reading model (UniT) can significantly reduce the number of false positives produced by combined multi-system models. This moves one step closer towards a universal high-performance cancer screening tool.

Early tumor detection save lives. Each year, more than 300 million computed tomography (CT) scans are performed worldwide, offering a vast opportunity for effective cancer screening. However, detecting small or early-stage tumors on these CT scans remains challenging, even for experts. Artificial intelligence (AI) models can assist by highlighting suspicious regions, but training such models typically requires extensive tumor masks--detailed, voxel-wise outlines of tumors manually drawn by radiologists. Drawing these masks is costly, requiring years of effort and millions of dollars. In contrast, nearly every CT scan in clinical practice is already accompanied by medical reports describing the tumor's size, number, appearance, and sometimes, pathology results--information that is rich, abundant, and often underutilized for AI training. We introduce R-Super, which trains AI to segment tumors that match their descriptions in medical reports. This approach scales AI training with large collections of readily available medical reports, substantially reducing the need for manually drawn tumor masks. When trained on 101,654 reports, AI models achieved performance comparable to those trained on 723 masks. Combining reports and masks further improved sensitivity by +13% and specificity by +8%, surpassing radiologists in detecting five of the seven tumor types. Notably, R-Super enabled segmentation of tumors in the spleen, gallbladder, prostate, bladder, uterus, and esophagus, for which no public masks or AI models previously existed. This study challenges the long-held belief that large-scale, labor-intensive tumor mask creation is indispensable, establishing a scalable and accessible path toward early detection across diverse tumor types. We plan to release our trained models, code, and dataset at https://github.com/MrGiovanni/R-Super

The application of ionizing radiation for diagnostic imaging is common around the globe. However, the process of imaging, itself, remains to be a relatively hazardous operation. Therefore, it is preferable to use as low a dose of ionizing radiation as possible, particularly in computed tomography (CT) imaging systems, where multiple x-ray operations are performed for the reconstruction of slices of body tissues. A popular method for radiation dose reduction in CT imaging is known as the quarter-dose technique, which reduces the x-ray dose but can cause a loss of image sharpness. Since CT image reconstruction from directional x-rays is a nonlinear process, it is analytically difficult to correct the effect of dose reduction on image quality. Recent and popular deep-learning approaches provide an intriguing possibility of image enhancement for low-dose artifacts. Some recent works propose combinations of multiple deep-learning and classical methods for this purpose, which over-complicate the process. However, it is observed here that the straight utilization of the well-known U-NET provides very successful results for the correction of low-dose artifacts. Blind tests with actual radiologists reveal that the U-NET enhanced quarter-dose CT images not only provide an immense visual improvement over the low-dose versions, but also become diagnostically preferable images, even when compared to their full-dose CT versions.