medical imaging developers

Abstract: Robust medical image segmentation across imaging modalities is challenging because of large differences in appearance and intensity distributions. Models trained on a single modality often show substantial performance drops when applied to unseen domains. In this work, we develop a unified 3D pancreas segmentation framework that applies domain-adversarial learning to 4,604 heterogeneous CT and MRI scans to learn anatomical representations. A shared nnU-Net encoder-decoder is trained for whole-pancreas segmentation, with a latent domain discriminator encouraging CT-MRI feature alignment. The learned encoder is subsequently transferred to pancreatic head-body-tail segmentation using limited MRI-only subregion annotations. An average Dice score of 87.31% on the in-distribution test set and Dice scores ranging from 84.20% to 88.09% across external OOD datasets were achieved in whole pancreas segmentation. Dice scores of 80.53% on MRI and 83.05% on CT were achieved for downstream subregion segmentation, without using CT subregion annotations. These results demonstrate that a unified anatomical representation can support both cross-modality pancreas segmentation and label-efficient downstream transfer.

Abstract: High-frequency ultrasound (HFUS) enables noninvasive visualization of superficial skin structures, but automated skin-layer analysis is limited by the scarcity of densely annotated data. Existing real HFUS datasets commonly provide annotations for superficial targets such as the epidermis and subepidermal low-echogenic band (SLEB), while dense labels for deeper structures such as dermis, subcutaneous tissue, fascia, and muscle are rarely available. We propose a physics-guided synthetic HFUS generation framework for skin layer segmentation. The framework constructs multilayer acoustic skin phantoms, assigns layer dependent acoustic properties, and uses k-Wave simulation to generate paired synthetic HFUS images, dense layer masks, and simulation metadata. To evaluate whether the generated data provide transferable supervision, we use it for downstream segmentation pretraining and fine-tune the models on real Mendeley HFUS data. Synthetic pretraining followed by real fine-tuning achieved real-domain performance comparable to real-only training and improved mean Dice/IoU in three of four evaluated trainable architectures. These results suggest that physics-guided synthetic HFUS images contain transferable anatomical and textural cues for real-domain skin layer segmentation, although further reduction of the synthetic-real appearance gap is needed to enable greater gains. The code and data are available at: https://github.com/Finn-02/synthetic-hfus-skin-layer-segmentation.

Abstract: Accurate identification of end-diastole (ED) and end-systole (ES) in echocardiography underpins the quantification of ventricular function, yet manual selection of these key frames is subjective and introduces clinically significant inter-operator variability. Recent self-supervised methods either prescribe strict periodic trajectories or learn an unconstrained low-dimensional motion subspace from reconstruction or registration objectives. The former offers interpretability but imposes restrictive assumptions on temporal progression, whereas the latter leaves cardiac phase implicit and ED/ES must be recovered through post-hoc geometric processing of the learned trajectory. We translate the physiological observation that cardiac phase is a one-dimensional signal into a prior by constraining the latent motion component to a single-parameter latent orbit, i.e., a global linear trajectory in latent space indexed by a bounded scalar phase variable. Mapping this variable through a sinusoidal nonlinearity yields an oscillatory motion signal with consistent temporal ordering, enabling direct identification of ED and ES from the learned phase signal. This inductive bias allows the model to capture an interpretable representation of the cardiac cycle, while maintaining flexibility to capture irregular heartbeats. Trained on EchoNet-Dynamic without annotations, our minimal single-parameter cardiac phase model learns an effective latent orbit, significantly improves upon the previous state of the art in ED localisation and matches it in ES localisation while using a more constrained representation and fewer training epochs. This demonstrates that a principled physiological inductive bias can match or exceed the performance of more complex representations. Code is available at: https://github.com/BonniciJ/OrbitalEcho/

Abstract: Three-dimensional ultrasound (US) is a safe, radiation-free complementary modality to CT and X-rays for longitudinal monitoring, yet its segmentation-derived partial point clouds are extremely artifact-laden. Consequently, it is challenging to recover a clean and complete anatomical structure from such US point clouds. In this paper, we present UBone3D, a novel framework based on physics-rectified conditional flow matching (CFM) that performs point cloud completion directly from partial US observations. UBone3D models deterministic physics artifacts (e.g., surface thickening, streaking, dropouts) via a simulated physics proxy, and introduces test-time physics rectification to steer the shape completion. At inference, the completion is jointly steered by two decoupled forces: (1) anatomical plausibility enforced by a CT-trained generative shape prior, BoneFM, and (2) physics consistency enforced by USimNet in the ultrasound formation space. Extensive experiments on simulated and in-vivo data demonstrate significant improvements in reconstruction accuracy and anatomical fidelity over existing baselines.

Abstract: Segmenting bruises is a challenging task in medical imaging due to limited data and annotations, diffuse boundaries, and highly variable appearance. In this work, we propose BruNet, a segmentation framework that combines a ViT-based visual encoder (a self-supervised DINOv3 or a pretrained LingBot-Vision backbone) with a SAM-based mask decoder. BruNet is trained on the HAM10000 skin lesion dataset and evaluated on a separate bruise dataset without additional fine-tuning. Although a small number of prior studies have explored machine learning and computer vision for bruise analysis, existing work has primarily focused on detection, classification, or colour analysis rather than pixel-level localisation. To the best of our knowledge, this is the first study to address automatic bruise segmentation. Our results show that BruNet outperforms CNN-based models, state-of-the-art segmentation models, ChatGPT-4o/5-assisted SAM2 zero-shot baselines, and the medical-oriented MedSAM model, demonstrating strong cross-domain generalisation to bruise segmentation.

Abstract: Uncertainty estimation for medical vision--language models (VLMs) using conformal prediction has gained increasing attention due to its distribution-free coverage guarantees. However, standard conformal prediction relies on exchangeability between calibration and test data and typically requires a sufficiently large calibration set to obtain reliable coverage. These assumptions are difficult to satisfy in few-shot transfer settings, where only a small labeled support set is available to adapt a pretrained VLM to a new medical task, while an unlabeled query set is used for evaluation. Supervised fine-tuning on the support set changes the model parameters and consequently shifts the nonconformity score distribution, breaking exchangeability between calibration and query samples and leading to unreliable coverage under distribution shift. Existing transductive conformal adaptation methods often preserve validity by avoiding supervised updates. While this helps maintain conformal assumptions, it underutilizes the scarce labeled support data and limits task adaptation, which is the primary objective in few-shot learning. In this setting, conformal prediction should serve as an uncertainty estimation layer that supports the adapted model, rather than preventing adaptation itself. To this end, we propose AlignCP, a framework that reconciles supervised few-shot adaptation with conformal uncertainty estimation under non-exchangeability. AlignCP learns a reweighted calibration distribution that reduces the score-level discrepancy between the labeled support set and the unlabeled query set. By aligning the one-dimensional nonconformity score distributions, AlignCP aims to close the coverage gap induced by adaptation without requiring query labels.

Abstract: Trochlear dysplasia (TD) is an abnormality of the femoral trochlea associated with anterior knee pain and patellar instability. The sulcus angle (SA) is used to assess trochlear morphology, but it is typically measured on a single axial MR slice with no clear guidance on which to select, making it sensitive to slice selection and landmark placement. We propose an automatic framework for continuous SA profiling from super-resolved MR volumes. Clinically acquired axial, coronal, and sagittal MR scans are combined using implicit neural representations to reconstruct a high-resolution volume. SA measurements are computed across the trochlear region using two landmark detection U-Net models. The approach was evaluated on the public fastMRI dataset and a small in-house cohort of patients with TD. Compared with conventional manual single-slice SA measurements, the proposed automated method yielded a mean absolute error of 11.6$^\circ$ while providing continuous characterization of trochlear morphology. Population-level analysis demonstrated distinct mean SA profiles between the public cohort and the in-house TD cohort, highlighting the potential of profile-based assessment to characterize TD. By reducing reliance on a single manually selected axial slice, the proposed framework extends conventional SA assessment to a continuous profile-based description of trochlear morphology without additional imaging, while remaining conceptually linked to current clinical assessment. Further validation is required. The code is available: https://github.com/wehrlimi/SA_Profile.

Abstract: Out-of-distribution (OOD) detection is crucial for safe deployment of medical AI systems, where domain shifts arise across institutions, acquisition protocols, and patient populations. VLMs enable zero-shot OOD detection by embedding images into a language-aligned latent space, where cross-modal similarity serves as a non-parametric confidence signal for identifying in-distribution samples. Yet existing methods rely almost exclusively on final-layer embeddings, implicitly assuming that the deepest representations are universally optimal. We first show that this assumption does not hold in medical imaging: intermediate layers provide complementary OOD signals, and the optimal representational depth depends on the respective image modality. While prior work selects layer combinations via entropy minimization of normalized histograms, we demonstrate that single-resolution entropy estimation is highly sensitive to binning choices, leading to performance variations of up to 19.3% AUROC. To address this instability, we propose a multi-resolution entropy estimation strategy that aggregates histogram statistics across multiple discretization scales, enabling robust and stable intermediate-layer selection. Across two medical OOD benchmarks, namely MIDOG and OASIS, covering distinct imaging modalities, diverse shift types, and different VLM backbones, our method consistently outperforms state-of-the-art approaches, offering a lightweight and stable solution for zero-shot OOD detection.

Abstract: Because dense frame-level annotation of colonoscopy videos is costly, we propose WSPolypNet, a weakly supervised framework for polyp localization using only video-level labels. WSPolypNet employs a 3D convolutional neural network trained with video-level supervision to generate class activation maps (CAMs), which identify candidate polyp regions without requiring frame-level spatial annotations. The CAM-derived localization cues are further enhanced using a multi-view strategy and provided to MedSAM2 as point prompts. MedSAM2 then propagates segmentation masks across the video, refining the coarse localization cues according to polyp boundaries. WSPolypNet achieved CorLoc scores of 47.80%, 43.68%, and 35.01% at IoU thresholds of 0.3, 0.5, and 0.7, respectively, compared with 36.87%, 33.72%, and 27.94% in the single-view setting. For small polyps, the multi-view strategy improved CorLoc@0.5 from 16.01% to 30.97%. The framework also achieved a recall of 94.51%. These results demonstrate the potential of weakly supervised spatiotemporal learning to substantially reduce spatial annotation requirements for polyp localization in colonoscopy videos.

Abstract: Deep learning has achieved state-of-the-art performance in echocardiographic video segmentation, with an increasing number of models incorporating temporal information. However, quantitative evaluation of temporal explainability remains largely unexplored. We propose a quantitative framework for evaluating Grad-CAM explanations using four complementary metrics measuring temporal consistency, saliency motion, anatomical overlap, and temporal overlap. Using EchoNet-Dynamic, we compare a baseline 2D U-Net with ConvLSTM U-Net models trained across multiple temporal strides. While segmentation performance remained comparable across all models, intermediate ConvLSTM explanations exhibited substantially lower saliency consistency and greater centroid motion than final prediction explanations. Temporal Bottleneck explanations were significantly more stable than Encoder Bottleneck explanations across all strides, while final ConvLSTM Decoder3 explanations were broadly comparable to those of the 2D U-Net. Importantly, conventional frame-wise explanation metrics cannot determine whether variation in intermediate explanations reflects meaningful temporal feature evolution or explanation instability. These findings establish a preliminary quantitative framework for temporal explainability and motivate temporal-aware XAI methods that explicitly account for evolving representations in medical video models.

Abstract: Segmentation of complex structures in X-ray tomographic data is a fundamental task in biomedical research, but it often requires large amounts of precisely annotated data, making fully supervised approaches costly and difficult to scale. In this study, weakly supervised deep learning is investigated as a strategy to reduce annotation effort while maintaining accurate segmentation. A two-dimensional convolutional neural network based on the nnU-Net framework was adapted to a weak supervision setting using sparse dot-based annotations, complemented by a limited number of fully segmented images. The approach was evaluated on high-resolution microCT slices of rat kidneys, targeting the segmentation of renal glomeruli, which are small, low-contrast anatomical structures. Results indicate that weak supervision provides a meaningful learning signal, enabling reliable localization of glomeruli even in the absence of dense labels. Incorporating a small set of high-quality annotations substantially improves segmentation performance, approaching that of a fully supervised model. These findings highlight the potential of weakly supervised learning as an annotation-efficient strategy for the analysis of complex structures in X-ray tomographic data, and suggest that alternative loss formulations tailored to sparse annotations may further enhance performance.

Abstract: Basal Cell Carcinoma (BCC) is the most common type of skin cancer, accounting for nearly 80% of skin cancer di- agnoses. Its optimal clinical management is guided by the distinct histopathologic subtype, with aggressive variants requiring more drastic measures. In current clinical practice, subtyping relies on skin biopsies, a procedure both costly and invasive. In this paper, we conduct a preliminary investigation into using deep learning for BCC subtyping, solely from a single dermatoscopic image of the lesion. Given the limited data at our disposal, we employ pre-trained vision transformers (ViTs), a state-of-the-art family of models highly effective for challenging downstream tasks with limited labeled data. Through repeated stratified k-fold cross-validation, we demonstrate that ViTs can achieve superior performance (AUC 0.784 on a dataset of 1271 dermatoscopic images of various BCC subtypes) over standard CNN-based baselines as well as previously-reported human reader perfor- mance, on the task of differentiating aggressive BCCs from other subtype families. These initial findings highlight the potential of combining deep learning and dermatoscopy to provide a biopsy- free alternative for BCC subtyping, thus aiding in improving treatment planning and patient outcomes.