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.

Radiology plays an integral role in modern medicine, yet rising imaging volumes have far outpaced workforce growth. Foundation models offer a path toward assisting with the full spectrum of radiology tasks, but existing medical models remain limited: they process volumetric CT and MRI as low-fidelity 2D slices, discard critical grayscale contrast information, and lack evaluation frameworks that reflect real clinical practice. We introduce Pillar-0, a radiology foundation model pretrained on 42,990 abdomen-pelvis CTs, 86,411 chest CTs, 14,348 head CTs, and 11,543 breast MRIs from a large academic center, together with RATE, a scalable framework that extracts structured labels for 366 radiologic findings with near-perfect accuracy using LLMs. Across internal test sets of 14,230 abdomen-pelvis CTs, 10,646 chest CTs, 4,906 head CTs, and 1,585 breast MRIs, Pillar-0 establishes a new performance frontier, achieving mean AUROCs of 86.4, 88.0, 90.1, and 82.9, outperforming MedGemma (Google), MedImageInsight (Microsoft), Lingshu (Alibaba), and Merlin (Stanford) by 7.8-15.8 AUROC points and ranking best in 87.2\% (319/366) tasks. Pillar-0 similarly outperforms all baselines in an external validation on the Stanford Abdominal CT dataset, including Merlin (82.2 vs 80.6 AUROC). Pillar-0 extends to tasks beyond its pretraining, such as long-horizon lung cancer risk prediction, where it improves upon the state-of-the-art Sybil by 3.0 C-index points on NLST, and generalizes with gains of 5.9 (MGH) and 1.9 (CGMH). In brain hemorrhage detection, Pillar-0 obtained a >95 AUROC when using only 1/20th of the data of the next most sample efficient baseline. Pillar-0 and RATE together provide an open, clinically rigorous foundation for building high-performance radiology systems, enabling applications that were previously infeasible due to computational, data, and evaluation constraints.

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.

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.

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.

Accurate and efficient 3D segmentation is essential for both clinical and research applications. While foundation models like SAM have revolutionized interactive segmentation, their 2D design and domain shift limitations make them ill-suited for 3D medical images. Current adaptations address some of these challenges but remain limited, either lacking volumetric awareness, offering restricted interactivity, or supporting only a small set of structures and modalities. Usability also remains a challenge, as current tools are rarely integrated into established imaging platforms and often rely on cumbersome web-based interfaces with restricted functionality. We introduce nnInteractive, the first comprehensive 3D interactive open-set segmentation method. It supports diverse prompts-including points, scribbles, boxes, and a novel lasso prompt-while leveraging intuitive 2D interactions to generate full 3D segmentations. Trained on 120+ diverse volumetric 3D datasets (CT, MRI, PET, 3D Microscopy, etc.), nnInteractive sets a new state-of-the-art in accuracy, adaptability, and usability. Crucially, it is the first method integrated into widely used image viewers (e.g., Napari, MITK), ensuring broad accessibility for real-world clinical and research applications. Extensive benchmarking demonstrates that nnInteractive far surpasses existing methods, setting a new standard for AI-driven interactive 3D segmentation. nnInteractive is publicly available: https://github.com/MIC-DKFZ/napari-nninteractive (Napari plugin), https://www.mitk.org/MITK-nnInteractive (MITK integration), https://github.com/MIC-DKFZ/nnInteractive (Python backend).

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) 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.

Influenced by the complexity of volumetric imaging, there is a shortage of established datasets useful for benchmarking volumetric deep-learning models. As a consequence, new and existing models are not easily comparable, limiting the development of architectures optimized specifically for volumetric data. To counteract this trend, we introduce MozzaVID - a large, clean, and versatile volumetric classification dataset. Our dataset contains X-ray computed tomography (CT) images of mozzarella microstructure and enables the classification of 25 cheese types and 149 cheese samples. We provide data in three different resolutions, resulting in three dataset instances containing from 591 to 37,824 images. While being general-purpose, the dataset also facilitates investigating mozzarella structure properties. The structure of food directly affects its functional properties and thus its consumption experience. Understanding food structure helps tune the production and mimicking it enables sustainable alternatives to animal-derived food products. The complex and disordered nature of food structures brings a unique challenge, where a choice of appropriate imaging method, scale, and sample size is not trivial. With this dataset we aim to address these complexities, contributing to more robust structural analysis models. The dataset can be downloaded from: https://archive.compute.dtu.dk/files/public/projects/MozzaVID/.

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.

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.

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 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.

Foundation models have demonstrated remarkable potential in medical domain. However, their application to complex cardiovascular diagnostics remains underexplored. In this paper, we present Cardiac-CLIP, a multi-modal foundation model designed for 3D cardiac CT images. Cardiac-CLIP is developed through a two-stage pre-training strategy. The first stage employs a 3D masked autoencoder (MAE) to perform self-supervised representation learning from large-scale unlabeled volumetric data, enabling the visual encoder to capture rich anatomical and contextual features. In the second stage, contrastive learning is introduced to align visual and textual representations, facilitating cross-modal understanding. To support the pre-training, we collect 16641 real clinical CT scans, supplemented by 114k publicly available data. Meanwhile, we standardize free-text radiology reports into unified templates and construct the pathology vectors according to diagnostic attributes, based on which the soft-label matrix is generated to supervise the contrastive learning process. On the other hand, to comprehensively evaluate the effectiveness of Cardiac-CLIP, we collect 6,722 real-clinical data from 12 independent institutions, along with the open-source data to construct the evaluation dataset. Specifically, Cardiac-CLIP is comprehensively evaluated across multiple tasks, including cardiovascular abnormality classification, information retrieval and clinical analysis. Experimental results demonstrate that Cardiac-CLIP achieves state-of-the-art performance across various downstream tasks in both internal and external data. Particularly, Cardiac-CLIP exhibits great effectiveness in supporting complex clinical tasks such as the prospective prediction of acute coronary syndrome, which is notoriously difficult in real-world scenarios.

Liver cancer is one of the leading causes of cancer death. To assist doctors in hepatocellular carcinoma diagnosis and treatment planning, an accurate and automatic liver and tumor segmentation method is highly demanded in the clinical practice. Recently, fully convolutional neural networks (FCNs), including 2D and 3D FCNs, serve as the back-bone in many volumetric image segmentation. However, 2D convolutions can not fully leverage the spatial information along the third dimension while 3D convolutions suffer from high computational cost and GPU memory consumption. To address these issues, we propose a novel hybrid densely connected UNet (H-DenseUNet), which consists of a 2D DenseUNet for efficiently extracting intra-slice features and a 3D counterpart for hierarchically aggregating volumetric contexts under the spirit of the auto-context algorithm for liver and tumor segmentation. We formulate the learning process of H-DenseUNet in an end-to-end manner, where the intra-slice representations and inter-slice features can be jointly optimized through a hybrid feature fusion (HFF) layer. We extensively evaluated our method on the dataset of MICCAI 2017 Liver Tumor Segmentation (LiTS) Challenge and 3DIRCADb Dataset. Our method outperformed other state-of-the-arts on the segmentation results of tumors and achieved very competitive performance for liver segmentation even with a single model.

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.

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.

Frontier artificial intelligence (AI) models, such as OpenAI's GPT-5 and Meta's DINOv3, have advanced rapidly through training on internet-scale public data, yet such systems lack access to private clinical data. Neuroimaging, in particular, is underrepresented in the public domain due to identifiable facial features within MRI and CT scans, fundamentally restricting model performance in clinical medicine. Here, we show that frontier models underperform on neuroimaging tasks and that learning directly from uncurated data generated during routine clinical care at health systems, a paradigm we call health system learning, yields high-performance, generalist neuroimaging models. We introduce NeuroVFM, a visual foundation model trained on 5.24 million clinical MRI and CT volumes using a scalable volumetric joint-embedding predictive architecture. NeuroVFM learns comprehensive representations of brain anatomy and pathology, achieving state-of-the-art performance across multiple clinical tasks, including radiologic diagnosis and report generation. The model exhibits emergent neuroanatomic understanding and interpretable visual grounding of diagnostic findings. When paired with open-source language models through lightweight visual instruction tuning, NeuroVFM generates radiology reports that surpass frontier models in accuracy, clinical triage, and expert preference. Through clinically grounded visual understanding, NeuroVFM reduces hallucinated findings and critical errors, offering safer clinical decision support. These results establish health system learning as a paradigm for building generalist medical AI and provide a scalable framework for clinical foundation models.

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