Tomography

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.

The experimental reconstruction of the 3D two-photon momentum density (TPMD) via angular correlation of electron-positron annihilation radiation (ACAR) is a particularly useful method for studying material Fermi surfaces. It does not rely on low temperatures, UHV conditions, or strong magnetic fields, and enables the study of the spin-resolved electronic structure of materials. Yet, it remains a challenging inverse problem. Typically, 10^8 positron annihilation events are measured for 3--6 projections of the TPMD at different angles. The standard reconstruction approach is an ACAR adaptation of Cormack's method (the MCM) that leverages the inherent symmetry in the crystal's structure. However, the poor signal-to-noise ratio means collecting data of sufficient quality for Fermi surface studies can take months per sample. We present DeepCormack, a family of data-driven model-based reconstruction algorithms that augments the MCM by integrating supervised deep-learning models (CNN, MLP, and UNet) at various stages. To overcome the lack of large experimental training sets, we propose a method which leverages singular value decomposition with dynamic mode decomposition to generate realistic synthetic TPMD volumes, requiring only a single reference momentum density computed via density functional theory. On test data, DeepCormack improves reconstruction quality over MCM by about 8.5 dB PSNR at 200M counts and remains stable at reduced counts, enabling significantly faster acquisition times. Generalisation to experimental data depends strongly on how well the training distribution from the reference momentum density matches the sample. We therefore recommend pairing DeepCormack with a DFT calculation of the target material to create sample-specific training data. Our proposed method offers either much higher quality reconstructions, or enables significantly faster ones, on the order of weeks.

X-ray tomography enables nondestructive characterization of material microstructures, while advances in micro-CT imaging have accelerated volumetric data acquisition and reconstruction. However, rapid interpretation remains limited by image segmentation, which often requires manual thresholding, user prompting, or material-specific model training. We present a zero-setup framework for multi-phase segmentation of synchrotron X-ray tomography data that generates interpretable masks for previously unseen datasets without user input or retraining during deployment. The framework combines a material-agnostic mask preparation strategy with a pretrained semantic segmentation network. It represents commonly occurring structural regions as background, sample, bright, dark-gray, light-gray, and porosity masks. Unlike conventional deep learning pipelines that require dataset-specific annotations and retraining, the proposed framework can be applied directly to new scans and produce diagnostic-level segmentations within minutes of reconstruction. This enables rapid assessment of scan quality, sample morphology, porosity, and attenuation variations during ongoing beamline experiments. The generated masks can later be manually refined or used to fine-tune application-specific models when greater accuracy or material-specific labeling is required. Evaluation on held-out synchrotron micro-CT images and qualitative testing on additional datasets demonstrate consistent and physically meaningful segmentations across varying samples and imaging conditions. The framework also substantially outperforms conventional intensity-based thresholding. By connecting high-speed reconstruction with immediate interpretation, the approach supports near-real-time beamline feedback and scalable AI-assisted scientific imaging workflows.

This paper proposes a Gaussian-Based Shift-Variant filtered backprojection (FBP) neural network, which is designed for the efficient reconstruction of non-circular trajectory cone beam computed tomography. The traditional differentiable shift-variant FBP model consists of a filtering component and a backprojection process. The filtering component includes operations such as weightings, differentiations, a 2D Radon transform, and a 2D backprojection. The proposed methods build on this framework by introducing a trainable 2D Gaussian model to represent the trajectory-related part in the filtering process, achieving a substantial reduction in the number of trainable parameters. Experimental results demonstrate that the proposed model reduces the parameter count by 99%, while only sacrificing a slight amount of reconstruction quality. Furthermore, the training time for each trajectory is reduced to one-fourth of the original, significantly accelerating convergence. These enhancements demonstrate a considerable augmentation in the model's practicality and effectiveness, making it a valuable asset for real-world applications.

Quantum state tomography is sample-starved, and the states one prepares live on a narrow, learnable manifold. A $k{=}0$ prior-only control shows that on concentrated families a prior estimate is already near-optimal, so ``high fidelity at few measurements'' can be family memorization rather than tomography; genuine measurement-efficiency needs a model that conditions on the measurements and demonstrably uses them. On a shared matrix-product-state (MPS) core parameterization we study two routes. ApproachA learns a generative prior over MPS cores with measurement-guided posterior inference (gold-standard-validated, but whose few-measurement accuracy the control shows is largely the prior). ApproachB, our main proposal, is a \emph{fixed-protocol amortized} MPS estimator trained once with a gauge-invariant fidelity loss; we deliberately do not rest it on a permutation-invariant set encoder (a plain MLP matches it). The decisive lever is the measurement design: motivated by the fact that local reduced density matrices determine a $χ$-MPS, conditioning on an \emph{informative local} Pauli set rather than random strings turns a modest, memorization-prone estimator into a high-fidelity one ($\approx\!0.95$, up to $+0.59$ over prior-only, decisively passing a shuffled-measurement control). A dropout ensemble, conformally recalibrated, gives $\approx\!90\%$-coverage intervals -- including for observables never measured, where a shot-based interval does not exist. Quality holds as the system grows (fidelity $0.90$ at $n{=}10$, gain \emph{growing} in $n$; $0.88$ at bond dimension $χ{=}4$), the parameterization is polynomial (native contraction to $20$ qubits), and we close the loop on IBM hardware ($5$ states at $0.97$ from hardware-measured Paulis).

Computed Tomography (CT) diagnosis often relies on dynamic selection of imaging phases, such as non-contrast, arterial, or venous phases, based on preliminary findings, clinical suspicion, and diagnostic guidelines. This phase-wise decision process is critical for reducing unnecessary radiation exposure while supporting timely staging and treatment planning. However, phase-selection protocols can vary across hospitals, regions, and guidelines, while most existing CT-based AI methods assume that all phases are available and focus on static tasks under a fixed imaging phase, failing to model whether additional phases are required. This limitation stems from heterogeneous multi-phase representations, the need for knowledge-guided phase control beyond visual cues, and the lack of supervision for phase-sufficiency decisions in existing datasets. To address these challenges, we propose Policy-Driven CT-Agent (PD-CTAgent) for clinically consistent CT phase selection and diagnostic reasoning. PD-CTAgent introduces a Clinical Structure Abstraction Module (CSAM) to harmonize heterogeneous CT phases into a unified, phase-aware evidence representation. Based on this representation, a Knowledge-Guided Diagnostic Control Model (KDCM) evaluates phase sufficiency and iteratively requests additional phases when necessary. The policy-driven agent design further allows PD-CTAgent to flexibly follow different institutional, regional, or guideline-specific diagnostic protocols. Together, PD-CTAgent bridges static CT analysis and real-world clinical workflows. Experiments on two public datasets, LIDC and MCT-LTDiag, and one private dataset demonstrate its effectiveness and clinical consistency. Code will be made public upon acceptance.

Objective. Existing quadratic unconstrained binary optimization (QUBO)-based sparse-view computed tomography (CT) reconstruction neglects photon-counting statistics and anatomical heterogeneity. We address both limitations within the QUBO framework.Approach. We propose a quantum compressed-sensing CT method combining penalized weighted least squares (PWLS) and guided total variation (GTV). PWLS weights projection residuals by photon-count reliability, whereas GTV uses gradients from a prior image reconstructed by the simultaneous algebraic reconstruction technique (SART) to preserve edges and suppress noise in homogeneous regions. After binary encoding, both terms form a unified QUBO model. Experiments used four 40 times 40 CT images under a 10-view fan-beam geometry with Poisson noise. Comparisons included conventional reconstruction methods, QUBO variants, gradient descent, simulated annealing, and a D-Wave hybrid quantum-classical solver.Main results. PWLS-GTV achieved the best reconstruction quality across all cases. In the representative chest case, it reached a peak signal-to-noise ratio (PSNR) of 36.64 dB, compared with 22.48 dB for SART, the best conventional baseline. GTV consistently outperformed conventional total variation. Simulated annealing and the D-Wave hybrid solver produced similar reconstructions, whereas gradient descent was ineffective. Repeated hybrid-solver runs showed stable performance.Significance. The framework incorporates photon-statistical weighting and structure-guided regularization into QUBO-based CT reconstruction without changing its quadratic form, providing a proof of concept for quantum-assisted sparse-view CT reconstruction.

The differentiable shift-variant filtered backprojection (SV-FBP) framework enables data-driven estimation of redundancy weights for cone-beam CT reconstruction under general source trajectories, removing the need for analytically derived weighting schemes. In this work, we present a systematic study of the robustness and adaptability of differentiable SV-FBP under challenging acquisition settings. We show that the framework remains stable across highly irregular and discontinuous trajectories, indicating that reconstruction performance is largely insensitive to trajectory ordering or continuity. Instead, the spatial distribution of sampling points plays a more dominant role. Under sparse-view conditions, differentiable SV-FBP achieves competitive reconstruction quality while providing an order-of-magnitude reduction in computation time compared to iterative reconstruction methods at moderate sampling densities. However, we identify a clear transition regime under severe undersampling, where the absence of iterative data consistency leads to performance degradation. Furthermore, we demonstrate that the framework remains applicable to non-planar multi-isocenter geometries, such as Lissajous-saddle trajectories, without requiring architectural modifications. These findings provide new insights into the behavior and limitations of the differentiable SV-FBP model and highlight it as a flexible and efficient solution for non-standard and robotic CBCT acquisition scenarios.

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.

Mobile C-arm cone-beam computed tomography (CBCT) has been widely used for real-time intraoperative 3D imaging. However, current practice often mechanically applies the fan-beam CT criterion of "180° plus fan angle" in pursuit of "data completeness" in reconstruction. This review argues that, under the single circular trajectory of three-dimensional cone-beam geometry, complete data are mathematically unattainable; moreover, blindly increasing sampling may exacerbate the trade-off among intraoperative image quality (Q), imaging time (T), and radiation dose (D). Against this background, this review reframes the evaluation of intraoperative CBCT around "data sufficiency" rather than "data completeness." This perspective moves beyond the excessive pursuit of absolute mathematical and analytic accuracy, and instead emphasizes task-specific minimum image-quality thresholds required for clinical decision-making. By synthesizing evidence from multiple clinical scenarios, this review suggests that approximation errors can be acceptable when clinical decision-making requirements are satisfied, thereby achieving a Q-T-D balance.

Computed Tomography (CT) is indispensable in clinical diagnostics, yet minimizing radiation dose without compromising image quality remains a critical challenge. Conventional low-dose protocols often rely on fixed, uniform angular sampling, independent of the underlying structural complexity of organs of individual patients. We propose ``Stochastic Adaptive Variance-Driven Exploration and Reconstruction'' (SAVER), an adaptive data acquisition framework that selects projection angles in real-time based on the statistical variance of acquired data. Utilizing a Softmax-based stochastic scheduling scheme with simulated annealing, SAVER prioritizes directions with high structural information while maintaining necessary exploration. Numerical experiments across 8 diverse phantoms demonstrate that SAVER achieves consistently higher reconstruction fidelity than conventional random sampling, particularly for objects with high structural anisotropy. Furthermore, the proposed method exhibits robust performance under significant measurement noise. By dynamically reallocating radiation dose to the most informative projections, SAVER provides a mathematically-grounded approach to maximize diagnostic quality per unit of radiation dose, marking a shift toward sample-dependent, data-driven CT acquisition.

Generating a 3D dental volume from a single panoramic radiograph (PXR) could provide a low-radiation alternative to Cone-Beam Computed Tomography (CBCT), but the problem is highly underdetermined: panoramic acquisition integrates 3D attenuation along curved X-ray paths into a 2D image, leaving depth-resolved anatomy unobserved. Existing implicit and generative approaches often produce oversmoothed geometry or anatomically inconsistent hallucinations, lacking geometry-driven supervision and relying on smooth representations unable to precisely localize sharp anatomical boundaries. We propose X-Splat, the first Gaussian Splatting framework for generating CBCT-like 3D dental volumes from a single PXR. X-Splat uses the known panoramic acquisition geometry as a generation scaffold: learnable anisotropic Gaussian primitives are initialized along the X-ray paths that formed the input image and adjusted in a single feed-forward pass, constrained by Beer-Lambert reprojection and multi-view radiographic training supervision. A lightweight residual refiner adds dataset-level anatomical priors without overriding the geometry already resolved by the Gaussians. We train on synthetic PXR-CBCT pairs, enabling direct volumetric supervision without paired real scans. We further introduce segmentation-based geometry-aware metrics, providing the first evaluation of PXR-based generation over maxillofacial anatomy. X-Splat outperforms NeRF- and GAN-based baselines, recovering individual teeth, cortical boundaries, and alveolar structure, including the mandibular canal which prior methods fail to reconstruct. Code will be available at https://github.com/tomek1911/X-Splat

Colored sectors in a microbial range expansion encode more than lineage survival counts. We formulate a computer-vision inverse problem: from one endpoint image of an accretive multi-type expansion, recover the radius-indexed pairwise boundary-flow field and test whether the visual pattern is compatible with a transitive scalar fitness hierarchy. The observable is a geometric signal extracted from sector-boundary curves in log-polar coordinates. We prove endpoint observability and stability for frozen fronts, weighted transitive/cyclic decomposition, contact-complete circular design, physical-clock and mechanism non-identifiability, exact Gaussian cyclicity testing, and Bonferroni-valid interval scanning. The benchmark is deterministic: analytic endpoint images, blurred/noisy pixel round trips, scalar-null stress tests, public-image tracing, multi-resolution mechanistic endpoints, and a non-learning frozen-front simulator. The implementation recovers pairwise edge-flow histories from endpoint images, detects cyclic residuals in a mechanistic four-type expansion, and uses those residuals as forcing signals for a dimensionless active design-control layer covering reaction-diffusion control, phenotype-frontier optimization, protocol synthesis, Monte Carlo robustness, and a downstream population-state bridge.

Dual-energy CT (DECT) exploits attenuation differences across different X-ray spectra to provide richer material information and has been widely used in medical imaging. While sparse-view acquisition can lower radiation exposure, it makes DECT material decomposition even more challenging, as the problem is nonlinear and ill-posed. Existing deep unrolling approaches generally do not explicitly incorporate the Jacobian operator induced by the nonlinear forward model, and their sparsity priors are still mainly built on conventional convolutions, which are insufficient for modeling global structural information. This study addresses the challenge of DECT multi-material decomposition in sparse-view settings by representing it as a sparse-regularized nonlinear least-squares problem. To solve it, we propose an iterative dual-domain refinement network (DECT-DRNet). In each iteration, the filtered back-projection (FBP)-based Jacobian approximation module is used first to generate an intermediate material decomposition result. Here, we characterize the forward process of material decomposition using a nonlinear operator, and then construct a theoretically grounded learnable approximation of the adjoint Jacobian operator by integrating the FBP algorithm with a U-Net into the backward process. In addition, to address the limitation of existing deep learning-based decomposition methods in globally suppressing noise and artifacts, we introduce a learnable sparse dual domain regularization term that incorporates Fourier convolutional residual blocks. This refinement block combines geometric feature extraction in the image domain with noise suppression in the frequency domain, allowing the model to capture both global and local features while maintaining structural details. DECT-DRNet demonstrates its ability to achieve more accurate material decomposition under sparse-view conditions.

A synthetic measurement of model competence is useful only if it survives the move to real data, yet the real labels that would verify it are exactly what medical imaging lacks. We ask whether transfer can be predicted in advance, label-free, and answer with a mechanism: on synthetic digital twins, competence that is donor-driven (a property of the transplanted nodule) survives the synthetic to real change of host, while host-driven competence (a property of the surrounding anatomy) need not. We test this on three lung CT vision-language tasks chosen to span that axis, across five public VLMs, four guidance conditions, and seven real datasets. The prediction holds in every case: presence and size orderings transfer (R2 >= 0.96), lobe does not; the split survives leave-source-out calibration, and the diagnostic names that boundary before any real label. TrialCouncil, a training-free council calibrated only on synthetic CT, confirms it by matching the best fixed model exactly where transfer is predicted. The contribution is not the router but the finding that transfer itself is predictable, label-free, from synthetic data alone.

The carbonized papyri from Herculaneum preserve the only large-scale library to survive from classical antiquity, but many unopened rolls remain unread because physical opening risks irreversible damage. X-ray computed microtomography ($μ$CT) and virtual unwrapping offer a non-invasive route to their texts, yet previous work on sealed Herculaneum scrolls has recovered only localized readings or limited surface regions. Here, using high-resolution phase-contrast $μ$CT acquired on the BM18 beamline at the European Synchrotron Radiation Facility (ESRF), together with improved computational unrolling and machine learning, we achieve the complete virtual unwrapping and reading of PHerc. 1667 under explicit coverage and papyrological-review criteria. This makes PHerc. 1667 the first Herculaneum papyrus to be fully digitally unrolled and read for extended scholarly study without physical opening. In PHerc. Paris 4, the optimized scan protocol makes ink directly visible in the tomographic volume, allowing three-dimensional ink segmentation and independent validation of surface-conditioned ink recovery. In PHerc. 139, we recover title and author-attribution evidence identifying the scroll as Philodemus, On Gods, Book 8. These results move virtual unwrapping of the Herculaneum scrolls beyond isolated demonstrations towards a scalable framework for systematic recovery of the still-unopened library.

Ovarian cancer is frequently diagnosed at an advanced stage, making preoperative contrast-enhanced computed tomography (CT) central to staging and surgical planning; yet the scarcity of annotated imaging data, compounded by privacy regulations, limits the development of generalizable computational models in this domain. Text-conditioned 3D CT synthesis has shown promise, but existing pipelines depend on paired radiology reports and have been evaluated only on chest CT. We propose OvESyn (Ovarian Evidence-based Synthesis), a framework that constructs standardized Findings and Impression sections directly from CT-derived imaging descriptors and routine clinical metadata, without any original radiology report, and uses them to condition a latent diffusion model adapted to 493 high-grade serous ovarian carcinoma patients. This is the first text-conditioned 3D CT synthesis framework adapted to an abdomino-pelvic oncologic setting. A systematic ablation over two adaptation axes, vision-language encoder alignment and generator fine-tuning, identifies generator domain adaptation as the operative mechanism for crossing the domain gap and establishing the target anatomy: without it, synthesis remains anchored to the thoracic pretraining domain, with Precision and Recall collapsing to zero and FID2.5D exceeding 140, regardless of encoder alignment. Encoder alignment instead refines intensity and fine detail. The full OvESyn attains the best distributional and intensity fidelity (FID2.5D 29.35, Precision 0.671, Wasserstein-1 0.044), while the generator-only variant maximizes coverage (Recall 0.645), reflecting a fidelity/coverage trade-off governed by encoder adaptation. Requiring only automatic segmentations and routine preoperative metadata, OvESyn supports transferability to report-scarce settings and provides a foundation for synthetic cohort generation in abdomino-pelvic oncologic imaging.

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.

X-ray computed tomography reconstruction is an ill-posed inverse problem, particularly in low-dose and sparse-angle settings where measurements are noisy and incomplete. While learned reconstruction methods such as the Learned Primal-Dual algorithm achieve strong performance, they typically rely on supervised training with access to ground-truth data, which is often unavailable in practice. In this work, we propose a self-supervised reconstruction method by extending the Noise2Inverse framework to the Learned Primal-Dual algorithm. The resulting approach, called Noise2Inverse Learned Primal-Dual (N2I-LPD), enables training of a learned iterative reconstruction operator without ground-truth images by exploiting the statistical independence of noise in distinct measurements with respect to angular rotation of the CT-scan. We compare the proposed method with classical reconstruction methods, as well as neural network-based approaches such as a U-Net trained within the same N2I framework. The results demonstrate that N2I-LPD achieves improved reconstruction quality, highlighting the potential of combining learned reconstruction operators with self-supervised training strategies for practical CT imaging scenarios where ground-truth data is unavailable.

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.

Sparse-view computed tomography (SVCT) reduces radiation exposure and acquisition time, but the limited number of projection views makes the reconstruction problem severely ill-posed and leads to streak artifacts when analytical methods are used. Plug-and-Play (PnP) methods provide an effective way to combine data fidelity with learned image priors, while stochastic PnP methods further improve robustness by matching the denoiser input distribution through re-noising. However, these methods often require many iterations to converge, which limits their practical efficiency. In this work, we propose a multilevel (ML) stochastic PnP method for SVCT that accelerates stochastic PnP reconstruction. We highlight that, in the stochastic setting, directly enforcing prior coherence across levels would require accurately estimating fine-level prior gradients through multiple denoiser function evaluations, which substantially increases the computational cost. Motivated by this observation, we perform the multilevel steps in multiresolution analysis (MRA) approximation spaces. This choice is supported by the structure of the wavelet decomposition, which causes the prior-coherence correction to vanish in expectation, thereby avoiding costly estimation of fine-level stochastic prior gradients for the coarse-level corrections. Experiments on SVCT reconstruction show that our method, called Multilevel Stochastic Plug-and-Play (ML-SPnP), achieves reconstruction quality comparable to state-of-the-art methods while substantially reducing runtime.

Quadratic unconstrained binary optimization (QUBO)-based quantum computed tomography (CT) casts reconstruction as a binary quadratic problem for quantum annealing and hybrid quantum--classical solvers. For grayscale CT, however, image encoding is constrained by the binary-variable budget: fixed global bit-plane encodings increase QUBO size and coupling complexity as gray-level precision improves, whereas low-bit encodings introduce quantization error. We propose a QUBO-based grayscale CT reconstruction framework that combines dynamic interval encoding with prior-balanced optimization. Each refinement round encodes active pixels only within local gray-level intervals around the current estimate, and a boundary-hit-guided update rule adaptively switches between search expansion and local refinement. To improve optimization stability, the method balances projection-domain data consistency and an edge-preserving quadratic prior before forming the final QUBO. Sparse-view and limited-angle fan-beam CT experiments show that the proposed method recovers structures and gray-level distributions more faithfully than the evaluated analytic, iterative, variational, and representation-based baselines. Expressivity analysis and ablation studies further indicate that the improvement mainly arises from effective gray-level representation through dynamic local encoding and more stable data-fidelity--prior coupling. Experiments on the D-Wave hybrid binary quadratic model (BQM) solver further demonstrate that the formulation is executable on a hardware-backed hybrid quantum--classical backend.

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.

Precise knowledge of nuclear structure is essential across fundamental physics, yet probing these structures is notoriously difficult. To address this challenge, ultra-peripheral collisions (UPCs) provide a femtoscopic tomography for imaging the atomic nucleus. UPCs offer a pristine electromagnetic pathway: coherent vector-meson photoproduction generates patterns of diffraction and two-source interference that directly encode the nuclear spatial density. Turning these patterns into quantitative constraints is, however, a challenging inverse problem, complicated by correlated sensitivities to deformation and neutron skin, phase smearing, and experimental backgrounds. Here we introduce an interpretable Multitask deep-learning framework that maps transverse momentum distributions to multiple nuclear-structure indicators simultaneously and identifies the kinematic regions driving each inference. We demonstrate the approach with coherent $J/ψ$ photoproduction in $^{96}_{40}\text{Zr} + ^{96}_{40}\text{Zr}$ collisions, showing that the learned features separate diffraction-dominated and interference-dominated information and provide analysis-ready observables for future high-luminosity data.

Sparse-view computed tomography is a severely ill-posed inverse problem, where recent 3D Gaussian Splatting methods offer an efficient explicit representation for tomographic reconstruction. However, we find that projection-domain optimization can be misleading in this setting: the rendered projections may continue to improve while the reconstructed volume deteriorates. We identify this failure mode as Projection-Volume Fidelity Divergence (PVFD), a representation-level optimization drift caused by anisotropic Gaussian deformation and view-specific primitive co-adaptation under sparse Radon constraints. To characterize this behavior, we introduce geometry- and volume-level diagnostics that measure needle-like Gaussian degeneration and the stability of the voxelized density field. Based on these observations, we propose LADES, a ground-truth-free optimization controller for sparse-view Gaussian tomography. LADES combines Linearly Annealed Dropout, which applies strong stochastic masking in early training to disrupt premature primitive co-adaptation and gradually restores full capacity for structural consolidation, with Structure-Aware Early Stopping, which terminates densification according to the saturation of Gaussian population growth rather than validation PSNR. Experiments on sparse-view CT reconstruction show that LADES improves volumetric fidelity, suppresses structural degeneration, and substantially reduces training time while maintaining competitive projection accuracy. These results suggest that robust Gaussian-based tomography requires monitoring and controlling volumetric structure, rather than optimizing projection fit alone.

Sexual identification of decomposed cadavers challenges traditional methods dependent on visual anthropological analysis. This study evaluates state-of-the-art deep learning (including YOLO26, YOLO11, ConvNeXt-Tiny, EfficientNetV2, ViT-B16, VGG16, and ResNet50) with transfer learning to automatically determine biological sex from forensic computed tomography (CT) scans. We analyzed 141 autopsied cadavers from the Forensic Medical Institute of Goiânia-GO, including a broad age range and varying conditions of preservation. The three-dimensional reconstructions of the pelvis and skull were converted into standardized two-dimensional profile projections, contributing to the study of this new technical approach. Data augmentation techniques compensated for sample limitations. Two scenarios were validated: binary and quaternary classification (one class per sex vs. one class per anatomical region of each sex). The best-performing model achieved highly consistent results on the pelvis region and still satisfactory performance on the skull region, reaching an overall patient-level accuracy of 95.65%, recall of 92.86%, F1- score of 94.36%, and precision of 97.22%, maintaining consistent performance across the evaluated cases, including those with trauma-related artifacts. Results indicate the technical feasibility of the methodology, demonstrating that deep learning models can provide objective, high-speed skeletal analysis. Since the study was conducted using data from a single institution and a single computed tomography scanner, further validation across multiple centers and scanners is required to assess the generalizability of the proposed approach

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.

In X-ray tomography, reconstruction quality generally improves with larger numbers of projections. However, more projections increase experiment costs, acquisition time and the radiation dose imparted to the sample. One mitigation to these trade-offs is to adopt a sequential design of experiments, in which each subsequent measurement is determined as a function of previously acquired data in order to maximize information gain. In practice, a widely used heuristic to maximize information is to align beams with the edges of the sample. A key challenge, however, is that the true sample is unknown, so identifying edge-aligned beams typically requires reconstructing the sample based on available measurements. This work proposes a novel sequential design method that identifies edge-aligned measurements directly from the sinogram, bypassing any reconstruction, thereby improving computational efficiency and reducing the experimental design's susceptibility to reconstruction errors. Our method dynamically selects the next set of measurement beams by maximizing an acquisition function that balances exploration and exploitation over the domain of all possible measurements, improving reconstruction quality while reducing measurement redundancy.

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.

Organ segmentation from PET/CT is critical for quantitative analysis and radiotherapy planning in oncology. To ease the high annotation cost of PET/CT segmentation, semi-supervised learning (SSL) provides a practical and effective solution for developing deep models with limited labeled data. Recent developments in visual foundation models have demonstrated remarkable adaptability with improved efficiency. In this work, we propose a mutual distillation framework that seamlessly exploits both structural and functional foundation models, which act as modality-specific generalists for distilling knowledge from structural CT and metabolic PET imaging. By bridging the gap between the task-specific precision of student models and the segmentation priors of generalist foundation models, we propose \textbf{MuDuo}, a mutual distillation framework that synergistically leverages SAM-Med3D for CT and SegAnyPET for PET to distill their knowledge into a lightweight student network. Our approach eliminates the need for manual prompts while maximizing the utility of unlabeled data for automatic segmentation, achieving state-of-the-art performance on the AutoPET dataset with only 5 labeled cases. Our source code is available at https://github.com/Wu-beining/MuDuo.

Energy Dispersive X-ray (EDX) tomography in Scanning Transmission Electron Microscopy (STEM) enables 3D compositional and elemental mapping at the nanoscale, but its use is limited by restricted tilt ranges and low-dose conditions required to avoid beam damage. Limited-angle acquisition introduces missing-wedge artefacts such as elongation and anisotropic resolution, while noisy low-dose data further degrade reconstruction quality and quantitative reliability. Here, we introduce an unsupervised deep learning framework based on Deep Image Prior with total variation regularization (DIP-TV) for limited-angle STEM-EDX tomography. We extend it to a multi-channel formulation (DIPm-TV) that jointly reconstructs multiple elemental maps by exploiting spatial correlations. Using a synthetic 3-channel phantom, we show that the method compensates for severe missing-wedge artefacts corresponding to approximately $100^\circ$ of missing angular range under moderate noise, outperforming simultaneous iterative reconstruction technique and compressed sensing approaches. We apply the method to 3D chemical analysis of Ge-Sb-Te (GST) memory devices in virgin (as-fabricated) and SET (crystalline) operational states. Samples were prepared as cross-sectional focused ion beam lamellae and acquired under a limited-angle tilt range from $-40^\circ$ to $+40^\circ$ with $5^\circ$ steps and a dose of $2.0\times10^5$ $e^-/Ang^2$. The multi-channel approach enables voxel-by-voxel elemental reconstruction using only EDX signals without external structural priors such as high-angle annular dark-field imaging. The reconstructed volumes show near-isotropic spatial resolution and reveal compositional heterogeneities associated with device operation. This approach enables 3D chemical characterization in experimentally accessible sample geometries where conventional methods fail due to severe angular limitations.

Head computed tomography (CT) typically uses sub-millimeter in-plane resolution but 2-5 mm through-plane spacing, creating substantial anisotropy that degrades multiplanar reconstructions, volumetric measurements such as hematoma volume estimation, and downstream algorithms that assume near-isotropic voxels. We present a deep learning system that synthesizes intermediate CT slices from pairs of neighboring axial slices, halving the effective through-plane spacing. The system improves three-dimensional visualization while simultaneously producing inherently denoised outputs, yielding two complementary benefits from a single inference pass. To build a reliable system, we systematically evaluate pixel-wise losses, namely mean squared error (MSE) and mean absolute error (L1); structural-similarity losses, namely the structural similarity index (SSIM) and its multi-scale variant (MS-SSIM); and hybrid combinations. On a held-out test set, all converged models outperform classical interpolation baselines and pretrained video frame interpolation methods (RIFE, FILM) on all structural measures, with MS-SSIM+L1 offering the strongest balanced profile. We also document training instability in SSIM-family losses and identify partial remedies: the standard numerical fixes eliminate the dominant failure mode but leave residual divergence at smaller batch sizes. All results are reported with patient-level bootstrap confidence intervals and paired statistical tests. As an illustration, we apply the system to an out-of-distribution head CT series from Hospital Universitario Virgen del Rocío: the model synthesizes intermediate slices and exhibits on the real slices the implicit-denoising signature predicted by our theoretical analysis, supporting in a single external case that interpolation quality and implicit denoising are not confined to the training distribution.

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.

Physics-informed learning is increasingly used for partial differential equation (PDE)-governed inverse problems, but its reliability remains difficult to certify. This paper develops a no-harm certification-and-selection framework for physics-informed inverse learning. A learned reconstruction is accepted only when its residual-calibrated radius is no worse than the baseline radius, namely when $R_{\mathrm{learn}}\le R_{\mathrm{base}}+\varepsilon_{\mathrm{safe}};$otherwise, the method returns the baseline. The certificate combines data, physics, boundary or initial-condition, and optimization residuals. Under a conditional stability estimate, these residuals yield an a posteriori reconstruction-error bound and a deterministic uncertainty radius. A high-probability certificate is also derived for physics residuals estimated from independent random collocation points. Numerical tests on Poisson source recovery, inverse heat reconstruction, limited-angle tomography, elliptic coefficient identification, and stochastic residual validation show that the selector accepts certified improvements, rejects shifted, hallucinated, or unfinished candidates, and becomes conservative in strongly ill-posed regimes. The framework is therefore a certification-and-selection layer, not another reconstruction architecture.

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.

Pretrained diffusion models demonstrate impressive potential in solving highly ill-posed 3D computed tomography (CT) inverse problems, while the inference process suffers from significant computational overhead. Furthermore, existing uniform timestep schedules fail to capture the non-uniform evolution of the reverse conditional diffusion stochastic differential equation, thereby introducing substantial truncation errors. To overcome this limitation, we propose Tracing the Oracle (TrO), a plug-and-play framework for improved timestep scheduling. Specifically, we treat densely sampled numerical integration trajectories on a few samples as the reference oracle. The optimized schedule is extracted by leveraging dynamic programming to globally minimize the cumulative error between the few-step approximation and the oracle. This mechanism precisely allocates the limited sampling steps to critical evolution stages that are highly susceptible to truncation errors. Our extensive experiments on the AAPM dataset across multiple 3D CT reconstruction tasks demonstrate that, when combined with the state-of-the-art 3D CT reconstruction method DDS, our optimized timesteps significantly improve reconstruction fidelity and computational efficiency compared to existing heuristic schedules, especially under a strict budget of no more than 10 sampling steps.

Cone-beam computed tomography (CBCT) frequently suffers from data truncation, which introduces severe artifacts and limits the effective field of view (FOV). Existing deep learning methods for truncated cone-beam computed tomography (CBCT) reconstruction suffer from serious limitations, including a strict reliance on supervised ground truth and a failure to account for continuous 3D spatial truncation variations. To address these challenges, we introduce a self-supervised 3D reconstruction framework based on neural scene representations. By directly mapping spatial coordinates to radiodensity under projection supervision, our approach inherently bypasses traditional filtering and backprojection operations, thereby fundamentally eliminating truncation-induced ring artifacts while enabling robust continuous 3D data extrapolation. However, coordinate networks are susceptible to an inherent spectral bias, which leads to a severe loss of clinically vital high-frequency textures. To resolve this bottleneck, we further incorporate a physics-based iterative refinement module into the neural scene representation architecture. Leveraging the artifact-free, extrapolated volume from the coordinate network as an optimal initialization, this module progressively re-extracts and injects high-frequency structural information from the original projections back into the volume. Extensive experiments on both simulated and real-world datasets demonstrate that our method successfully unifies the exceptional artifact suppression and extrapolation capabilities of neural networks with the high-fidelity detail preservation of iterative algorithms.

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.

Radiology reports describe kidney lesions by type, size, enhancement, and attenuation, yet existing 3D methods predict only at the patient or organ level. We reformulate kidney CT characterization as a per-lesion set-prediction task: one model emits a variable number of lesions per kidney, each with four clinical attributes. We curated 2,619 CT volumes from 788 patients at one academic medical center, with multi-granularity side- and per-lesion labels, and used KiTS23 (489 cases) for zero-shot external validation. We propose \textbf{LesionDETR}, a DETR-style architecture with size-distance Hungarian matching and a hierarchical loss that aggregates per-slot outputs to side-level objectives. Across four input representations and six encoder initializations, two design choices dominate: a segmentation mask as an input channel, and same-domain abdominal pretraining (SuPreM); generic large-corpus pretraining is no better than random initialization. LesionDETR reaches bilateral side-level abnormality AUC $0.799 \pm 0.009$ on UF-Health and $0.817 \pm 0.072$ on KiTS23. A count-conditioned variant reaches per-lesion mAP $0.190 \pm 0.083$ on cystic lesions; rare solid-lesion AP stays at the noise floor, pointing to targeted data collection, not architecture, as the next bottleneck. The framework yields verified per-lesion predictions for downstream structured report generation.

Reconstructing thin 3D structures is challenging due to their sparsity, scale variation, and complex geometry. Such structures arise in a wide range of domains, including medical imaging of vascular systems and industrial pipe systems. While recent neural methods perform well on dense surfaces, they often fail to recover fine thin geometries. We propose a reconstruction approach based on local depth projections, which provide an efficient and informative 2D representation of thin structures. Specifically, we traverse the 3D model with a sliding box to generate local orthographic depth projections, which are processed by a neural network to reconstruct missing thin structures in 2D. The local reconstructions are subsequently fused back into the 3D model to produce a coherent and detailed shape. Experiments on pulmonary artery reconstruction from CT volumes and industrial pipeline recovery from synthetic and real scans demonstrate improved preservation of fine structural details over existing methods.

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.

Accurate registration of CAD models to CT scans is essential for establishing ground truth geometry in volumetric imaging. Obtaining reliable object masks is of growing importance in machine learning settings; as recent architectures grow more capable, huge datasets are required to fully utilise their capabilities. Traditional intensity-based methods fail when CT grayscale values lack calibration references, while point-based algorithms (e.g., ICP, RANSAC) require feature correspondence unavailable between idealized CAD geometry and noisy volumetric CT data. We propose a two-stage geometric registration method for cylindrical objects (ionization chambers) that takes advantage of the distinctive geometric features of the objects. First, we estimate the 3D rotation axis by detecting elliptical cross-sections across CT slices, fitting ellipses to edge-detected contours, and performing PCA on the fitted ellipse centers after RANSAC outlier removal. Second, we voxelize the CAD model, orient it along the detected axis, and maximize volumetric overlap with the CT scan through translational adjustment. This approach achieves robust registration with tilt and orientation errors below $0.1^\circ$ without intensity calibration or feature matching. Once registered, the aligned CAD model provides ground truth geometry for applications including machine learning-based object localization and automated analysis in industrial CT workflows.

Generative models are increasingly used as priors for inverse problems, but their ability to produce realistic images creates a basic trust problem: a plausible reconstruction may be supported by the measurements, or it may be filled in by the prior along unobserved directions. This distinction is especially important in medical imaging, where acquisition operators are designed under scan-time, dose, and calibration constraints. We study generative inverse problems from a measurement-geometry perspective. The central question is whether a fixed measurement operator can distinguish nearby images that are plausible under the generative prior, and whether this relationship can guide better measurements. We introduce a local measurement-manifold compatibility measure that quantifies how well the operator observes prior-relevant tangent directions. Under local regularity assumptions, we prove that this quantity controls the stable part of the reconstruction error, while the generative prior controls off-manifold drift. This worst-direction certificate motivates practical fixed and sequential acquisition rules based on overall local volume preservation, including a posterior-cloud design that adapts measurements at test time without training a sampling policy. Across row-sampling, tomographic, and MR acquisition settings, the proposed scores predict failure modes, explain measurement-induced hallucinations, and guide better sampling. In fastMRI Cartesian sampling, posterior-cloud measurement design improves over strong non-learned ACS-preserving baselines, including variable-density and Poisson-like masks.

We introduce Echo-POSED, a self-supervised framework for real-time transthoracic echocardiography (TTE) guidance that recommends probe adjustments directly from 2D ultrasound images, without the need for expert-labelled views or tracked probe trajectories. Instead, it trains on 2D views sliced from routinely acquired 3D echocardiography volumes, enforcing equivariance to probe motions while remaining invariant to cardiac phase, yielding a pose representation on $\mathrm{SO}(3)\times\mathrm{SO}(3)$. Across a held-out split and public external 3D--TTE datasets (including vendor shift), Echo-POSED maintains geometric consistency under virtual perturbations and enables intra- and inter-patient guidance simulations, achieving a combined mean angular error of 8.2 degrees between the guided and target views in intra-patient simulations with cardiac motion.

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

Dual-energy CT (DECT) enables virtual monochromatic imaging (VMI) and improved contrast resolution, but its clinical adoption is limited by hardware complexity and cost. In this work, we propose a unified deep learning framework that synthesizes contrast-phase-specific virtual monochromatic 50 keV images from single-energy CT (SECT) data by leveraging contrast phase information as a prior. The model is trained using DECT-derived 70 keV and 50 keV image pairs across four contrast phases -- Angio, Arterial, Portal, and Delayed -- using a novel prior conditioning architecture that integrates contrast phase priors into the energy transformation process. We demonstrate that the proposed unified model achieves contrast enhancement and generalizes well across contrast phases. Additionally, we show that the model can generate 50 keV-like images from SECT inputs, preserving contrast phase-specific dynamics.

The goal of this work is to reduce the effect of photon noise in dental cone-beam CT reconstruction. We consider an inverse problem formulation and develop a databased prior. To this end, we simulate fan-beam acquisitions and add photon noise to the projection data. The prior is obtained by training a gradient-step denoiser using reconstructed simulated acquisitions. The trained model is integrated into a plug-and-play gradient-step algorithm to reconstruct images from simulated projections. Experiments on synthetic data demonstrate the denoising capabilities of the trained model, while qualitative evaluations on real images showcase the algorithm's performance and generalization ability.

Volcanoes emit large amounts of CO2, directly influencing human lives. Mapping volcanic gas emissions helps to forecast eruptions and understand the impact of volcanoes on climate and the environment. Drone-based gas sensing significantly reduces risks in volcanic monitoring but faces technical limitations when measuring gas, as rotor downwash disperses the gas plume before detection. Gas Tomography using remote gas sensing addresses this challenge. At the Salinelle dei Cappuccini mud volcanoes, we demonstrate that while drone-mounted in-situ sensors failed to detect CO2 emissions due to aerodynamic disturbance, open-path sensing successfully enabled remote gas distribution mapping. We present a novel model-based gas tomographic reconstruction approach that incorporates a Lagrangian model to compensate for wind-induced advection. The resulting gas distribution maps align with manually collected in-situ measurements, confirming that model-based gas tomography effectively overcomes downwash limitations and enables accurate mapping of volcanic emissions.

Electron tomography (ET) plays an important role in the three-dimensional (3D) characterization of nanomaterials. However, under limited-angle and sparse-view conditions, conventional algorithms produce degraded reconstructions, which compromise the quality and interpretability of resulting 3D data. In this paper, we present deep image prior (DIP), an unsupervised deep learning (DL) approach, for highly degraded tomography acquisitions and demonstrate, using simulated data, that its performance is comparable to that of supervised approaches requiring training datasets, even for tilt ranges as limited as 60° and tilt increments of 10°. We then apply it to experimental data and show that it enables reliable 3D quantification under both sparse-view and limited-angle conditions, highlighting its potential for a wide range of materials and acquisition modalities.

Low-dose computed tomography (LDCT) reconstruction faces a critical tradeoff between reconstruction quality and resource requirements. While recent deep learning methods achieve state-of-the-art performance, they typically rely on over 500,000 parameters trained on large-scale datasets exceeding 35,000 scans. This work investigates whether graph-based regularization can provide meaningful noise reduction under strict resource constraints. We propose Deep Graph Laplacian Regularization (Deep GLR), integrating quadratic graph regularization into a Proximal Forward-Backward Splitting optimization framework with three lightweight CNN modules. Evaluated on the LoDoPaB-CT benchmark, Deep GLR achieves 30.70 dB PSNR, representing a 6.33 dB improvement over filtered backprojection, while using only 91,848 parameters trained on 1000 samples (2.8% of standard training set). Compared to benchmark methods, this represents 5.8 times better parameter efficiency and 30 times better data efficiency per dB improvement. The learned graph bandwidth parameter ($ε$=1.25) converges to interpretable values, suggesting the method captures meaningful image priors rather than overfitting. While a 13 dB gap remains versus state-of-the-art methods, results demonstrate that graph-based regularization provides a favorable efficiency-quality tradeoff for resource-constrained medical imaging scenarios.

A panoramic X-ray compresses a 3D jaw into a 2D strip; we aim to recover the missing depth cleanly and fast. Existing implicit neural representations render realistic volumes but are slow to train, sensitive to sampling and positional encodings, and costly in practice. Pure CNN baselines are efficient yet struggle with the dental arch's long-range geometry, blur fine enamel-dentin boundaries, and offer little interpretability. We present K-U-KAN, a three-stage pipeline that (i) lifts 2D features into depth-aware observables with Kolmogorov-Arnold Networks, (ii) advances these observables by a stable, phase-aware linear evolution via a Koopman token block, and (iii) places the predicted depth bins onto focal-trough rays before a lightweight 3D attention U-KAN refines the volume. This marriage of physics (Beer-Lambert image formation), geometry (horseshoe focal trough), and learned linear dynamics yields sharp anatomy, fewer artifacts, and robust behavior on native radiographic intensities with batch size one. On held-out data, K-U-KAN matches transformer/implicit baselines on signal and structure metrics, clearly improves perceptual quality, and trains in roughly half the time-making single-view PX $\to$ CBCT reconstruction more practical for clinical pipelines.

Ultrasound computed tomography (UCT) via full waveform inversion (FWI) enables high-resolution quantitative imaging for tissue characterization and disease diagnosis. However, UCT suffers from large computational burden and severe convergence issues due to highly nonlinear optimization. Deep learning can accelerate UCT reconstruction, but supervised training requires large-scale labeled datasets difficult to obtain in vivo. To address these limitations, we propose SDA-UCT, a two-stage self-supervised domain-adaptive framework for rapid and accurate UCT imaging of musculoskeletal tissues. SDA-UCT employs an attention-enhanced network (AttUCT) pre-trained on simulation datasets and transfers to in-vivo data via physics-informed self-supervised learning, effectively bridging the simulation-to-real domain gap. A Low-Rank Adaptation (LoRA) mechanism is integrated to enable efficient adaptation across diverse clinical scenarios. Results showed that AttUCT achieved high-quality SOS reconstruction for simulated human forearm with a PSNR of 29.23 dB and SSIM of 0.928, outperforming conventional FWI and existing deep learning methods. Validated on in-vivo data, SDA-UCT successfully reconstructed SOS images revealing complex anatomical structures (skin, fat, muscle, tendon, bone and bone marrow) for human forearm, in high concordance with MRI references. The LoRA mechanism adjusting only 3% of parameters achieved comparable performance to full fine-tuning. The rapid reconstruction (5 ms per frame) enables real-time 3D visualization, achieving five-orders-of-magnitude improvement over traditional FWI. This work represents the first self-supervised domain-adaptive deep learning for rapid, high-resolution in-vivo UCT imaging, showing potential for musculoskeletal disease diagnosis.