clinical imaging teams

Abstract: In real-world clinical settings, dental X-ray segmentation using deep learning methods suffers from reliability issues. Even when the segmentation quality is bad, deep learning models show high confidence in their predictions (calibrational blindness). Moreover, in real use, doctors do not have ground-truth masks to check their accuracy. To address this problem, we introduce a simple quality-checking engine called HUS-QA with three stages. We train it on the PRAD (Periapical Dental X-ray) dataset to build our SimCLR self-supervised ResNet-18 U-Net model, which generates the segmentation mask and then evaluates its quality. Our HUS-QA checks the segmentation mask quality without a ground-truth mask. Prediction confidence, edge sharpness, shape connectivity, and area-size penalty are the simple indicators considered in this research. Results show that standard confidence methods fail (r = -0.1394, p = 1.7864e-3, ROC AUC = 0.4275). By contrast, our HUS-QA shows a positive correlation with actual Dice scores (r = 0.4647, p = 3.7510e-28) and achieves a strong ROC-AUC of 0.8405. Therefore, HUS-QA serves as a practical tool for clinical quality control.

Abstract: Medical severity estimation commonly relies on absolute grade annotations, which are fundamentally ordinal, yet existing methods often treat the grades as independent categories. Learning-to-rank methods, which can be trained using relative annotations based on severity comparisons of image pairs, can provide continuous severity rankings but cannot directly predict discrete severity grades. We propose Dominance-guided Ordinal Severity Estimation from Sparse Relative Annotations (DOSE), a framework for learning ordinal medical severity from sparse pairwise comparisons without using absolute annotations. DOSE aggregates the observed comparisons through a global comparison graph to estimate a dominance score for each image. Differences between dominance scores set cumulative margins in the embedding space, so that pairs with larger estimated severity differences are separated more strongly, and also generate pseudo-pairs that supervise a scalar severity head alongside the observed comparisons. The learned continuous severity axis is converted into discrete grades via label-free score calibration, with tie-anchored segmentation as the main calibration method. In the experiment, DOSE consistently outperformed pairwise-ranking baselines on ACNE04, IDRiD, and LIMUC under different pair budgets. Code is available at https://github.com/TushirSahu/DOSE

Abstract: Alzheimer's disease (AD) diagnosis may benefit from gut metabolic information associated with brain-gut interactions, yet existing models largely analyze cerebral glucose metabolism alone. Although whole-body fluorodeoxyglucose positron emission tomography (FDG-PET) can provide paired brain-gut observations, routine brain examinations rarely include gut imaging, limiting direct use of this information for diagnosis. In this paper, we present BRIDGE (Brain and Gut Representation Integration via Distribution-Guided Enhancement), a two-stage framework for transferring brain-gut metabolic knowledge to brain-only diagnosis. Specifically, BRIDGE integrates a conditional brain-to-gut latent transport module and a disease-evidence-guided cerebral pathway to capture subject-specific cross-organ correspondence and disease-relevant cerebral representations. For the cerebral pathway, a large language model (LLM) helps organize literature-derived descriptors into human-approved semantic anchors that guide feature learning. Additionally, we introduce a counterfactual-guided residual fusion mechanism, which uses matched and non-matched virtual-gut evidence to supervise a confidence gate and dynamically regulate the contribution of transported cross-organ information. At inference, BRIDGE exploits complementary gut-related context using brain PET alone, without measured gut PET. Extensive experiments across public and private cohorts demonstrate that BRIDGE outperforms brain-only and cross-organ baselines, achieving AUC gains of 6.0% and 5.2% over its brain-only counterpart for CN/MCI and CN/AD diagnosis, respectively. Notably, its ability to transfer complementary brain-gut metabolic context while preserving brain PET as the sole inference input highlights its potential for clinically practical diagnosis. Our code is available at https://github.com/CUHK-AIM-Group/BRIDGE.

Abstract: Lung tumor segmentation plays a vital role in early detection and treatment planning of lung cancer. Although state-of-the-art deep learning models achieve high dice score coefficients (DSC), each forward pass requires computing large amounts of floating point operations, making them computationally expensive, requiring GPU acceleration, and having slow inference speed, limiting real-world clinical deployment. We propose a lightweight, energy-efficient model that leverages the ENet architecture for its real-time inference capability and low computational cost, enhanced with UNet-style skip connections between encoder and decoder stages for feature reuse and the lightweight Convolutional Block Attention Module (CBAM) for improved feature representation. The model is trained on publicly available data from The Cancer Imaging Archive (TCIA) via the Medical Segmentation Decathlon Challenge (MSD) and evaluated on the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) dataset. Our model achieves a DSC of 0.90812 (threshold of 0.5) with its compact architecture of 430,052 parameters and 0.549 Giga Multiply-Accumulate operations (GMAC), making it up to 10 times faster, requires 79 times less GMAC than UNet, and has 22 times fewer parameters than SegNet. These characteristics make it well-suited for deployment in clinical settings where computational resources are limited and decrease the cost of utilizing such a system. Additionally, the explainable AI technique of Grad-CAM is used to provide visual interpretability of the model's predictions and to identify regions where segmentation performance requires improvement.

Abstract: Combined optoacoustic (OptA) and ultrasound imaging is a promising modality across a wide range of pathologies. Its use in clinical research, however, is limited by a lack of analysis software accessible to users without programming expertise. Existing tools are either script-based engineering frameworks or proprietary vendor applications. We present OPTARI, an open-source graphical software application to facilitate large-scale clinical optoacoustic-ultrasound (OPUS) studies. OPTARI builds on the napari image viewer and the PATATO toolkit for OptA data processing. It supports native vendor and open HDF5 data formats, aligns with the IPASC standard, and is distributed as a standalone executable. Features include region-of-interest annotation, reconstruction, chromophore unmixing, deep-learning-based tissue segmentation, and temporal and spectral analysis modules. OPTARI offers a combination of features for clinical study analysis that none of the compared tools provide. The automated tissue segmentation produced results comparable to expert labeling for muscle tissue, and batch processing reduced analysis time from minutes to under one second per scan. The tool is used in ongoing clinical OPUS studies. OPTARI connects engineering frameworks with medical research and provides an open-source basis for reproducible and standardized analysis in clinical OptA imaging studies.

Abstract: Current evaluation protocols for medical image segmentation remain largely anchored in sample-wise comparisons, e.g., Dice and Hausdorff distance, which require each prediction to be paired with a ground-truth mask. Yet two limitations arise in practice: they are inapplicable when predictions are made on unlabeled data; and even when annotations are available, they cannot assess whether a collection of predictions matches the distributional structure of the ground-truth population. We introduce MID (Mask-Image Distributional Divergence), a distribution-level evaluation metric for medical image segmentation. MID builds upon the observation that segmentation quality is a property of the joint image-mask distribution: a mask may be anatomically plausible in isolation yet incorrect for the image it accompanies. MID compares the joint distribution of images and masks between a reference set and a set of predictions, without requiring sample-wise correspondence. This captures both mask realism and image-mask consistency. We evaluate MID across 13 publicly available datasets spanning CT, MRI, and MRA. Under anatomically realistic corruptions across 56 organ groups, MID tracks mean Dice and Hausdorff distance without per-sample ground-truth pairing. MID also detects distributional shifts across modalities and anatomies, identifies image-mask misalignment through controlled shuffling experiments, and produces reliable model rankings across real segmentation models. Official implementation available at github.com/erc-caravel/pytorch-mid

Abstract: Surface-based cortical analysis is useful in many applications as it is a natural way to model the highly folded structure of the cerebral cortex, allowing quantities such as curvature and thickness to be easily calculated. Existing deep learning (DL) methods have focused on 1x1x1 mm3 T1-weighted (T1w) scans, thus replicating classical pipelines. Here we present a neural network that is trained exclusively on synthetic scans with random contrast and resolution. Consequently, it can be applied to almost any kind of magnetic resonance imaging (MRI) scan. In addition, our model provides vertex-wise uncertainty estimates of the predicted surface as well as a spherical registration to fsaverage space. Our model performs on par with other state-of-the-art DL methods on 1x1x1 mm3 T1w scans and outperforms the only other method capable of estimating cortical surfaces from low resolution, non-T1w scans. The predicted uncertainty, moreover, correlates with overall scan quality on low resolution scans and highlights areas of poor surface reconstruction on 1x1x1 mm3 T1w scans, suggesting that it can be used for quality control. Finally, the predicted spherical registrations prove comparable to other DL and classical registration methods. These qualities, when combined with the fast inference time, will provide the ability to analyze large, existing databases of clinical MRI scans, with the potential for finding disease-specific patterns that would otherwise be infeasible in a research setting.

Abstract: Biomedical imaging modalities often require a trade-off among resolution, field of view (FOV), and acquisition speed. Video mosaicking offers a strategy to overcome this limitation by computationally stitching sequential high-resolution frames into a wide-FOV composite. However, existing methods struggle with non-rigid deformations, and modality-specific artifacts arising in clinical and research imaging. Here, we present FloVMos, a generalizable, optical-flow-based deep learning framework for real-time video mosaicking across diverse biomedical imaging modalities. FloVMos achieves robust, pixel-level registration by fine-tuning an optical flow model on synthetic training data with ground-truth deformation fields. We introduce a pipeline for generating this training data, simulating realistic tissue motion and imaging distortions from existing mosaics or raw videos. Our automated synthetic data generation and optical flow model training based on this data allow users to adapt FloVMos to different imaging modalities. To demonstrate this, we applied FloVMos to seven diverse imaging modalities: reflection confocal microscopy, open-top light-sheet microscopy, fetoscopy, laparoscopy, dermoscopy, sparse spectral microscopy, and endoscopy. FloVMos outperforms conventional baselines in accuracy, robustness, and speed for all the tested modalities. This adaptable and training-efficient framework enables large-area visualization with real-time performance and may support broader use of video-based biomedical imaging in research and clinical workflows.

Abstract: Vessel segmentation in medical images is essential for many clinical tasks, ranging from diagnosis to treatment planning. However, it remains challenging due to complex vascular morphology and diverse imaging conditions. Existing deep learning methods rarely aim at building a generalizable vessel segmentor across anatomies and modalities. While the Seg- ment Anything Model (SAM) has shown promise for med- ical image segmentation, its original design does not fully exploit vascular morphology and struggles with fine-grained vascular structures, leading to suboptimal performance. In this paper, we propose ReG-SAM, a SAM-based framework tailored to 2D vessel segmentation that leverages reference graph set for enhancing vascular representations. Specifically, we introduce two modality-aware representations derived from the reference masks: graph prompt embeddings (GPEs) that encode global spatial features from graphs, and vascu- lar prototype embeddings (VPEs) that capture fine-grained modality-specific vessel characteristics from multi-scale fea- ture maps and vascular masks. Since both require vascular masks that are unavailable during inference and require robust modality-aware vascular feature representations, we construct a modality-wise vascular database and develop two reference graph-guided representation learning schemes for estimating GPEs and VPEs using samples from the database rather than ground-truth masks. Extensive experiments across 19 datasets demonstrate that ReG-SAM consistently outperforms existing baselines, even those using manual prompts, particularly on challenging thin vessels.

Abstract: Optimizing fMRI scan duration and spatial resolution is critical for experimental design, yet traditional correlation-based approaches cannot quantify uncertainty or disentangle scanner measurement noise from true neural variability across subjects. Without principled uncertainty bounds, researchers cannot know whether a protocol is long enough to reliably estimate connectivity, or whether between-subject differences reflect biological variation or noise. We present a Bayesian framework modeling BOLD dynamics as coupled Ornstein-Uhlenbeck processes, using Sequential Neural Posterior Estimation to obtain connectivity posteriors while accounting for frequency-independent measurement noise across the BOLD spectrum. Applied to N = 28 healthy controls (55 scans) at 7T using a functional network atlas (65 DMN regions), the framework quantifies uncertainty across its sources: scanner noise, subject variability, and acquisition length. Spatial analysis identifies a mean of 46 voxels per ROI, roughly half of typical region sizes, as sufficient to achieve 90% of asymptotic precision. At the single-subject level, 7T reaches its within-session precision plateau in approximately 7 minutes versus 10 minutes for 3T, a 40% reduction in required scan time, providing the first direct, model-based quantification of the scan-time advantage conferred by higher field strength. At the population level, 3T requires roughly 37 times more per-subject scan time than 7T for the pooled curves to converge, confirming a consistent advantage of higher field strength at every timescale. Together these findings provide concrete, scanner-specific guidance for protocol optimization, with direct implications for reducing acquisition costs and improving the reliability of connectivity-based clinical biomarkers. We provide code enabling researchers to derive these bounds from their own data.

Abstract: Deep learning segmentation of renal tumors requires large annotated datasets, yet clinical deployments typically offer only a handful of tumor-positive cases from the target site. We propose a diffusion-based inpainting framework that synthesizes anatomically plausible renal tumors within healthy CT scans, requiring no additional annotation, and provide the first systematic comparison of 2D, 2.5D, and full 3D (MAISI) synthesis strategies for this task. Training the diffusion model on public data (KiTS23, KIRC) and evaluating nnU-Net segmentation on a internal cohort across three low-data regimes, we find that 2.5D and 3D augmentation substantially reduce false positives (from $\sim$18--20\% to $\sim$3--6\%) while maintaining Dice, whereas 2D provides no consistent benefit. Crucially, the proposed 2.5D method matches full 3D synthesis on every metric at substantially lower computational cost, indicating that local volumetric consistency alone is sufficient for effective augmentation in data- and resource-scarce clinical settings.

Abstract: Over the years, Convolutional Neural Networks (CNNs) have demonstrated strong capability in cancer detection and classification using medical images. However, CNN-based models often struggle to capture long-range contextual dependencies. In such scenarios, integrating Compact Convolutional Transformer (CCT) architectures after the CCT layer allows CNN-extracted features to reshape into compact patch tokens using a CCT tokenizer, followed by the addition of positional embeddings to preserve spatial structure. Using 5-fold cross-validation, the model was tested on 3 sets of breast cancer mammography. With only 250,435 parameters, the model achieved 99%-100% accuracy across 3 datasets, indicating robust generalization. Explainable AI (XAI) was integrated into the model to explain the breast cancer classification process to enhance clinical trust. The results indicate that the proposed framework is suitable for computer-aided diagnosis systems, particularly in resource-constrained clinical environments. The novelty of the proposed CNN-integrated CCT overcomes the limitation of CNN's gradient degradation in the last layers by integrating convolutional tokenization with transformer-based learning. Lighter than ViT, which is effective in capturing long-range dependencies, the model has also proven efficient in breast cancer classification by capturing long-range dependencies among breast tissue regions.

Abstract: Deep networks trained on structural MRI for Alzheimer's disease (AD) staging often reach reasonable accuracy while attending to anatomically irrelevant regions, and multimodal models that add clinical tables frequently rely on variables that were used to assign the diagnostic label in the first place. We study both issues with a deliberately lightweight slice-based encoder (ResNet18 with a one-layer Transformer over slices) on 1,075 baseline T1-weighted scans from ADNI-1. First, we use FastSurfer segmentations as an anatomical reference: YOLOv8 models trained on segmentation-derived labels localize Alzheimer-relevant structures with mAP_50 above 0.96, and a Grad-CAM comparison shows that the image-only classifier frequently attends to the skull, orbits and background. Second, we adapt a CLIP-style image - tabular contrastive framework and organize ADNIMERGE variables along a label-leakage spectrum. Fusion with cognitive scores yields 87.3% three-way accuracy, which we treat as a leakage-driven upper bound rather than an imaging result; fusion with regional volumes yields 73.0%. We observe that the choice of contrastive target changes what the image encoder learns: on MCI vs. CN, the image-only head reaches 52.4% when the encoder is aligned to cognitive scores and 73.8\% when aligned to volumes, although no tabular input is used at inference. Third, restricting the input to a per-subject crop of the medial temporal lobe raises image-only three-way accuracy from 58.7% to 65.1%. All results come from single runs on a small balanced test set, and we report confidence intervals and the protocol differences that prevent direct comparison with published numbers.

Abstract: Multi-shell diffusion MRI (dMRI) unlocks more expressive microstructural modeling than single-shell scans, yet its longer acquisition time hinders deployment in large-scale cohorts and time-constrained clinical settings. Synthesizing an unobserved shell from a single-shell input is fundamentally ill-posed and further complicated by protocol mismatch, where source and target gradient direction sets may not align. We propose DTI-SHNet, a single-to-multi-shell synthesis framework that operates in the real symmetric spherical harmonics (SH) coefficient domain and performs spatially aware volumetric regression. Given a source shell, we estimate diffusion tensor imaging (DTI) and use direction-agnostic parametric maps along with a brain mask as conditioning priors to guide a 3D U-Net regressor from source-shell to target-shell SH coefficients. To couple coefficient accuracy with signal fidelity, we introduce a signal consistency regularization that reconstructs signals on randomly sampled canonical directions from predicted coefficients and enforces agreement in the signal domain. Experiments on UK Biobank and Cam-CAN data for b=1000 to b=2000 dMRI synthesis show that DTI-SHNet achieves competitive visual quality compared to advanced methods, while better preserving downstream diffusion measures. Our code is available at https://github.com/xiaovhua/dti-shnet.

Abstract: Single Ventricle Physiology (SVP) is a rare subtype of congenital heart disease characterized by the presence of a single functional cardiac ventricle with atypical anatomic configurations that challenge conventional image segmentation approaches. The scarcity of clinical data and the morphological diversity across SVP subtypes make the development of robust segmentation methods particularly difficult. To address these limitations, we propose a cardiac MRI segmentation framework focused on ventricular chambers and myocardium segmentation tailored for SVP. First, we introduce a data augmentation pipeline that generates synthetic 3D cardiac meshes using SDF4CHD and corresponding synthetic cardiac MRI through generative modeling. Second, we introduce SV-Cine, a diagnosis-conditioned adaptation of the foundation model CineMA that incorporates patient-level diagnostic information through Feature-wise Linear Modulation layers, enabling diagnosis-aware feature adaptation during segmentation. We evaluated the framework on an internal cohort with varying SVP subtypes. SV-Cine achieved median Dice scores of 0.89 (IQR: 0.80--0.91) for the left ventricle and 0.72 (IQR: 0.54--0.84) for the right ventricle, outperforming the strongest baseline, nnU-Net, by 0.39 Dice points on right ventricle segmentation. It also yields a median ejection fraction error of 5.55 percentage points (IQR: 3.41--7.69) for the dominant ventricle. Compared with the internal cohort, LV and myocardium segmentation performance was lower for the external cohort; whereas RV Dice scores were comparable for both cohorts. Our findings suggest that a pretrained foundation model can be adapted for highly specialized downstream tasks through usage of diagnosis priors while leveraging anatomic knowledge learned from large-scale MRI datasets during pretraining.

Abstract: Accurate biomedical image segmentation requires not only high global overlap but also reliable delineation of clinically meaningful boundaries. In blood-smear microscopy, cytoplasm and nucleus contours provide the structural basis for downstream morphology analysis; however, deep segmentation models may remain uncertain or overconfident near ambiguous boundary regions even when achieving strong Dice scores. This work proposes a Reliability-Aware Boundary Refinement Network (RABR-Net), a two-stage framework for trustworthy image segmentation. A strong UNet++ EfficientNet-B4 base segmenter first produces initial class probabilities and logits. Predictive entropy, test-time augmentation variance, margin uncertainty, probability gradients, and soft boundary cues are then combined into a boundary-aware reliability representation. This representation guides a gated residual refiner that selectively corrects uncertain boundary pixels while preserving confident regions of the base prediction. The framework is evaluated using overlap accuracy, class-wise Dice, Boundary Dice, HD95/ASSD, calibration, risk--coverage analysis, robustness under image perturbations, qualitative correction maps, and paired statistical testing. On the held-out test set, the proposed method improves Dice from 0.9602 to 0.9614, Boundary Dice from 0.3448 to 0.3611, and HD95 from 3.0354 to 2.8274 compared with the cached base prediction. Statistical analysis confirms significant improvements in Dice, Boundary Dice, and HD95. Qualitative results show that the learned gate concentrates around uncertain cytoplasm and nucleus boundaries, and correction maps confirm localized boundary refinement. Although calibration does not automatically improve after refinement, the proposed framework provides an interpretable and reliability-focused strategy for boundary-sensitive biomedical image segmentation.

Abstract: Brain age estimation has become a popular research proxy for assessing brain health and disease, yet longitudinal trajectories of brain ageing are still poorly defined, and clinical use is limited. Building on existing Siamese longitudinal frameworks, we develop Brain-Predicted Age Acceleration (Brain-PACE) to directly estimate the pace of structural brain ageing from paired T1-weighted MRI. Brain-PACE identified accelerated ageing in $42.6$% of participants with mild cognitive impairment. Faster Brain-PACE was associated with greater functional and cognitive impairment (FAQ; $r=0.35$, ADAS13; $r=0.30$, CDR-SB; $r=0.32$) and greater regional tau burden in the posterior cingulate ($r=0.59$), precuneus ($r=0.47$), and entorhinal cortex ($r=0.37$). These associations were stronger than those observed when pace was calculated indirectly from repeated cross-sectional brain age estimates, suggesting that direct longitudinal modelling captures complementary information relevant to ongoing pathological change. Methodologically, Brain-PACE extends the LILAC framework by combining spatial attention with soft label distribution learning and a Cramér distance objective, improving probabilistic performance and reducing prediction bias while providing measures of predictive uncertainty. Together, these findings support Brain-PACE as a complementary longitudinal imaging phenotype with sensitivity to relevant clinical and biological changes in early neurodegeneration.

Abstract: Wireless Capsule Endoscopy (WCE) enables non-invasive visualization of the gastrointestinal tract, but its miniaturized optics, sensor limitations, and wireless transmission constraints result in low-resolution images with reduced visibility of diagnostically important structures. This paper proposes CEM-TUDASR, a computationally efficient unsupervised Transformer-based super-resolution framework for WCE image enhancement without paired low-resolution (LR) and high-resolution (HR) training data. A domain-adaptive degradation network synthesizes realistic WCE-like LR images from HR conventional endoscopy images, reducing the domain gap and enabling effective unpaired learning. The SR generator integrates Deep Attention Blocks (DABs) and a Fusion Attention Block (FAB) to capture long-range contextual dependencies and fine local structures while preserving perceptual and structural fidelity. The model is trained on a curated dataset derived from Kvasir Capsule and evaluated on KID and GIANA for cross-dataset generalization. No-reference quality metrics, including BRISQUE, PIQE, NIQE, and the domain-specific EndoQM, show that CEM-TUDASR consistently outperforms existing unsupervised SR methods. Qualitative results further demonstrate improved restoration of mucosal textures, vascular patterns, and clinically relevant anatomical details. Cross-domain experiments on retinal images additionally demonstrate the adaptability of the framework. With only 2.67 million parameters and 169.94 GFLOPs, CEM-TUDASR achieves high-quality reconstruction while maintaining computational efficiency, making it suitable for resource-constrained clinical and embedded endoscopic applications.