Computed Tomography Dataset

Recent innovations in deep learning have significantly enhanced the diagnosis of medical images, although they are based on the use of centralized data storage that pose severe threats to patient privacy and medical data security. To address this issue, this research proposes a Federated Learning (FL) model that is coupled with an optimized YOLOv8 network to detect the kidney stones on a computed tomography (CT) image and at the same time, protect privacy of the patients. The suggested system can help various medical organizations to jointly train a common model without exchanging the information about the patients. This is to ensure that data protection laws like GDPR and HIPAA are adhered to. The residual feature fusion and DropBlock regularization among other architectural improvements are also included in YOLOv8 to enhance detection robustness and minimize overfitting. Experimental analysis carried out on a distributed CT dataset demonstrated that the federated YOLOv8 model has a mAP at 50 of 0.733 and is able to keep the data confidential. Moreover, its lean design facilitates fast edge deployment and real-time inference across a clinical setting. Altogether, these findings indicate that Federated Learning is a safe and efficient solution to AI-assisted diagnosis in contemporary healthcare when combined with the use of sophisticated object detection models.

The joint interpretation of metabolic function and anatomical structure is essential for clinical diagnosis in whole-body PET/CT. Although recent advances in 3D medical vision-language models have demonstrated remarkable progress, current efforts are limited to regional CT imaging, leaving a critical void in comprehensive whole-body PET/CT analysis. In this work, we introduce MetaStructAtlas, a large-scale dataset for grounded whole-body PET/CT interpretation that synthesizes multimodal imaging with integrated anatomical, metabolic, and semantic annotations. MetaStructAtlas provides 490 co-registered 3D PET and CT volumes with 50,470 organ-level segmentation masks and grounded radiology reports. To facilitate interactive reasoning, we further developed MetaStructVQA, a standardized 3D grounded visual question-answering benchmark containing 100,565 QA pairs. This framework explicitly links diagnostic queries to visual evidence across modalities, encompassing anatomical, morphological, and metabolic characteristics. Finally, we evaluate state-of-the-art 3D medical VLMs on MetaStructVQA, establishing a robust foundation for multimodal representation learning and integrated whole-body reasoning in nuclear medicine.

Accurate 3D abnormality segmentation in chest CT requires dense spatial supervision, but obtaining expert voxel-level labels is costly. Radiology reports, however, are routinely generated during clinical interpretation and contain instance-specific descriptions that can provide additional guidance without new dense annotation. Existing vision-language grounding methods typically require report-derived findings at inference, making localization dependent on paired text and limiting each forward pass to a queried finding. We propose Instance-Guided Report Anchoring (IGRA), a model-agnostic module that preserves the correspondence between each annotated abnormality instance and the report finding that describes it. IGRA pools each instance representation and anchors it to the corresponding finding embedding during training; all text-related components are discarded at inference. We further reformulate free-text grounding on ReXGroundingCT as multi-label volumetric segmentation by merging same-category instances, allowing all abnormality categories to be predicted in one image-only forward pass. IGRA improves Dice by 22.5% over the strongest image-only baseline (30.93 vs. 25.25) and is comparable to VoxTell on the single-finding subset (30.29 vs. 30.43). Applied unchanged to four standard 3D segmentation backbones, IGRA improves Dice and hit rate across all architectures. Zero-shot evaluation on LIDC-IDRI, PleThora, and a private in-house dataset further shows consistent gains over image-only baselines.

Background: Patient details and acquisition metadata are important for clinical decisions, image quality control, and automated research pipelines, but may be missing or unreliable in imaging archives. Purpose: To develop and evaluate a fast open-source model that predicts patient and acquisition characteristics directly from CT and MR images. Materials and Methods: Separate 3D ResNet-10 ensembles for CT and MR were trained on 57,291 and 43,200 clinical examinations acquired from 2011 to 2025. Both predicted weight, height, age, sex, contrast presence, vertebral coverage, and image noise. The CT model additionally predicted scanner manufacturer, tube voltage, tube current, convolution kernel, and post-injection time; the MR model predicted sequence class. Performance was evaluated on internal CT (n=501) and MR (n=636) test sets and an external CT dataset (n=54). Results: Internal CT MAEs were 3.90 kg, 3.68 cm, and 4.42 years for weight, height, and age, with sex F1=0.990; corresponding MR results were 4.34 kg, 4.62 cm, 7.13 years, and F1=0.970. The CNN outperformed a segmentation-derived XGBoost baseline for all four core targets in both modalities (adjusted P<=.042). F1 scores were 0.963 for CT contrast, 0.953 for MR sequence, and 0.823 for MR contrast. External CT MAEs were 4.45 kg, 4.05 cm, and 5.17 years, with sex F1=0.971. CPU inference required 20 seconds for CT and 12 seconds for MR. Conclusion: One 3D multitask model per modality can rapidly recover patient and acquisition characteristics from heterogeneous CT and MR examinations. Models are available in TotalSegmentator: https://github.com/wasserth/TotalSegmentator

In medical imaging, the clinical value of Computed Tomography (CT) lies not only in depicting current disease status, but crucially in enabling longitudinal comparison of serial scans to determine disease evolution, a process that underpins response assessment, recurrence detection, and ongoing patient management. Yet, despite this central role of temporal comparison in clinical decision-making, existing medical foundation models remain largely confined to single-study understanding, leaving temporally grounded cross-examination insufficiently addressed. To address this gap, we study longitudinal imaging difference reporting, a task in which a model takes two temporally separated scans from the same patient and generates a clinically meaningful report describing interval changes between them. We introduce CT-$Δ$Bench, a dedicated benchmark for this task with patient-level splitting to prevent information leakage. To better evaluate this task beyond surface-level text similarity, we further develop change-aware metrics specifically designed to capture clinically meaningful longitudinal changes, and conduct an independent physician validation to assess the reliability of the synthesized references and event extraction pipeline. We also compare direct paired-CT reasoning with an indirect two-stage pipeline that first generates single-timepoint reports and then performs textual differencing. Finally, we propose DeltaMed, a baseline model for direct paired-CT difference reporting, and train it on the benchmark training set. Together, these contributions lay the groundwork for temporally aware medical foundation models that better reflect real-world longitudinal clinical reasoning.

Automated lesion segmentation in whole-body PET/CT imaging can assist clinicians with cancer detection, staging, and treatment planning across radiotracers and cancer types. However, training lesion segmentation models that capture variations in lesion size, distribution, and appearance requires large annotated datasets, whose creation is both time- and expertise-intensive. As a result, models trained on limited labeled PET/CT data often lack the accuracy and generalizability needed for clinical use. We present FEEDS (Foundation model-Enabled Efficient Data Sampling), a label- and compute-efficient learning strategy that uses vision foundation model embeddings to select the most informative and diverse unlabeled cases for expert annotation. Unlike unsupervised, semi-supervised, and active learning approaches, FEEDS is a one-step training paradigm requiring only a limited, representative training set, making it label- and compute-efficient. We train and validate FEEDS using the AutoPET-III dataset. We test its accuracy and generalizability on three held-out sets: AutoPET-III, DeepPSMA, and an internal Dartmouth-Hitchcock Medical Center dataset. We evaluate clinical utility at the voxel, lesion, and anatomic region level to assess performance in high-risk areas and treatment planning utility. FEEDS outperforms random-sampling-based labeling, pseudolabel-based semi-supervised learning, and training with limited labeled data alone. It generalizes across all three test sets, FDG and PSMA tracers, and multiple diseases, matching fully-labeled (100%) training performance with 70% less annotation burden. FEEDS addresses the challenge of label scarcity in an automatic lesion segmentation framework by providing a practical approach for constructing representative and diverse annotation queues from large, unannotated clinical repositories.

Routine CT interpretation is inherently comprehensive, capturing incidental findings across the entire scan volume. 3D CT foundation models could assist this process by providing generalizable representations of anatomy and pathology. To evaluate their diagnostic breadth, we benchmark ten frozen CT encoders across three cohorts of thoracic CT scans, including an unseen internal clinical dataset, using $k$-nearest neighbors, zero-shot prompting, and linear probing. We find no universal state-of-the-art, with rankings fluctuating significantly depending on the evaluation context. While models combining fine-grained image tokenization with vision-language alignment generally perform best, a lightweight supervised encoder remains highly competitive, demonstrating that explicit labels can effectively substitute for scale. Crucially, rather than model architecture, we observe that the primary determinant of performance is a physical bottleneck: a finding's detectability scales with its contrast against surrounding tissue and its spatial extent. Through controlled within-organ comparisons, we empirically demonstrate that widespread or high-contrast abnormalities, such as devices and effusions, are reliably recovered. Conversely, small, low-contrast focal lesions remain a persistent challenge across all evaluated encoders. We attribute this to the inherent limitations of globally pooled embeddings, suggesting that accurately representing small, low-contrast structures will require region- or lesion-level pretraining.

Medical images are routinely de-identified---names, dates, and other metadata removed---and then shared for research, teaching, and public benchmarks under the assumption that this renders them anonymous. Such de-identification protects the metadata but not the pixels, and---apart from scans that directly contain facial structures---whether the image content itself identifies the patient has received little scrutiny. We investigate this question by learning a cycle-consistent correspondence between a cross-sectional medical image and a non-medical, patient-identifying image, using a pair of coupled, cycle-consistent variational autoencoders. From a held-out scan, the model recovers a recognisable likeness of the patient (identity-region MAE = 0.163); conversely, it synthesises a scan from such an image. These results indicate that a de-identified medical scan remains identifying---it is, in effect, a photograph of the patient---and that imaging data should be governed as biometric data rather than as anonymisable records. To support reproducibility, the code and trained models are shared at https://github.com/attilasimko/public-repository.

A 3D CT scan entering a vision-language model produces a long sequence of visual tokens, often thousands to tens of thousands per volume, and this sequence must be compressed before a language model can consume it. Token compression is well studied in general vision, but little of it targets 3D CT specifically. A common baseline is grid average, which pools regular grid cells and can blend distinct anatomy, lesion, and air into one token. We present \textbf{ORCA} (ORgan-Centroid Aggregation), a token compressor for 3D CT. It merges adjacent tokens with organ guidance and adds a sinusoidal encoding of each region's centroid to preserve spatial layout. This preserves the anatomical information a downstream model needs. ORCA is training-free and plug-and-play, producing an adjustable token set without any model change or text query. We evaluate it across two datasets (CT-RATE and Merlin) and five encoders. The evaluation spans two task types: attribute prediction over five families (size, density, location, texture, and disease) and text generation (visual question answering and report generation). At matched token budgets, ORCA improves consistently over existing compression methods. It shrinks the visual context $64\times$ and its KV-cache $50\times$, and is $31\times$ faster to process each volume. Code released at https://github.com/renjie-liang/ORCA-3DCT.

Volumetric CT vision-language pretraining learns 3D representations from scan-report pairs, but global and anatomy-aware objectives supervise only correspondence: they establish what is present and leave how much unconstrained. Nothing separates a mild from an extensive case of the same finding along a consistent direction, so the graded burden language in reports collapses into a present/absent signal. Longitudinal supervision would supply this order, but patient-matched CT pairs are scarce at scale; cross-sectional cohorts already encode weak burden cues across different patients. We introduce Spectrum, an anatomy-conditioned framework that represents each study at whole-study and organ scopes. For each organ-mapped pathology, a rule-based scorer mines confidence-filtered lower-to-higher pairs of different patients, and Burden-Direction Alignment (BDA) aligns the pathology-conditioned image delta with the report delta at each scope, separating that direction from its reverse. Because the endpoints are different people, a target-conditioned aligner first makes them comparable, so the delta reflects burden rather than between-patient variation. BDA further separates the selected direction from its reverse, anchors it to the observed higher-burden endpoint, and enforces consistency across ordered triplets. Since every pair is drawn within a single pathology, BDA is designed to constrain intra-class structure that image-report contrast alone never touches. Spectrum attains 85.6 zero-shot AUROC on CT-RATE and 72.7 on external RAD-ChestCT, with consistent gains in linear probing and retrieval. Weak cross-patient order is thus a scalable complement to anatomy-aware correspondence, yielding burden-aware CT representations without longitudinal data.

Medical image quality plays a critical role in diagnostic accuracy, especially in X-ray-based imaging modalities such as cone-beam computed tomography (CBCT), where image quality must be balanced against radiation dose. While expert visual evaluation remains the clinical standard for image quality evaluation, it is time-consuming, subjective and affected by inter-observer variability, emphasizing the need for reliable quantitative image quality assessment (IQA) methods. However, the development and validation of such IQA methods have been limited by the lack of publicly available CBCT datasets with expert image quality annotations. In this study, we provide the first open-access CBCT IQA dataset containing 1,764 annotated image slices acquired using systematic variations in image acquisition and reconstruction parameters. Three clinical experts graded the overall image quality and a predefined regions of interest (ROI) using a four-level scoring scheme. In addition, we benchmark 26 full reference- and no reference-based IQA measures against expert annotations and introduce an exploratory IQA measure-based ranking capable of distinguishing subtle image quality differences. This dataset introduced a standardized benchmark for future CBCT IQA research and provides a valuable resource for the development and validation of new IQA methods, enabling reproducible research and advancing CBCT IQA.

This paper proposes an automated classification method of COVID-19 chest CT volumes using improved 3D MLP-Mixer. Novel coronavirus disease 2019 (COVID-19) spreads over the world, causing a large number of infected patients and deaths. Sudden increase in the number of COVID-19 patients causes a manpower shortage in medical institutions. Computer-aided diagnosis (CAD) system provides quick and quantitative diagnosis results. CAD system for COVID-19 enables efficient diagnosis workflow and contributes to reduce such manpower shortage. In image-based diagnosis of viral pneumonia cases including COVID-19, both local and global image features are important because viral pneumonia cause many ground glass opacities and consolidations in large areas in the lung. This paper proposes an automated classification method of chest CT volumes for COVID-19 diagnosis assistance. MLP-Mixer is a recent method of image classification using Vision Transformer-like architecture. It performs classification using both local and global image features. To classify 3D CT volumes, we developed a hybrid classification model that consists of both a 3D convolutional neural network (CNN) and a 3D version of the MLP-Mixer. Classification accuracy of the proposed method was evaluated using a dataset that contains 1205 CT volumes and obtained 79.5% of classification accuracy. The accuracy was higher than that of conventional 3D CNN models consists of 3D CNN layers and simple MLP layers.

This paper proposes an automated classification method of chest CT volumes based on likelihood of COVID-19 cases. Novel coronavirus disease 2019 (COVID-19) spreads over the world, causing a large number of infected patients and deaths. Sudden increase in the number of COVID-19 patients causes a manpower shortage in medical institutions. Computer-aided diagnosis (CAD) system provides quick and quantitative diagnosis results. CAD system for COVID-19 enables efficient diagnosis workflow and contributes to reduce such manpower shortage. This paper proposes an automated classification method of chest CT volumes for COVID-19 diagnosis assistance. We propose a COVID-19 classification convolutional neural network (CNN) that has a 2D/3D hybrid feature extraction flows. The 2D/3D hybrid feature extraction flows are designed to effectively extract image features from anisotropic volumes such as chest CT volumes for diagnosis. The flows extract image features on three mutually perpendicular planes in CT volumes and then combine the features to perform classification. Classification accuracy of the proposed method was evaluated using a dataset that contains 1288 CT volumes. An averaged classification accuracy was 83.3%. The accuracy was higher than that of a classification CNN which does not have 2D and 3D hybrid feature extraction flows.

The rapid emergence of 3D CT foundation models has opened new avenues for predictive modeling from CT imaging, offering a compelling alternative to traditional radiomics which is known to suffer from reproducibility issues and sensitivity to acquisition protocol variations. Yet, as these models grow in availability, a critical need arises to evaluate how well their learned representations generalize across diverse clinical settings and whether adaptation to specific downstream tasks is necessary to unlock their full potential. To address these questions, we benchmarked several 3D CT foundation models for predicting recurrence-free survival in head and neck cancer across two public datasets totaling 3,644 patients, evaluating various adaptation strategies and modality fusion mechanisms. Our findings reveal persistent difficulty in identifying features that generalize consistently across different imaging distributions, as evidenced by significant performance drops on external validation cohorts. Ultimately, the integration of imaging features with clinical data remains the most accurate approach for prognostic prediction, though achieving universal generalization across varied clinical contexts continues to represent a substantial challenge for the current generation of models.

Self-supervised pretraining is central to 3D medical image analysis, where unlabeled CT volumes are abundant but expert annotations are scarce. Yet existing volumetric encoders often fail to preserve the coarse spatial and geometric structure that downstream reasoning depends on, limiting their performance on organ disentanglement, abnormality detection, and spatial understanding when paired with language models. We introduce Rad-JEPA 3D, a joint-embedding predictive framework that learns volumetric CT representations by predicting the latent features of a complete scan from a masked view. At its core is a hybrid H-Mamba encoder that fuses a Mamba state-space branch, which models inter-slice continuity through sequential scanning, with a grouped-query attention branch, which captures cross-plane spatial context, combined through a lightweight per-token router. To improve the quality of intermediate representations, we further propose Hidden States Orthogonal Regularization (HSOR), which aligns student-teacher hidden states and reduces feature redundancy throughout the encoder. This layer-wise regularization produces more consistent and discriminative volumetric representations, leading to improved performance on organ recognition and spatial reasoning tasks. Pretrained on approximately 120,000 CT scans, Rad-JEPA 3D attains state-of-the-art results despite its compact size: with only 4.0B total parameters, it achieves competitive results with state-of-the-art on closed-ended VQA and the best average spatial-reasoning score on the Spatial-Med benchmark. Ablation studies confirm that the hybrid block and HSOR contribute complementary gains, and that the induced spatial structure can substitute for raw language-model scale on volumetric reasoning tasks.

We introduce a method for training a text-conditioned segmentation model for CT scans, which combines voxel-level supervision with coarse but scalable slice-level supervision from reports. We extract, from a large database of scan-report pairs, descriptions of findings with indices of slices where those findings occur. We then finetune a general-purpose 2D image segmentation model, SAM3, with standard segmentation losses from strongly labeled data and with a slice-level classification loss from the extracted weak supervision. Our results on the ReXGroundingCT dataset illustrate that this strategy improves the segmentation dice score: from an 8% relative gain when there are 1000 fully labeled volumes to 22% when there are 250 fully labeled volumes.

A CT examination captures multiple organs, but many biomedical questions concern abnormalities, prognosis, or longitudinal change in a specific organ. These questions require a separate representation for each organ within the same CT volume. Existing CT foundation models commonly produce a single volume-level representation, while recent anatomy-aware methods either encode pre-separated organ volumes or explicitly disentangle images into organ token groups. The former may remove clinically relevant surrounding context, while the latter does not condition a shared encoder on a selected organ before its features are formed. We introduce OrganLens for organ-specific representation learning through self-supervision. An organ identity conditions a shared CT encoder, while organ-specific distillation and anatomy-mask supervision shape features for anatomy-weighted pooling into organ-specific representations. At inference, the shared model produces 11 organ-specific representations without external segmentation masks. We evaluate OrganLens on CT-RATE, RAD-ChestCT, INSPECT, and NLST across diverse acquisitions and downstream evaluations. Relative to CT-pretrained DINOv2, heart representations raise CT-RATE cardiomegaly AUROC from 0.910 to 0.953, while lung representations improve the Harrell C-index for NLST lung-cancer mortality by 14.2%. The global representation reaches INSPECT Recall@10 of 33.09% and 32.04% for text-to-image and image-to-text retrieval, respectively. Across organ-related tasks, anatomically matched representations provide stronger task-relevant signal, while the global representation retains broad utility. OrganLens offers a scalable approach to organ-specific CT representation learning with a shared encoder. More broadly, it provides the medical research community with a reusable framework for studying organ-specific disease across cohorts and clinical endpoints.

18F-FDG PET/CT plays a central role in staging, treatment planning, and response assessment for head and neck cancer by providing functional information that complements anatomical CT imaging. However, PET acquisition requires radiotracer administration, specialized infrastructure, and additional cost, limiting its availability for repeated imaging. We present a proof of concept deep learning framework for synthesizing PET like images directly from routine CT scans with the goal of providing complementary metabolic information that may support imaging triage and clinical decision support rather than replace diagnostic PET. Forty-four patients from the publicly available QIN-HEADNECK dataset were retrospectively analyzed using five fold cross-validation. We propose a fully three dimensional dual path architecture consisting of (i) a regression U-Net optimized for voxel-wise quantitative SUV estimation and (ii) a conditional generative adversarial network optimized for realistic PET texture. Their outputs are integrated using hotspot guided Laplacian pyramid blending, allowing quantitative information from the regression pathway to be preserved within metabolically active regions while leveraging adversarial texture synthesis elsewhere. The proposed framework achieved a mean absolute error of 0.00395, PSNR of 39.19 dB, and SSIM of 0.9634 on reconstructed three dimensional PET volumes. Qualitative evaluation demonstrated accurate localization of many FDG-avid lesions while producing anatomically realistic background texture. Consistent with previous CT to PET synthesis studies, the principal limitation was systematic underestimation of SUV within highly metabolically active tumor regions.

Purpose: To develop and validate a deep learning ensemble for estimating adult sex, age, height, and weight from coronal digitally reconstructed radiographs (DRRs) generated from diagnostic CT. Materials and Methods: This retrospective study included 128,621 CT examinations from 80,004 adults at nine institutions in Japan. Three multitask models-ConvNeXt-Base, ViT-Base/16, and MaxViT-Base-were fine-tuned using coronal DRRs and combined by weighted averaging. Data were split by institution into training (114,147 examinations; seven institutions), tuning (4,305; one institution), and test (10,169; one institution) sets; generalizability was assessed on two non-Japanese datasets. Accuracy and mean absolute error (MAE) were used to evaluate sex classification and age, height, and weight regression, respectively. Body surface area (BSA)-corrected heart and liver volume trends were compared using true versus estimated height and weight. Results: In the test set (median age, 69.9 years; 4,899 of 10,169 [48.2%] male), overall sex-classification accuracy was 0.997 (95% CI, 0.996-0.998), and MAEs were 3.57 years (3.51-3.63), 2.59 cm (2.54-2.64), and 3.40 kg (3.34-3.47) for age, height, and weight, respectively. In examinations covering the chest through pelvis, accuracy was 1.000, and MAEs were 3.15 years, 2.28 cm, and 3.18 kg, respectively. BSA calculated from estimated values reproduced age-related heart and liver volume trends obtained using true values. On non-Japanese datasets, height error increased but was reduced by continued fine-tuning. Conclusion: The ensemble estimated adult sex, age, height, and weight from CT-derived DRRs, with generally lower errors in examinations with broader anatomical coverage.

3D CT vision-language models (VLMs) classify abnormalities from text prompts in a zero-shot manner, enabling cross-institution deployment where labels are scarce and clinical tasks shift faster than supervised models can be retrained. A real CT scan, however, typically contains several co-occurring abnormalities, and the reliability of zero-shot multi-label prediction under distribution shift remains poorly understood. Test-time adaptation (TTA) updates a model on unlabeled target scans without source data or target annotations, yet existing TTA methods target multi-class softmax prediction on natural images or 2D medical segmentation, and none addresses unsupervised multi-label adaptation for zero-shot 3D CT VLMs. We study when TTA helps zero-shot 3D CT VLMs. A controlled diagnostic analysis shows that TTA is conditional: the volumetric input must preserve the encoder's depth structure, and the base representation must transfer to the target cohort, with depth reduction alone lowering internal AUROC by more than 0.12. We then focus on the regime where the base model already separates present from absent abnormalities. We introduce CARVE (Cardinality-Aware Retained-View Entropy), the first TTA method for this setting. CARVE estimates a sample-specific positive-label cardinality $\hat{k}$, optimizes a top-$\hat{k}$ objective to preserve co-occurring abnormalities, and performs memory-efficient multi-view adaptation by scoring weak 3D views without gradients before updating on a retained subset. Across contrastive CT-CLIP and anatomy-aware fVLM, CARVE provides the most consistent improvements across multi-label, three-class, and binary CT tasks when the base model is already discriminative. These results establish multi-label TTA for zero-shot 3D CT VLMs as a distinct problem and CARVE as a cardinality-aware solution.

Computed tomography (CT) vision-language pretraining from paired volumes and radiology reports is a scalable yet challenging task. Existing methods commonly adopt global scan-report contrast, which is scalable but obscures heterogeneous organ evidence. Meanwhile, direct organ-level alignment remains coarse, since the same anatomy can exhibit multiple distinct radiological appearances. Therefore, pretraining requires a finer alignment unit: the organ-conditioned radiological pattern. In this work, we propose OCP-CT, an organ-conditioned pattern-token alignment framework for CT vision-language pretraining. Specifically, OCP-CT preserves a stable global CT-report contrastive branch and introduces an organ pattern interface: sparse Mixture-of-Experts (MoE) routes image and text tokens according to latent radiological patterns, learnable slots query the routed tokens into continuous pattern tokens, and paired token contrast aligns image-text pattern tokens with structured soft targets built from report-derived clinical similarity. On the publicly available CT-RATE and RAD-ChestCT benchmarks, OCP-CT achieves average AUROCs of 84.5% and 69.9% for zero-shot abnormality diagnosis, respectively. Compared with the strongest prior reported results, these results yield absolute AUROC gains of 6.7 and 0.8 percentage points.

Automatic voxel-level grounding of free-text findings in 3D chest Computed Tomography (CT) is critical for clinical interpretability. However, this task remains highly challenging due to the intricate spatial complexity of large 3D volumes and the heterogeneity of free-text findings. Existing end-to-end approaches often struggle to simultaneously learn the localized feature representations required for accurate 3D segmentation and the complex semantic understanding needed for text alignment, leading to suboptimal grounding performance. To overcome this fundamental limitation, we propose a novel decoupled framework that disentangles the problem into two specialized stages: (1) class-agnostic lesion segmentation and (2) text-volume reasoning. This structural separation allows the model to first extract candidate sub-volumes by localizing potential abnormalities. Subsequently, intensive cross-modal reasoning is performed to align these localized sub-volumes with free-text medical findings. To resolve the spatial ambiguities inherent in local regions, the reasoning module is augmented with explicit anatomical guidance, utilizing relative spatial coordinates and lung lobe priors. Evaluated on the ReXGroundingCT benchmark, our method achieves state-of-the-art performance in overall grounding quality on the official leaderboard. These results demonstrate that decoupling detection from reasoning is a highly effective paradigm for handling the complexity of 3D medical visual grounding. Our code is publicly available at https://github.com/khuhm/DAGG.

Background: Automated 3D segmentation of muscles and adipose tissue from CT is vital for body composition analysis, but multi-source data heterogeneity and high CPU memory demands hinder clinical deployment. Methods: We propose a coarse-to-fine hierarchical framework to segment ten tissue structures. Efficiency is optimized using Dynamic Spacing and Anisotropic Patching, a Group Inference mechanism for low-memory sliding-window processing, and Topology-Aware Asymmetric Resampling for fast post-processing. Results: The framework was trained on 1,558 CT volumes from seven public and two private datasets, and evaluated on an independent test cohort (N=105), per-structure Dice coefficients ranged from 0.924 to 0.982. Eight major structures met the +-10% relative error clinical acceptance limit. On a 12-core CPU workstation, the GPU-free pipeline averaged 44.5 seconds per volume with 4.73 GB peak memory. Conclusion: This framework balances accuracy and efficiency, enabling robust, large-scale body composition analysis on standard CPU workstations.

Reliable organ localization in abdominal CT can provide spatial priors for downstream trauma analysis. We propose CT-3GDINO, a lightweight 3D detector that adapts a Grounding-DINO-style query-based architecture to fixed organ localization using frozen pseudo-text class tokens instead of a real text encoder. The model combines a Swin3D visual backbone, bidirectional feature enhancement, pseudo-text-guided query selection, and a cross-modality decoder to predict normalized 3D boxes for liver, spleen, left kidney, right kidney, and bowel. We train and evaluate on 193 matched RSNA/RATIC CT volumes with segmentation-derived boxes. The best multi-scale model, trained from scratch, achieves 0.5830 overall top-1 class-wise mAP over 3D IoU thresholds from 0.1 to 0.7, outperforming fixed- and trainable-backbone classification-pretrained variants with 0.5570 and 0.4657 mAP. Performance is strong for coarse localization, with 0.9649 AP at IoU 0.1, but remains limited for strict box alignment, with 0.1552 AP at IoU 0.7. These results establish CT-3GDINO as an open-source baseline for pseudo-text-conditioned 3D organ localization and motivate future work on localization-aware pretraining, richer multimodal conditioning, and injury-focused detection.

Vision-language pre-training (VLP) holds great promise for general-purpose medical AI by leveraging radiology reports as rich textual supervision, yet existing methods struggle with 3D CT imaging due to inefficient visual backbones and coarse semantic alignment. To address these issues, we propose a tailored VLP framework featuring three key components: (1) a CNN-ViT hybrid encoder that replaces ViT's patch embedding with a 3D CNN backbone to efficiently capture local anatomical details while preserving global attention and compatibility with pre-trained cross-modal priors; (2) a disease-level contrastive learning mechanism using learnable query tokens to dynamically extract disease-specific semantics from full reports and align them with corresponding visual features, thereby disentangling distinct diseases within the same anatomical region; and (3) a diagnosis-aware prompt strategy that employs real clinical phrases and aggregated disease prototypes to bridge the pre-training-inference gap and enhance zero-shot diagnostic reliability. Our model achieves state-of-the-art performance on CT-RATE (84.4% AUC, +5.1%) and Rad-ChestCT (75.4% AUC, +5.4%), with even larger gains (+9.8% AUC) on a challenging 60-disease benchmark, and demonstrates strong transferability to radiology report generation, underscoring the generality and clinical utility of our approach.

Novel view synthesis (NVS) is an active research topic in computer vision, owing to the success of neural radiance field (NeRF) and 3D Gaussian splatting (3DGS) methods. While NVS opens the door to potential applications in gastroendoscopy, such as extending the field of view of endoscopic images and enabling digital twins for 3D archiving and endoscopist manipulation training, the dataset is insufficient to evaluate NVS for gastroendoscopy. In this paper, we present the first real gastroscopy dataset for NVS, namely the GastroNVS dataset, which contains a set of gastroscopic images, camera poses, and a point cloud for real gastroendoscopy inspection. To assess the suitability of the GastroNVS dataset, we evaluate several 3DGS methods and discuss the challenges for future development. The dataset is available on request from our project page.

Automated diagnosis of 3D brain CT scans is essential for critical care, yet it remains challenging due to the heavy reliance on manual annotations and the limited semantic understanding of conventional models. While 2D foundation vision-language models (VLMs) have shown remarkable generalization, effectively transferring their representational power to 3D volumes remains an open problem. In this paper, we propose Brain-Adapter, a novel dual-stream multiple instance learning (MIL) framework that leverages pre-trained 2D biomedical VLMs and raw diagnostic reports for robust scan-level multi-label classification. Specifically, we introduce a Text-Conditioned Attention (TCA) mechanism, utilizing raw diagnostic sentences as semantic queries to dynamically align visual cues with specific disease concepts. Concurrently, a parallel visual MIL stream captures global scan characteristics, supervised by structured labels extracted via a Large Language Model (LLM). To ensure representation coherence, a consistency constraint enforces synergy between the two streams. During inference, an Uncertainty-Aware Refinement (UAR) module dynamically calibrates and fuses these dual-stream predictions to resolve ambiguous cases. Extensive experiments demonstrate that our method significantly outperforms state-of-the-art 3D models and standard MIL approaches. By eliminating the reliance on dense annotations, Brain-Adapter provides a highly scalable and clinically viable solution for 3D acute intracranial pathology analysis.

Medical expert annotators are scarce, and blind reliance on artificial intelligence (AI) can be misleading, motivating approaches in which humans, particularly junior medical trainees or even non-medical personnel, collaborate with AI to achieve robust medical segmentation. Although the Segment Anything Model (SAM) shows promise for general-purpose image segmentation, its performance in human-AI collaboration for specialized medical tasks has not been thoroughly evaluated. Here we present Hi-Seg, a human-in-the-loop segmentation framework for pulmonary nodules built on SAM. Humans iteratively refine prompts through trial-and-error learning and semantic reasoning, progressively guiding SAM toward higher-quality masks. Using chest CT scans from 1,179 patients across 12 centers, we conducted the first large-scale external validation of collaborative human-SAM segmentation. Across all annotator groups, Hi-Seg achieved a mean Dice score of almost 85%, outperforming five state-of-the-art deep learning models by 10-22% and 13 SAM variants by 1-29%. Hi-Seg improved segmentation accuracy while reducing annotation time for medical annotators, and briefly trained non-medical annotators achieved performance comparable to that of the junior medical student. These findings suggest that human-in-the-loop segmentation can reduce clinician workload, enable scalable crowdsourced annotation, and transform clinical workflows by facilitating the safe and efficient integration of foundation models into routine clinical practice.

Recent advances in multimodal learning, including large language models (LLMs) and vision-language models (VLMs), have demonstrated strong adaptability to natural images. However, extending their use to the medical domain, particularly for volumetric (3D) images, is challenging due to high computational complexity, volumetric dependencies and the semantic gap between visual features and clinical terminology. Naively fine-tuning LLMs on limited medical data often leads to overfitting and clinical hallucination, where linguistic fluency is prioritized over clinical factuality. In this study, we investigate parameter-efficient adaptation strategies for volumetric CT report generation and introduce RAD3D-Prefix, a lightweight diagnostic-prior conditioning framework that minimizes the need for extensive parameter training. This module integrates image embeddings with multi-label diagnostic classification logits, preserving critical clinical details while bridging the semantic gap. By keeping the LLM frozen, our method requires minimal trainable parameters and mitigates the risk of overfitting on small, domain-specific datasets. Through a systematic study spanning LLMs from 96.1M to 1.6B parameters, we find that fine-tuning is most beneficial for smaller LLMs, whereas freezing larger (~1B+ LLMs and training only lightweight projection layers provides a superior trade-off between performance, generalization, and computational efficiency. Across multiple automatic metrics and a clinical reader study, RAD3D-Prefix outperforms comparable parameter-efficient baselines and demonstrates strong out-of-domain generalization while using substantially fewer trainable parameters than fully fine-tuned alternatives.

Multiphasic contrast-enhanced CT (CECT) is widely used for abdominal lesion characterization, yet it carries inherent risks of contrast-induced nephropathy, escalates acquisition burden, and heavily contributes to radiologist workload. To address these challenges, we introduce a novel multi-center benchmark for multi-organ abdominal disease diagnosis and automated radiology report generation, which learns to synthesize contrast-enhanced findings from single-phase non-contrast CT (NCCT). To support this, we curated a large-scale dataset of paired NCCT-CECT studies and their corresponding contrast-enhanced radiology reports from two centers, partitioned into internal sets and an external validation cohort. Under a unified evaluation protocol, we benchmarked five contemporary deep learning architectures encompassing chest-specific, abdomen-specific, and general-purpose multimodal domains. Extensive experiments demonstrate that NCCT retains diagnostic signals, achieving an average multi-organ AUC of 69.1% on the internal cohort and 63.1% on the external cohort, respectively. By releasing this dataset and standardized benchmark publicly, this study aims to catalyze future research into safer, resource-efficient, and globally accessible contrast-free abdominal imaging workflows. Code is available at: https://github.com/xmed-lab/TriALS-Report.

Temporomandibular joint osteoarthritis (TMJ OA) is a prevalent degenerative condition whose osseous changes are often subtle on cone-beam CT (CBCT), making automated detection challenging. We study how well the DINO family of self-supervised vision transformers -- DINOv1, DINOv2, DINOv2+reg, and RAD-DINO (a radiology-pretrained variant) -- transfers to CBCT, asking how much backbone adaptation is needed and of what kind. We propose a simple slice-based pipeline using Vision Transformer (ViT) backbones: axial CBCT slices are encoded per-slice by a frozen or partially adapted ViT and aggregated via attention-based multiple instance learning (MIL) for patient-level binary OA/Normal classification. Through systematic ablation across unfreezing strategies and aggregation designs on a multi-source CBCT dataset, we find that partial unfreezing of the final two transformer blocks is the decisive factor, improving AUC from 0.671 (fully frozen DINOv2) to 0.902. This outperforms DINOv1 (0.867), DINOv2+reg (0.774), and a supervised ImageNet ViT-B/16 baseline (0.843). Our results provide practical guidance for adapting DINO-family foundation models in low-data medical imaging settings, showing that adaptation strategy is a stronger driver of performance than backbone choice alone.

3D reconstruction could improve colonoscopy by estimating mucosal coverage and alerting clinicians to missed regions during screening. However, algorithm development is limited as no current datasets provide both a realistic in vivo appearance and dense, time-resolved 3D ground truth, especially under non-rigid deformation. We present C3VD-DEFCOL, a framework and dataset for evaluating deformable colonoscopy reconstruction with paired geometry and realistic texture. Starting from C3VD/C3VDv2 colon meshes and camera trajectories, we generate controlled deformations of the colon surface, including peristaltic waves and centerline motion, and render per-frame depth, surface normals, optical flow, camera poses, and time-stamped 3D meshes. We then use the rendered geometry, primarily depth, to condition an LTX-2.3-based sim-to-real translation model that produces RGB clips with in vivo-like mucosal color, texture, vasculature, and specular appearance while preserving the underlying 3D scene structure. The resulting dataset contains 110 videos from 11 unique colon mesh geometries, with varying camera trajectories, appearances, and parameterized deformation regimes, including three peristaltic severity levels that serve as controlled evaluation axes. We evaluate the generated videos using appearance realism, geometric consistency, and temporal consistency metrics, and use the paired ground truth to benchmark the downstream task of pose estimation in deformable 3D reconstruction. Our experiments show how pose estimation error increases with increasing deformation severity, providing a controlled stress test that is not possible with existing in vivo datasets. Overall, C3VD-DEFCOL is designed as a reproducible, quantitative evaluation platform for testing deformable 3D reconstruction algorithms, with the goal of reducing the domain gap between synthetic datasets and in vivo colonoscopy.

Recent breakthroughs in self-supervised learning (SSL), such as the Latent-Euclidean Joint-Embedding Predictive Architecture (LeJEPA), alongside successes in integrating visual encoders with language models, have driven the demand for adaptable, high-capacity vision encoders in Computed Tomography (CT). In this work, we explore 2D slice-based architectures as a flexible alternative to native 3D models for processing volumetric CT data. Using the CT-RATE dataset, we trained DALE-CT (Depth-Aware Latent-Euclidean Computed Tomography), a 2D model family built entirely from scratch using LeJEPA, and compared its performance against a continually pre-trained DINOv2 baseline. To enhance representation quality, we developed a novel 3D depth-aware pre-training strategy anchored by dense auxiliary supervision from both automated anatomical masks and human-annotated abnormalities. Under linear probe evaluation with Multiple Instance Learning (MIL) for multi-abnormality detection, the frozen backbone of this dual-supervised model (DALE-CT-2S) achieves a Macro AUROC of 0.833. This performance demonstrates near-parity with state-of-the-art 3D vision-language models, achieved entirely from scratch with significantly less data and no textual supervision. To ensure reproducibility, all training code, evaluation scripts, and model weights have been made publicly available.

This work proposes a lightweight 2D-U-Net-based framework for segmenting five abdominal organs in large field-of-view 3D CT scans. The method combines coarse-to-fine segmentation, predictions from multiple anatomical planes, and additional fuzzy 3D spatial maps that provide anatomical location cues to improve segmentation accuracy. We combine multi-planar 2D-U-Net models augmented by a spatial occurrence map. The approach involves two main stages. First, the abdominal volume of interest region is detected by traversing the whole scan axially with a 2D-U-Net and determining the x-y-z-minimum and -maximum extents of the 5 abdominal organs of interest. Second, we use spatial occurrence maps to enhance our multi-planar 2D-U-net architecture inside the bounds from the former stage. The method is evaluated on 80 CT scans from various public sources. The results show Dice improvements of about 4% at maximum compared to the same model trained without spatial occurrence maps.

Three-dimensional models are widely assumed preferable for volumetric medical imaging, yet their practical value depends on whether performance gains justify added computational cost and complexity. Rather than proposing a new architecture, we study how input dimensionality (2D, 2.5D, 3D) affects model behavior across convolutional neural networks (CNNs) and Vision Transformers (ViTs) under a fixed training protocol. Using a leakage-free NLST cohort (n = 1,977) with supporting LIDC-IDRI data, we find that the 2.5D CNN offers the most favorable discrimination-stability trade-off in our comparison (ROC-AUC 0.682, 95% CI [0.546, 0.799]) with a stable operating point. In contrast, 3D CNNs show threshold instability, and transformers exhibit degenerate predictions, such as all-positive predictions. Confidence intervals are wide and overlapping, so we present these results as a controlled resource-performance frontier and a failure-mode taxonomy rather than as definitive superiority claims. For class-imbalanced lung cancer screening classification, 2D and 2.5D inputs provide a more reliable trade-off between performance, stability, and computational efficiency than full 3D representations.

In this paper, we present a robotic ultrasound acquisition system that integrates stereo vision, touch-based feedback, and expert-informed strategies to perform autonomous and adaptive abdominal scans. The system records freehand motion and force data from expert radiologists, creating a framework to capture transducer motion, applied forces, and anatomical scanning strategies. This expert data is replayed to replicate characteristic scans with the robot, forming a foundation for further autonomous capabilities. Using stereo vision, the system generates three-dimensional topography maps of the patient's abdomen, which are refined through stiffness measurements at key points to delineate the rib cage boundary. These combined techniques enable the robot to execute two distinct scanning paths: an upward-angled sweep beneath the rib cage to visualize structures near the upper abdomen and a perpendicular sweep across soft tissue regions. A compliant, torque-controlled seven degree-of-freedom robotic manipulator is controlled to maintain consistent probe contact through closed-loop force control over the varied anatomical surfaces. Physical experiments demonstrate that the system achieves high-quality imaging comparable to expert scans while dynamically adapting to patient-specific topographies. Furthermore, the robotic system surpasses expert capabilities by enabling three-dimensional volume acquisition, which enhances diagnostic potential and provides volumetric data for advanced analyses. This work highlights the integration of expert knowledge into autonomous robotic systems and underscores the potential of combining perception-based autonomy with physical reasoning for enhanced diagnostic performance.

Abdominal CT disease classification is challenging because each scan is a large 3D volume with many possible findings, while diagnostic evidence is often confined to specific organs or anatomical compartments. Most study-level classifiers aggregate encoder features using anatomy-agnostic pooling or attention, creating a mismatch between localized disease evidence and global evidence aggregation. We propose ORACLE--CT, an encoder-agnostic anatomy-aware aggregation framework that uses multi-organ segmentation to define label-specific anatomical supports and restrict attention pooling to relevant regions. The framework supports single-organ, multi-organ union, comparative, localized, and global support strategies. We evaluate ORACLE--CT with three encoder families: DINOv3, I3D--ResNet-121, and the radiology-native Pillar--0 encoder. Models are trained end-to-end on MERLIN and evaluated internally and under frozen external transfer to Duke--Abdomen and AMOS. Compared with global average pooling, support-masked pooling improved MERLIN macro-AUROC/AUPRC from 0.838/0.638 to 0.858/0.676 for DINOv3 and from 0.829/0.617 to 0.848/0.659 for I3D--ResNet-121. On harmonized 10-label external evaluation, DINOv3 improved on Duke--Abdomen from 0.802/0.628 to 0.835/0.683 and on AMOS from 0.742/0.313 to 0.762/0.350, with similar gains for I3D--ResNet-121. For Pillar--0, most gains came from learned attention, with smaller additional benefit from anatomical masking. ORACLE--CT improves discrimination and external robustness while preserving an auditable link between predictions and anatomical evidence.

Ischemic stroke is a major global disease. Treatment decisions are highly time-sensitive, as eligibility for reperfusion therapies relies on the interval between stroke onset and intervention. However, the true onset time is often uncertain in clinical practice, necessitating imaging-based assessment of tissue age as a surrogate marker. Early ischemic changes on routinely acquired non-contrast CT (NCCT) are often subtle, and real-world clinical datasets exhibit pronounced onset-time class imbalance and center-scanner-related heterogeneity. In this work, we propose StrokeTimer, a fully automated framework for onset-time estimation in acute ischemic stroke. StrokeTimer integrates self-supervised disentanglement learning with energy-guided contrastive learning to capture subtle ischemic patterns while addressing long-tailed data distributions under acquisition variability. Onset time is categorized into three clinically relevant windows: <4.5 h, 4.5-6 h, and >6 h. Experimental results on a large multi-center NCCT dataset from two national cohorts, MR CLEAN Registry and MR CLEAN LATE, show that StrokeTimer achieves a macro AUC of 0.69 and a macro F1-score of 0.57, improving the strongest baseline by nearly 50% (p < 0.005). In this realistic, challenging setting, representative baseline approaches exhibit near-chance macro performance. Model explanations further highlight subtle gray-white matter blurring and hypodense regions consistent with established radiological biomarkers. These findings demonstrate the potential of StrokeTimer to support treatment decision-making in acute ischemic stroke. Code is available at https://github.com/BrainVas/StrokeTimer.

Self-supervised learning has enabled large-scale pre-training on 2D natural images, producing general-purpose visual representations that transfer effectively across tasks. However, many medical imaging modalities, such as CT scans, are inherently three-dimensional and differ fundamentally from natural images in both structure and semantics. Volumetric modalities capture spatial continuity, organ anatomy, and intensity-based tissue properties (e.g., Hounsfield Units), which are not adequately modeled by 2D pre-training. To bridge this gap, we introduce CoralBay, a self-distillation framework that extends DINO by using a hierarchical 3D Swin backbone and applying self-distillation to concatenated multi-scale features, enabling data-efficient self-supervised learning of rich spatial representations that encode both global semantics and fine-grained local structure. As a result, CoralBay transfers effectively to a wide range of downstream radiological tasks, demonstrating strong and consistent performance across diverse anatomical targets. In addition, we contribute to the open-source \eva framework by introducing a public, reproducible 3D radiology leaderboard that unifies multiple datasets and establishes a standardized benchmark for evaluating volumetric representation learning methods.

Lower extremity computed tomography (CT) contains clinically relevant information for body composition analysis, sarcopenia assessment, and musculoskeletal disease monitoring, but extracting these measurements at scale requires accurate tissue segmentation and an automated quantification workflow. Existing public segmentation tools are not designed for comprehensive lower extremity CT analysis, particularly for clinically important inter/intramuscular adipose tissue, and most public methods only provide mask prediction rather than an end-to-end quantification system. To address this problem, we present LegSegNet, a deep learning system for lower extremity CT tissue segmentation and body composition quantification. Given an input CT scan, LegSegNet segments bone, skeletal muscle, subcutaneous adipose tissue, and inter/intramuscular adipose tissue. It then computes quantitative tissue measurements for downstream analysis. We developed the segmentation model using 1,302 manually annotated CT slices and evaluated it on 900 held-out test slices, with all annotations reviewed by radiologists. We benchmark LegSegNet against a broad set of 2D segmentation methods, including CNN-based models, transformer-based models, and finetuned foundation models, and further evaluate its generalization on an external public CT dataset. LegSegNet achieves the best overall segmentation performance, with an average Dice score of 89.31 on the held-out test set. To our knowledge, LegSegNet is the first publicly available end-to-end system for lower extremity CT tissue segmentation and quantification, providing a practical evaluation tool for future computer vision research in medical image analysis. The code and model weights are available at: https://github.com/mazurowski-lab/LegSegNet

Computed tomography (CT) is a central to three-dimensional medical imaging, yet CT-based artificial intelligence remains fragmented across task-specific models for segmentation, classification, registration, and report analysis. Here we present FlexiCT, a family of CT foundation models trained by agglomerative continual pretraining on 266,227 CT volumes from 56 publicly available datasets, forming a large-scale public resource for CT representation learning. FlexiCT uses agglomerative pretraining across three stages: two-dimensional axial pretraining, three-dimensional anatomical pretraining and report-guided semantic alignment. This training strategy supports slice-level, volume-level and vision-language analysis. Across five downstream task families (segmentation, classification, registration, vision-language understanding and clinical retrieval), FlexiCT matches or exceeds prior task-specific approaches on multiple benchmarks. Its embeddings further organize CT scans along gradients associated with various tumor stages, suggesting that CT foundation models can capture imaging features relevant to disease phenotype characterization. Project page and code are available at: https://ricklisz.github.io/flexict.github.io and https://github.com/ricklisz/FlexiCT.

In recent years, there has been a notable increase in the level of attention that is given to algorithms based on deep learning in the context of medical image segmentation. Nevertheless, the reliability of the field has been hindered due to the absence of a standardized methodology for performance analysis and the utilization of different datasets in previous research. The primary objective of the research is to comprehensively evaluate contemporary segmentation frameworks combined with state-of-the-art pre-trained backbones in order to accurately predict COVID-19 lesions in CT images. Moreover, this evaluation can serve as a point of reference for the segmentation of images in various other imaging scenarios. In order to accomplish this, we integrate four distinct deep learning architectures, namely Unet, PSPNet, Linknet, and FPN, with six pre-trained encoders, including VGG 19, DenseNet 121, Inception ResNet V2, MobileNet V2, SeresNet 101, and EfficientNet B0. This approach enables the development of diverse testing architectures. In the context of image segmentation, our research encompassed both binary and multi-class experimentation. The findings derived from our analysis of three distinct COVID-19 CT segmentation datasets indicate that deep learning architectures yield precise and efficient segmentation outcomes. Significantly, a maximum F1-Score of 98% was attained for binary class segmentation, while multi-class segmentation yielded F1-Scores of 75% and 77% across two separate datasets. The utilization of artificial intelligence and deep learning enhances the diagnostic process for pandemic diseases across multiple dimensions.

COVID-19 was a significant challenge that led to the loss of numerous lives daily. Not only a certain country was involved in this outbreak, but even the world has suffered because of the coronavirus. Imaging techniques using computed tomography (CT) and X-rays of the lungs are the most useful tools for the COVID-19 or any other pandemic disease screening process. Technology today has revolutionized the world by using artificial intelligence to replace manual processes with automated machines, which enable the system to imitate the human brain by making wise decisions based on experience. Motivated by this, our work proposes to use convolutional neural networks (CNN) based models for designing a computer-aided diagnosis (CAD) system that differentiates between COVID-19 and healthy lung pictures. We used two different sets of X-ray images of the lungs in addition to two different sets of CT scans and the classification is done using a variety of networks that have been pre-trained such as VGG (16, 19), Densenet (121), Resnet (50, 50 V2, 101 V2), Mobile net (V2), Xception Inception (V3, Resnet V2), Efficient net (B0) and Nasnet (Large). On the X-ray and CT image datasets, Resnet and VGG architecture have shown the ability to properly differentiate COVID-19 from normal images, with an average accuracy of 95 to 98 percent respectively. Our acquired results on the classification datasets are competitive and superior to previously reported findings in the literature.

Medical vision-language models (VLMs) have rapidly advanced as general-purpose multimodal assistants, yet their deployment in 3D Computed Tomography (CT) analysis remains constrained by a persistent mismatch between optimization objectives and clinical rigor. Current Reinforcement Learning (RL) paradigms still rely on lexical proxy signals that induce \textit{Evaluation Hallucinations}'', where models optimize linguistic fluency rather than factual clinical correctness, leading to diagnostically critical errors. To bridge this gap, we introduce the \textbf{Clinical Abnormality Benchmarking Substrate (CABS)}, a structured system that decomposes radiology reports into verifiable clinical semantic units. Using CABS, we identify a \textit{Mechanistic Divergence}'' in standard RL, where surface-similarity rewards drive policy gradients to bypass medical facts. We therefore propose \textbf{Trajectory-Integral Feedback GRPO (TIF-GRPO)}, a novel framework integrating control-theoretic principles into policy optimization. By formulating clinical reasoning as a pseudo-temporal trajectory for anomaly discovery, TIF-GRPO regulates anatomy-aware rewards via an integral feedback loop that penalizes persistent omissions as cumulative state errors and suppresses hallucinations as excessive control effort. Experiments on 3D CT benchmarks demonstrate that our approach significantly enhances abnormality detection and clinical faithfulness, establishing a new paradigm for fine-grained regulation in medical VLMs. Our project is available at \href{https://github.com/ZJU4HealthCare/TIF-GRPO}{GitHub}.

Accurate segmentation and statistical shape modeling of hand anatomy have significant implications for medical diagnostics, ergonomics, and biomechanics. This study proposes an AI-assisted reconstruction pipeline for segmenting and analyzing hand anatomy from 1,271 elbow-to-hand (e2h-CT) computed tomography scans. A Pix2Pix-based conditional generative adversarial network is first employed to remove plaster cast and background artifacts from CT volumes. The cleaned scans are then processed in 3D Slicer to extract skin and bone masks, which are converted into closed-surface mesh models. Segmented bone meshes are used to construct skeletal representations, enabling implicit skinning to align all hand models into a standardized anatomical configuration. Subsequently, non-rigid registration is performed on the hand skin surfaces using the Geodesic Based Coherent Point Drift++ (GBCPD++) algorithm to establish point-wise correspondence across subjects. Principal Component Analysis (PCA) is then applied to the registered models to quantify anatomical shape variability. The Pix2Pix preprocessing stage achieved a Dice coefficient of 0.9856 and an IoU of 0.9720 on the held-out test set. Statistical modeling was performed on a subset of 90 scans in which the fingers were fully visible and anatomically separated. The resulting statistical shape distributions demonstrate strong agreement with the U.S. Army Anthropometric Survey (ANSUR II), supporting the anatomical validity of the reconstructed models. The proposed methodology demonstrates significant potential for advancing biomechanical modeling, ergonomic optimization, prosthetic design, and precision medical diagnostics.

Automated segmentation of liver lesions on non-contrast computed tomography (NCCT) is clinically important but fundamentally challenging, particularly in low-resource settings across Africa and Asia where contrast agents are frequently unavailable. Progress has been limited by the absence of annotated NCCT benchmarks. Here we describe the TriALS challenge for automated liver lesion segmentation under contrast-limited conditions, supported by a multi-centre dataset of 150 cases with four-phase CT acquisitions (600 volumes) from Egyptian and Chinese institutions. Algorithms were evaluated on 70 cases from three institutions, including an independent external cohort. The top-performing method achieved a mean venous-phase Dice of 0.754, consistent with human-level performance, yet dropped to 0.57 on NCCT. On external validation, the leading method outperformed off-the-shelf models by up to 28% in Dice on NCCT. Algorithm performance was most strongly predicted by training data scale and pre-training strategy. A cross-year comparison exposed a persistent perceptual barrier on NCCT that scaling pre-training alone cannot overcome. Data, annotations, and code are available at https://github.com/xmed-lab/TriALS.

Recent progress in deep learning has significantly advanced CT image analysis, particularly for segmentation tasks. However, these advances are largely confined to image-level pattern recognition, with most methods lacking explicit anatomical or contextual reasoning. Large vision-language models introduce linguistic context into image analysis, yet most approaches typically focus on a single task, which is insufficient for clinical workflow analysis that requires multiple fine-grained types of analysis, such as anatomy detection and segmentation. In this paper, we propose a unified autoregressive framework that integrates language-guided visual reasoning into CT interpretation. Our method introduces task-routing tokens that trigger detection and segmentation heads conditioned on the hidden states of a large vision-language model, enabling coherent generation of visual outputs (e.g., masks and bounding boxes) and textual reasonings. To progressively enhance localisation accuracy and semantic clarity, we further design a "closer-look" mechanism that allows the model to perform progressive coarse-to-fine visits to regions of interest under refined fields of view. To support model training and evaluation, we curated a new multimodal CT dataset containing pixel-wise masks, bounding boxes, spatial prompts, and structured descriptions for visual objects constructed through an AI-assisted annotation process with human verification. Experiments on public benchmarks demonstrate consistent improvements over the SoTA, achieving up to 1.0% Dice on BTCV and 1.7% Dice on MosMed+, while additionally providing appearance reasoning outputs. The code and dataset will be available.

This work studies lung tumor growth prediction from sparse and irregular longitudinal computed tomography (CT) observations with measurement variability. A Bayesian physics-informed neural network is developed by combining Gompertz growth dynamics with low-dimensional Bayesian inference in the log-volume domain. The framework employs a two-stage inference strategy combining maximum a posteriori (MAP) estimation and Hamiltonian Monte Carlo (HMC) sampling to estimate posterior predictive distributions and uncertainty intervals. The method was evaluated on longitudinal data from the National Lung Screening Trial (30 patients). Results show that the model captures heterogeneous tumor growth patterns while maintaining reasonable prediction accuracy under limited observations. Compared with deterministic modeling approaches, the proposed approach additionally provides calibrated uncertainty estimates. The inferred posterior parameter correlations were consistent with expected biological growth behavior. The proposed framework achieved a cohort-level log-space RMSE of approximately 0.20 together with well-calibrated 95% credible interval coverage across 30 patients. These findings suggest that Bayesian physics-informed modeling may be useful for uncertainty-aware tumor growth assessment when only limited longitudinal follow-up scans are available.

Multi-window CT imaging captures complementary pathological information across anatomical structures of differing densities, yet existing deep learning methods fuse representations only at later stages, missing cross-density interactions. We propose a cross-window knowledge distillation framework in which student encoders learn latent clinical priors from a teacher trained on the most informative window. Evaluated retrospectively on three cohorts - COPD-CT-DF (n=719), RSNA PE (n=1,433), and an in-house CTEPD dataset (n=161) - distillation improved per-window AUC by 10.1-16.5 percentage points on COPD-CT-DF (0.75-0.81 to 0.90-0.94; all P<0.001), with ensemble AUC reaching 0.9960. Similar gains were observed on RSNA PE (0.80-0.83 to 0.90-0.92) and CTEPD (AUC 0.7481 vs. 0.6264). Cross-window distillation internalises pathological signatures invisible to supervised approaches, offering a generalisable solution for multi-window pulmonary CT analysis.

Recent advances in 3D medical vision-language models have enabled joint reasoning over volumetric images and text, showing strong performance in medical visual question-answering (VQA) and report generation. Despite this progress, it remains unclear whether these models learn spatially grounded anatomy from 3D volumes or rely primarily on learned priors and language correlations. This uncertainty stems from the lack of systematic evaluation of semantic-spatial reasoning in volumetric medical VLMs for clinically reliable decision support. To address this gap, we introduce CT-SpatialVQA, a benchmark designed to evaluate semantic-spatial reasoning in 3D CT data. The benchmark comprises 9077 clinically grounded question-answer (QA) pairs derived directly from 1601 radiology reports and CT volumes, which are validated via a robust LLM-assisted pipeline with a 95% human consensus agreement rate. Our dataset requires explicit anatomical localization, laterality awareness, structural comparison, and 3D inter-structure relational reasoning. We also introduce a standardized evaluation protocol and benchmark eight 3D medical VLMs, finding severe degradation on semantic-spatial reasoning tasks, averaging 34% accuracy and often below random, highlighting the need for deeper integration of volumetric evidence for trustworthy clinical use.

We report the design and results of the third autoPET challenge (MICCAI 2024), which benchmarked automated lesion segmentation in whole-body PET/CT under a compositional generalization setting. Training data comprised 1,014 [18F]-FDG PET/CT studies from the University Hospital Tübingen and 597 [18F]/[68Ga]-PSMA PET/CT studies from the LMU University Hospital Munich, constituting the largest publicly available annotated PSMA PET/CT dataset to date. The held-out test set of 200 studies covered four tracer-center combinations, two of which represented unseen compositional pairings. A complementary data-centric award category isolated the contribution of data handling strategies by restricting participants to a fixed baseline model. Seventeen teams submitted 27 algorithms, predominantly nnU-Net-based 3D networks with PET/CT channel concatenation. The top-ranked algorithm achieved a mean DSC of 0.66, FNV of 3.18 mL, and FPV of 2.78 mL across all four test conditions, improving DSC by 8% and reducing the false-negative volume by 5 mL relative to the provided baseline. Ranking was stable across bootstrap resampling and alternative ranking schemes for the top tier. Beyond the benchmark, we provide an in-depth analysis of segmentation performance at the patient and lesion level. Three main conclusions can be drawn: (1) in-domain multitracer PET/CT segmentation is sufficient and probably approaching reader agreement; (2) compositional generalization to unseen tracer-center combinations remains an open problem mainly driven by systematic volume overestimation; (3) heterogeneity and case difficulty drive performance variation substantially more than the choice of algorithm among top-ranked teams.

We introduce iTRIALSPACE, a programmable evaluation framework for controlled assessment of lung CT models. Standard benchmarks are static retrospective collections that entangle lesion size, lobe prevalence, anatomy, and acquisition context, making it difficult to determine what structurally drives model accuracy. iTRIALSPACE addresses this limitation by composing real clinical CTs and lesion profiles into controlled virtual lesion trials through a four-stage pipeline: multidataset nodule profiling, explicit trial specification, anatomy-aware mask insertion, and ControlNet-conditioned CT synthesis. The framework is built on a unified 54-attribute nodule-profile dataset spanning 13,140 annotated nodules from seven public CT sources and instantiated as 13 trial modes. We evaluate iTRIALSPACE in a 55,469-sample Virtual Lesion Study spanning three medical VLMs, four spatialguidance conditions, and three clinical tasks. Across all 13 modes, the synthetic substrate remains within the real-to-real FID baseline, and synthetic performance rankings transfer strongly to real clinical data ($ρ$ = 0.93, p < 10$^{-15}$). Controlled trial modes expose findings unavailable to fixed-distribution benchmarks, including shortcut-driven size prediction collapse under lobe-equalized sampling and hostto-donor variance ratios of 8.9x and 3.3x in twin-cross analysis. These results position iTRIALSPACE as an auditable evaluation infrastructure for controlled, falsifiable testing beyond static retrospective benchmarks.

Cone Beam Computed Tomography (CBCT) is pivotal for 3D diagnostic imaging in dentistry. However, the development of robust AI models for volumetric analysis is often constrained by the scarcity of large, annotated datasets. Self-supervised learning (SSL), particularly Masked Image Modeling (MIM), offers a promising pathway to leverage unlabeled data. A limitation of standard MIM is its reliance on random masking, which fails to prioritize diagnostically critical regions in dental CBCT volumes, such as subtle pathological changes and intricate anatomical boundaries. To address this, we propose ATMask, a novel adaptive masking strategy. Instead of applying random masks or employing computationally intensive attention modules, ATMask computes an inter-slice texture variation map to identify regions with high structural or textural complexity. These high-variation areas are then selectively masked during pre-training, compelling the model to learn richer contextual representations essential for inferring complex 3D morphological transitions. Furthermore, we contribute the first large-scale CBCT dataset, curated from both public and private sources, comprising 6,314 scans, for the dental AI model pretraining. Extensive experiments on three downstream dental CBCT tasks demonstrate that our ATMask enables more data-efficient and powerful representation learning than standard random masking and other advanced SSL baselines. The dataset and code will be released.

Thoracic Computed Tomography (CT) scans offer detailed insights into the intricate branching network of the airway tree, which is essential for understanding various respiratory diseases. Airway bifurcations, where airway branches split, are crucial landmarks for understanding lung physiology, disease mechanisms and lesion localization. Despite the significance of bifurcation analysis, a notable lack of datasets annotated for this task hinders the development of advanced automated specialized detection or segmentation tools. In this paper, we introduce BifDet, the first publicly-available dataset specialized for 3D airway bifurcation detection, filling a critical gap in existing resources. Our dataset comprises carefully annotated CT scans from the ATM22 open-access cohort with bifurcation bounding boxes covering the parent and daughter branches. As a use-case for demonstrating the potential of BifDet, we fine-tune and evaluate RetinaNet and DETR for 3D airway bifurcations detection on CT scans. We provide detailed pipelines, including preprocessing steps and specific implementation design choices. Results are detailed over various categories of minimal bounding box sizes to serve as baseline to benchmark future research.

Chest computed tomography (CT) is central to the detection and management of thoracic disease, yet the growing scale and complexity of volumetric imaging increasingly exceed what can be addressed by scan-level prediction alone. Clinically useful AI for CT must not only recognize disease across the whole volume, but also localize abnormalities and provide interpretable visual evidence. Existing vision-language foundation models typically compress scans and reports into global image-text representations, limiting their ability to preserve spatial evidence and support clinically meaningful interpretation. Here we developed EXACT, an explainable anomaly-aware foundation model for three-dimensional chest CT that learns spatially resolved representations from paired clinical scans and radiology reports. EXACT was pre-trained on 25,692 CT-reports pairs using anatomy-aware weak supervision, jointly learning organ segmentation and multi-instance anomaly localization without manual voxel-level annotations. The resulting organ-specific anomaly-aware maps assign each voxel a disease-specific anomaly score confined to its corresponding anatomy, jointly encoding lesion extent and organ-level context. In retrospective multinational and multi-center evaluations, EXACT showed broad and consistent improvements across clinically relevant CT tasks, spanning multi-disease diagnosis, zero-shot anomaly localization, downstream adaptation, and visually grounded report generation, outperforming existing three-dimensional medical foundation models. By transforming routine clinical CT scans and free-text reports into explainable voxel-level representations, EXACT establishes a scalable paradigm for trustworthy volumetric medical AI.

Accurate prognostication and risk estimation are essential for guiding clinical decision-making and optimizing patient management. While radiologist-assessed features from CT scans provide valuable indicators of disease severity and outcomes, interpreting such images requires expert knowledge, and translating rich visual information into textual summaries inevitably leads to information loss. In this work, we propose a vision-language framework for 3D CT image understanding that leverages large-scale open-sourced CT images paired with radiology reports through visual instruction tuning. This pre-training enables the model to learn clinically meaningful visual-textual representations, which can then be adapted to downstream survival prediction tasks. By incorporating a survival prediction head on top of the pre-trained model, our approach improves survival prediction from CT images and clinical data while generating clinically meaningful language responses to predefined questions. Experimental results demonstrate that our method outperforms baseline methods in survival prediction, particularly, when clinical data alone is less predictive. The code will be released upon acceptance.

Automated medical report generation for 3D PET/CT imaging is fundamentally challenged by the high-dimensional nature of volumetric data and a critical scarcity of annotated datasets, particularly for low-resource languages. Current black-box methods map whole volumes to reports, ignoring the clinical workflow of analyzing localized Regions of Interest (RoIs) to derive diagnostic conclusions. In this paper, we bridge this gap by introducing VietPET-RoI, the first large-scale 3D PET/CT dataset with fine-grained RoI annotation for a low-resource language, comprising 600 PET/CT samples and 1,960 manually annotated RoIs, paired with corresponding clinical reports. Furthermore, to demonstrate the utility of this dataset, we propose HiRRA, a novel framework that mimics the professional radiologist diagnostic workflow by employing graph-based relational modules to capture dependencies between RoI attributes. This approach shifts from global pattern matching toward localized clinical findings. Additionally, we introduce new clinical evaluation metrics, namely RoI Coverage and RoI Quality Index, that measure both RoI localization accuracy and attribute description fidelity using LLM-based extraction. Extensive evaluation demonstrates that our framework achieves SOTA performance, surpassing existing models by 19.7% in BLEU and 4.7% in ROUGE-L, while achieving a remarkable 45.8% improvement in clinical metrics, indicating enhanced clinical reliability and reduced hallucination. Our code and dataset are available on GitHub.

Reported chest CT segmentation performance can be strongly inflated when train and test partitions mix slices from the same study. We present CTSCAN, a reproducible multi-source chest CT benchmark and research stack designed to measure what survives under patient-disjoint evaluation. The current four-class artifact aggregates 89 cases from PleThora, MedSeg SIRM, and LongCIU, and we show that the original slice-PNG workflow induces near-complete case reuse across train, validation, and test. Using the playground environment, we run a multi-seed protocol sweep with the same FPN plus EfficientNet-B0 control configuration under slice-mixed and case-disjoint evaluation. Across 3 seeds and 12 epochs per seed, the slice-mixed protocol reaches 0.6665 foreground Dice and 0.5031 foreground IoU, whereas the case-disjoint protocol reaches 0.2066 Dice and 0.1181 IoU. Removing patient reuse therefore reduces foreground Dice by 0.4599 absolute (69.00% relative) and foreground IoU by 0.3850 absolute (76.52% relative). CTSCAN packages the corrected benchmark with deterministic split manifests, explicit weak-supervision controls, a scripted multi-seed protocol sweep, and reproducible figure generation, providing a reusable basis for patient-disjoint chest CT evaluation.

Lung cancer remains the leading cause of cancer-related mortality worldwide, with survival outcomes critically dependent on early and accurate detection. When low-dose computed tomography (LDCT) findings are indeterminate, clinicians typically defer diagnosis pending follow-up CT imaging obtained up to 12 months later, inevitably delaying treatment for patients with malignant nodules. To address this clinical gap, we propose Nodule-Aligned Multimodal (Latent) Diffusion (NAMD), a novel generative framework that synthesizes one-year follow-up nodule CT images conditioned on the baseline CT scan, quantitative nodule biomarkers, and patient-level Electronic Health Records (EHR), enabling timely prediction of nodule malignant progression without requiring actual follow-up scans. NAMD introduces two key contributions: (i) a nodule-aligned latent space regularized so that embedding distances reflect clinically meaningful biomarker changes, and (ii) an LLM-driven multimodal conditioning mechanism encoding heterogeneous EHR data into the diffusion backbone. Evaluated on the National Lung Screening Trial (NLST), our method's synthetic follow-up images achieve an AUROC of 0.805 and an AUPRC of 0.346 for lung nodule malignancy prediction, outperforming both the baseline LDCT performance without virtual follow-up generation, and existing state-of-the-art conditional generation methods, while maintaining competitive image quality. These findings suggest that NAMD enables earlier and more accurate lung cancer diagnosis by capturing clinically meaningful features of nodule progression.

While foundation models in radiology are expected to be applied to various clinical tasks, computational cost constraints remain a major challenge when training on 3D-CT volumetric data. In this study, we propose TotalFM, a radiological foundation model that efficiently learns the correspondence between 3D-CT images and linguistic expressions based on the concept of organ separation, utilizing a large-scale dataset of 140,000 series. By automating the creation of organ volume and finding-sentence pairs through segmentation techniques and Large Language Model (LLM)-based radiology report processing, and by combining self-supervised pre-training via VideoMAE with contrastive learning using volume-text pairs, we aimed to balance computational efficiency and representation capability. In zero-shot organ-wise lesion classification tasks, the proposed model achieved higher F1 scores in 83% (5/6) of organs compared to CT-CLIP and 64% (9/14) of organs compared to Merlin. These results suggest that the proposed model exhibits high generalization performance in a clinical evaluation setting using actual radiology report sentences. Furthermore, in zero-shot finding-wise lesion classification tasks, our model achieved a higher AUROC in 83% (25/30) of finding categories compared to Merlin. We also confirmed performance comparable to existing Vision-Language Models (VLMs) in radiology report generation tasks. Our results demonstrate that the organ-separated learning framework can serve as a realistic and effective design guideline for the practical implementation of 3D-CT foundation models. The source code and pretrained models are publicly available at https://github.com/jichi-labo/TotalFM.