medical imaging software developers

Abstract: Healthcare institutions routinely accumulate high-dimensional computed tomography (CT) volumes, but only a fraction can be annotated by experts. We present L2GSSL, a local-to-global self-supervised learning framework that leverages unlabeled volumes by decomposing pretraining into intra-slice and inter-slice representation spaces. A slice encoder learns view-invariant local features, and a global encoder aggregates the resulting tokens to model volumetric context. The stop-gradient isolates the local space from the global objective, while slice-wise execution and a three-phase schedule support training under constrained GPU memory. On LIDC-IDRI lung nodule malignancy classification, L2GSSL reaches $0.9229$ AUROC with only $10\%$ of the labels and $0.9377$ with $25\%$, exceeding the volume-level VICReg by $0.0229$ and $0.0294$, respectively. With all labels, the strongest supervised baseline exceeds L2GSSL by only $0.0044$ AUROC, consistent with self-supervised pretraining providing its greatest value when annotations are limited. Without adaptation to the external LNDb cohort, a model fine-tuned on $25\%$ of LIDC-IDRI obtains $0.8138$ AUROC and $0.7589$ AUPRC, improving over the strongest evaluated self-supervised baseline by $0.1130$ and $0.0954$. Experiments across data sources, thoracic and abdominal anatomy, downstream tasks, and two backbones examine healthcare-data variety, while lesion-slice masking shows that the predictions depend on lesion-bearing content.

Abstract: Dynamic endoscopic reconstruction is fundamental to robotic surgery and computer-assisted interventions. While 3D Gaussian Splatting (3DGS) realises real-time rendering, its application to deformable intraoperative environments remains constrained by spurious geometry and varying illuminations. To address these limitations, we introduce EndoPrior-GS, a novel pipeline that explicitly couples frame-extracted vision heuristics and estimated depth maps. EndoPrior-GS derives a joint texture prior from a tool-filtered valid tissue mask, a non-specular photometric filter, and anatomical structural salience, yielding a probability map that guides primitive initialisation and subsequent density control. The prior is further extended to the temporal domain through a texture-aware term that dynamically weighs pairwise primitive contributions during training. We conduct extensive experiments on benchmark datasets EndoNeRF and SCARED, and the obtained results show that our method EndoPrior-GS reduces Flow Error by 27.7% and 25.8% over the representative approaches while preserving competitive rendering quality and real-time rendering speed. Our project website is available at https://jiaqi-huang-77.github.io/EndoPrior-GS/.

Abstract: Quantitative characterization of lymph node morphology is important for assessing axillary lymph node metastasis in breast cancer. However, surfaces reconstructed from computed tomography (CT) segmentation may contain geometric and topological defects that compromise subsequent analysis, while conventional shape descriptors predominantly characterize global morphology. To address these issues, we developed an integrated framework combining topology-aware surface processing with multi-resolution spherical harmonic (SH) analysis of CT-derived axillary lymph nodes. The processing pipeline produced topology-valid genus-0 surfaces with improved mesh quality, which were then represented at multiple SH degrees and characterized using 20 predefined geometric feature families. Geometric fidelity increased with SH degree, whereas predictive performance peaked at intermediate resolutions. Preferred SH degree also differed across feature families. A family-specific mixed-resolution model achieved an AUC of 0.918, compared with 0.884 for the conventional PyRadiomics Shape14 baseline, corresponding to an improvement of 0.0344. Controlled perturbation experiments showed that higher SH degrees transmitted more fine-scale geometric variation and yielded lower stability of curvature-based predictions. Representative geometric descriptors provided interpretable characterization of metastasis-associated surface morphology. Independent validation further supported the framework's transportability: label-free replication in a multicenter lymph node cohort reproduced the family-specific resolution effects, while a labeled LIDC-IDRI lung-nodule experiment reproduced the resolution-dependent relationship between SH degree and predictive performance. Altogether, the framework provides a topology-valid basis for quantitative characterization of lymph node morphology and metastasis-associated imaging phenotypes.

Abstract: Nuclei instance segmentation is a core task in digital pathology, yet high-accuracy models rely on large vision transformer (ViT) encoders whose inference speed cannot meet real-time clinical demands. We propose a lightweight scheme that distills the UNI2-h pathology foundation model into a ConvNeXt-Tiny student (Ours-T, 34.7M parameters, 1/20 of the teacher) via output-level knowledge distillation. Ours-T achieves an mPQ of 0.519 on PanNuke (98.8% of the teacher), a zero-shot bPQ of 0.668 on MoNuSeg, and an inference speed of 634.3 img/s, requiring only 0.045 s for full-resolution 1024^2 analysis (21.8x speedup). Experiments further show that multi-scale gated convolution (MALA) yields no gain under ViT encoders, and output-level distillation alone suffices for efficient knowledge transfer.

Abstract: Cross-site out-of-distribution (OOD) generalization in resting-state functional magnetic resonance imaging (rs-fMRI) often relies on learning task-discriminative representations from full-scan functional connectivity (FC) graphs and promoting invariance across source sites. However, FC graphs are estimated from finite, temporally correlated blood-oxygen-level-dependent (BOLD) sequences. Cross-site agreement therefore does not necessarily imply that predictive evidence remains supported under FC re-estimation within the same scan. In this paper, we propose Brain Network Re-estimation-Informed OOD Learning (BRIO), a framework that uses within-scan FC re-estimation to guide cross-site alignment. BRIO maps fullscan graphs and their re-estimates into consistently indexed connectome factors, enabling comparisons of their predictive contributions. It assesses re-estimation support from changes in these contributions relative to within-class subject variability and class separation. For each source-site pair and class, this task-calibrated support from both sites is combined with predictive relevance to form pairwise qualifications, which determine relative factor weights and overall alignment strength. Leave-one-site-out experiments on four real-world datasets (ABIDE, REST-metaMDD, SRPBS, and ABCD) show that BRIO consistently outperforms competitive baselines, with relative improvements of up to 3.8% in accuracy. These gains also persist under an alternative brain parcellation on ABIDE.

Abstract: Existing text-guided segmentation models in the medical domain cover only a narrow set of anatomical structures and lesions in chest X-rays (CXRs), and most of them assume that the queried target is always present in the image. Instruction-guided lesion segmentation (ILS) was introduced to overcome these limitations by segmenting diverse lesion types from simple user instructions while also recognizing when the queried lesion is absent, and ROSALIA was proposed as the first model for this task. However, the masks produced by ROSALIA remain of limited quality, often carrying scattered noise. Moreover, ROSALIA predicts the mask in a single shot, which differs fundamentally from how radiologists perceive and delineate lesions in practice. A radiologist first surveys the entire thorax, then localizes the approximate region of abnormality, and only then refines the lesion contour. Motivated by this coarse-to-fine, multi-level perception process, we present XFlow, a workflow model for ILS that combines box-based localization with multi-turn point refinement. XFlow detects the lungs, decides whether the queried finding is present in each of them, and prompts a fine-tuned SAM with the lesion box for an initial mask. It then corrects that mask through point prompts until its boundary follows the lesion, leaving every intermediate decision visible. Our experiments show that XFlow achieves the best segmentation quality on both internal and external evaluation. Notably, it surpasses ROSALIA in segmentation quality even when the two are trained on the same lesion annotations. Code and model weights will be made publicly available.

Abstract: Medical vision-language pre-training largely follows a visit-level image-report matching paradigm, aligning paired images and reports at individual visits. While effective for static cross-modal correspondence, this paradigm provides limited supervision for longitudinal clinical change, such as whether abnormalities improve, remain stable, or worsen over time. Learning such change is challenging because temporal semantics are implicit in free-text reports, and different abnormalities within the same patient may evolve asynchronously or even in opposite directions. We propose MedCTA, which reframes medical vision-language pre-training from visit-level cross-modal matching to learning clinical change. Rather than compressing a patient history into a single temporal representation, MedCTA models clinical change at two complementary scopes. At the abnormality scope, clinically grounded queries construct abnormality-conditioned visual and textual trajectories to capture heterogeneous abnormality evolution. At the patient-course scope, global image and report sequences are modeled to capture overall clinical progression beyond any individual abnormality. Structured trend supervision is extracted from longitudinal reports by an offline LLM parser, removing the need for manual temporal annotations. Combined with static image-report alignment, MedCTA learns representations that preserve visit-level cross-modal correspondence while encoding longitudinal change semantics. Experiments on temporal image classification, image-text retrieval, and zero-shot classification show consistent gains over strong medical vision-language baselines.

Abstract: Dynamic contrast-enhanced breast MRI (DCE-MRI) is rich in anatomical and perfusion information, but its reliance on gadolinium-based contrast agents raises safety concerns and adds cost. Virtual contrast enhancement, synthesizing post-contrast from pre-contrast images, is a promising alternative. We address the MAMA-SYNTH challenge task of predicting peak-enhancement breast MRI. Rather than adopting the full machinery of diffusion or flow matching, we observe that under a rectified, straight-line path the generative process collapses to a single difference prediction: the synthetic peak image is the pre-contrast image plus a predicted enhancement map, recovered in one forward pass. Around this we build Anguinus Sculpturae, a compositional pipeline in which nnU-Net segmentations of lesion, foreground and breast region guide two generators - one optimized for global fidelity, one for lesion structure through an asymmetric Tversky term routed via a frozen segmenter - composited region-wise with Gaussian-weighted blending. On the held-out Duke subset of MAMA-MIA our model achieves the best FRD and Dice among all evaluated variants, showing that single-step difference prediction with segmentation guidance suffices to recover both global fidelity and lesion structure. Code is available at https://github.com/MIC-DKFZ/AnguinusSculpturae.

Abstract: Accurate classification of anterior segment diseases is crucial for ophthalmic screening and diagnosis. However, slit-lamp image analysis remains challenging due to substantial variability in imaging conditions and the intrinsic anatomical-disease hierarchy of ocular pathologies. Existing methods typically formulate this task as a flat multi-class classification problem, ignoring the structured dependency between anatomical regions (e.g., cornea, conjunctiva, and lens) and disease manifestations.To address these limitations, we propose CFCH, a Coarse-Fine Collaborative Hierarchical learning framework that explicitly models anatomical context and disease semantics through a dual-branch architecture. To enable effective cross-granularity collaboration, CFCH introduces semantic and cross-granularity attention consistency constraints, encouraging aligned yet complementary feature learning across branches. In addition, we construct AS-9K, a large-scale anterior segment dataset with 8975 images covering 12 common disease categories. To the best of our knowledge, AS-9K is the largest publicly available dataset for anterior segment image classification. Extensive experiments on two anterior segment datasets demonstrate that CFCH outperforms state-of-the-art methods. Qualitative visualizations further show more focused and lesion-relevant activation responses, validating the effectiveness of the proposed framework. Code will be available at https://github.com/ybupengwang/CFCH.

Abstract: Background: Large volumes of unlabeled knee MRI scans are available across repositories but remain insufficiently leveraged. We developed KneePreM, a knee-specific 3D self-supervised model, and evaluated transfer and label efficiency for classification and segmentation. Methods: A 3D U-Net masked autoencoder was pretrained on 19,011 unlabeled Osteoarthritis Initiative (OAI) MRI series from 4,791 participants. Downstream fine-tuning used full and reduced training sets for fastMRI+ two-label classification (1,172 examinations), Arthroscopic Partial Meniscectomy (APM) eight-target classification (1,716 examinations), SKM-TEA segmentation (155 examinations), and APM segmentation (25 examinations). Baselines were random initialization and SuPreM. Deployment workflow was implemented with a Model Context Protocol interface. Evaluation metrics included balanced accuracy, F1 score, ROC AUC, PR AUC, and Dice score. Statistical analysis used bootstrap confidence intervals and paired bootstrap tests for classification and Wilcoxon signed-rank tests for segmentation. Results: KneePreM achieved higher full-data macro ROC AUC than both baselines for fastMRI+ and APM (all p < .001). For fastMRI+ classification, KneePreM achieved a ROC AUC of 0.722 using 50% of the training data, exceeding both full-data baselines. In APM classification, KneePreM reached a ROC AUC of 0.740 with 70% of the data, matching the full-data random baseline and outperforming SuPreM. For SKM-TEA segmentation, its 70%-data Dice of 0.838 exceeded the full-data random baseline (0.835) and both same-budget comparators. In APM segmentation, its 75%-data Dice of 0.746 exceeded the full-data random baseline (0.731) and both same-budget comparators. Conclusion: KneePreM improves transfer performance and label efficiency across knee MRI classification and segmentation tasks, particularly when labeled training data are limited.

Abstract: Congenital heart disease (CHD) is the most common birth defect, yet a large fraction of cases remain undetected on prenatal ultrasound, in part because current artificial-intelligence methods assume that the key diagnostic frames have already been isolated from a study, by a clinician or by a view classifier. We remove that assumption and address CHD screening directly at the level of the whole ultrasound study. We propose a two-stage framework that first learns transferable frame representations by self-supervised masked-autoencoder pre-training on unlabeled fetal ultrasound, then identifies cardiac frames with a disease-robust module and aggregates them with a transformer-based multiple instance learning (MIL) model that produces a case-level diagnosis from study-level labels alone. The model further returns its highest-scoring frames for clinician review, and a hierarchical head separates critical from non-critical CHD. On the internal test set of our multi-source development cohort (FUSE), the proposed cardiac-gated MIL model reaches an area under the curve (AUC) of 0.985 with a specificity of 0.990, outperforming the reproduced NATMED ensemble (AUC 0.861, specificity 0.600) and the FetalCLIP foundation model (AUC 0.867, specificity 0.710). On an independent external cohort, all models initially perform near chance, but label-free CORAL adaptation raises the proposed model from an AUC of 0.513 to 0.944, whereas whole-study and view-dependent baselines do not recover. These results indicate that whole-study MIL with disease-robust cardiac-frame identification is an accurate and deployable route to prenatal CHD screening.

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: A key challenge in medical image analysis is the scarcity of large annotated datasets for specific populations and diseases. As deep learning models rely heavily on labeled data, effective transfer learning strategies are needed to reduce the dependence on manual annotations. Self-supervised learning has emerged as a promising approach for developing foundation models by enabling the learning of transferable feature representations from large-scale unlabeled medical imaging datasets. In this study, we investigate voxel-level brain age prediction as a domain-specific self-supervised pretext task and compare it with image inpainting, a widely used non-domain-specific alternative. We further propose a multitask self-supervised pretraining framework that jointly optimizes both objectives to learn complementary neuroimaging representations. The pretrained models are evaluated on three downstream magnetic resonance image segmentation tasks: multiple sclerosis lesion segmentation, ischemic stroke lesion segmentation, and cortical brain structure segmentation. Overall, the proposed multitask pretraining framework consistently outperformed the single-task pretrained models and training from scratch across most experimental settings, demonstrating the benefit of combining domain-specific and general self-supervised learning pretext tasks for the development of generalizable neuroimaging foundation models.\ Code Availability: The source code used in this study is publicly available at https://github.com/TasneemN/Combining-General-and-Domain-Specific-Pretext-Tasks-for-Brain-MR-Image-Segmentation/

Abstract: Dermoscopy classifiers built on Vision Transformers process all image patches uniformly, although diagnostic evidence is concentrated in the lesion region. Existing token pruning methods reduce tokens using generic saliency or similarity signals, but rarely ask whether the retained subset still contains the lesion. This paper introduces MedTokenBudget, a supervised post-backbone token routing framework that learns to construct compact lesion-enriched representations when auxiliary lesion masks are available. Its Lesion-Aware Token Scoring (LATS) module fuses attention entropy, feature norm, and local feature contrast through a learned scorer, then routes the top-$K$ patches under a target budget. LATS is trained with budget curriculum learning, diversity regularization, attention distillation, and lesion-mask supervision. The trained router is evaluated with a lesion retention rate that directly measures how much ground-truth lesion evidence survives the token budget. On ISIC 2019, mask-supervised LATS consistently outperforms Random and ToMe at headline budgets while retaining substantially more lesion patches. Code is provided for reproducibility, and complete tabulated results are included in the supplementary material.

Abstract: Common segmentation losses aggregate errors voxel-wise, so lesions influence the objective in proportion to their volume, giving small but clinically critical lesions disproportionately little weight. Instance-aware losses aim to address this mismatch by assigning each lesion its own term. However, blob loss and CC-DiceCE derive their regions solely from annotations, so false-positive components receive no instance-level term. This matters in computer-assisted review, where each false-positive component may require separate inspection, making precision and false-positive burden important alongside recall. We introduce the bidirectional connected-component loss (BiCC), which pairs annotation- and prediction-derived partitions to score predicted components on their own scale. By deriving instances from the predictions, this branch directly penalizes false-positive components regardless of their size. The balance parameter $α$ allows control over the lesion-wise precision-recall trade-off. Across five datasets with five-fold cross-validation using nnU-Net, BiCC outperforms CC-DiceCE in lesion-wise F1 on four datasets and blob loss on all five. It significantly improves over DiceCE on three datasets and matches it on two; CC-DiceCE instead loses up to 0.363 precision by favoring recall. Code is available at https://github.com/TIO-IKIM/BiCC-Loss.

Abstract: Dense vessel annotation in digital subtraction angiography (DSA) is labor-intensive, yet every unlabeled sequence records how contrast passes through the vessels. Semi-supervised methods take their targets from the current model, and generic self-supervised pretexts reconstruct static appearance, so this signal goes unused. We propose ConPro, a self-supervised pretraining scheme whose target is a contrast projection, the normalized drop of every pixel below its temporal median over the sequence. On DIAS and DSCA, with 10%, 20% and 50% of the training cases labeled, ConPro improves on training from scratch at every label fraction and is the best of the compared methods on DSCA at 20% and 50% labels. Controlled comparisons show that the gain comes from the target. A temporal-median target with the same input, loss and budget stays at scratch level, and using the projection directly instead of learning it, as an input channel or a pseudo-label, helps little or hurts. ConPro provides pretrained weights without changing the segmentation architecture, so it combines with semi-supervised training, and UniMatch, the strongest baseline, gains 0.5 to 2.0 Dice and 0.9 to 2.3 clDice at every label fraction when started from ConPro weights, reaching 75.4 Dice on DIAS and 81.3 on DSCA.

Abstract: Resting-state functional connectivity (FC) is widely used to classify brain phenotypes and disorders. Most pipelines use the full connectome and seek gains through model design. We instead examine how FC geometry constrains classification and cross-site transfer. Across-subject FC variation concentrates in a small effective subspace, suggesting substantial redundancy in nominal dimensions. Across cohorts, these subspaces may differ in orientation even when their effective ranks are comparable, potentially limiting transfer. Across 2,330 subjects from HCP, ABIDE, and ADHD-200, effective-rank analysis reveals strong spectral concentration. Projection onto leading components at the effective-rank scale recovers most of the full-FC classification performance. In ABIDE, site-specific effective subspaces are weakly aligned, and their principal-angle overlap predicts pairwise transfer after covariate adjustment despite comparable per-site effective ranks. Controlled rotations that alter subspace orientation while preserving the mean and covariance spectrum drive transfer toward chance, whereas displacement-matched label-orthogonal rotations do not. These results identify subspace orientation as a key factor in transfer degradation under controlled perturbations. This study offers a geometric diagnostic of FC generalization and suggests evaluating cross-site harmonization by its ability to align effective subspaces alongside classification accuracy.

Abstract: Conventional image registration algorithms are robust to domain shifts and achieve low errors, but they are slow and computationally expensive. Deep-learning methods are efficient at inference-time, but face challenges in out-of-domain samples. We propose Recursive Uncertainty-Gated Image Registration (RUGI), an algorithm for iteratively refining deformation fields predicted by learning-based registration models. At each iteration, the registration model predicts an incremental deformation, and a gating map modulates the update. Refinements are hence concentrated in regions that remain difficult to register. We explore two gating strategies: a learned uncertainty-based approach and an image residual error approach. We evaluate RUGI on cardiac MRI and echocardiography datasets and show consistent improvements over single-step inference. Ablation experiments demonstrate that iterative refinement alone improves registration, but informative spatial gating provides a significant additional benefit. The error-gated variant of RUGI can also be applied directly to existing pretrained models; applied to VoxelMorph, TransMorph, and CycleMorph, it yields MSE reductions of 27-37% with no modification to the original training procedure. The improvements in registration performance are reflected in decreased errors in ejection fraction estimation relative to ground truths. These results demonstrate that spatially selective iterative refinement provides an effective strategy to improve registration accuracy at inference-time.

Abstract: Automated assessment of the Critical View of Safety (CVS) in laparoscopic cholecystectomy requires both recognition of the three CVS criteria and anatomical grounding in small, rare, and often occluded hepatocystic structures. Learning-based methods differ in the anatomical information they use, from image-level classification to detection, segmentation, or graph-based reasoning, yet grounding the safety-critical anatomy remains the main bottleneck. We propose CasCVS-Net, a staged multi-task cascade that jointly performs object detection, semantic segmentation, and CVS assessment, trained on the Endoscapes dataset. The model couples the tasks through predicted anatomy: predicted boxes guide segmentation, and predicted masks provide region-level features for CVS classification, so CVS assessment at inference uses only model predictions rather than ground-truth annotations. To reduce optimisation instability in this coupled setting, training progresses from detection to detection-segmentation and then to the full three-task cascade, followed by task-wise fine-tuning. Evaluation on the public unseen test set shows that CasCVS-Net improves over matched single-task baselines on all three tasks, achieving 32.0 detection mAP, 46.8 semantic mIoU, 15.3 rare-anatomy mIoU, and 67.2 CVS mAP. It outperforms the state-of-the-art LG-CVS and SV2LSTG by 6.3% and 4.5% relative CVS mAP, respectively, corresponding to 4.0 and 2.9 mAP points. These results show that staged task coupling through predicted boxes and masks improves anatomical grounding for CVS assessment, particularly for rare hepatocystic structures.

Abstract: Objective assessment of robotic surgery uses instrument kinematics, which must be reconstructed when only video is available. We introduce a kinematic reconstruction network for estimating instrument position, orientation and jaw angle from monocular video. Our visual representation combines global attention pooling of frozen DINOv3 features with local pooling at instrument landmarks from fine-tuned SAM 3.1 masks. Our shared Transformer encoder and temporal convolutional heads integrate this representation with mask geometry, monocular depth and visual state estimates from arm-specific multilayer regression networks. Our position branch predicts displacement magnitude and direction separately to preserve traveled distance. We fit trajectories to predicted state observations and motion increments by differentiable weighted least squares, expressing quaternion observations relative to cumulative predicted rotations to obtain a quadratic orientation objective. We evaluate reconstruction across 2,802 Open-H episodes. Compared with LiveMAE on the main Open-H benchmark, our method reduces path-length mean absolute error from 0.45 to 0.34\,cm and increases temporal mean average precision for motion segmentation from 44.54\% to 54.44\%.

Abstract: We developed an anatomy-aware deep learning framework to synthesize post-contrast breast MRI from pre-contrast images, emphasizing tumor and background parenchymal enhancement (BPE) regions. This retrospective study included 649 patients with 6,251 paired pre-contrast and post-contrast images. The framework integrates breast mask consistency, lesion-region supervision, and BPE-region supervision into an image-to-image translation model. Evaluation included quantitative image quality metrics, a reader study with two breast radiologists, and downstream Ki-67 classification. The proposed method outperformed Pix2Pix, Pix2PixHD, diffusion-based synthesis, and mask-supervised baselines in whole-image and regional evaluations. Ki-67 classification showed no statistically significant performance differences across real- and synthetic-image training and testing settings, although this does not establish equivalence. These findings suggest that anatomy-aware supervision improves synthesis fidelity and support further investigation of synthetic post-contrast MRI for contrast-free imaging workflows.

Abstract: Radiomics provides quantitative descriptions of tumour appearance that may complement disease-specific foundation models in small labelled cohorts. We investigate this complementarity for computed tomography-based classification of clear cell renal cell carcinoma. Our framework uses radiomics to modulate RenalCLIP features through feature-wise linear modulation (FiLM), while retaining a direct radiomics contribution. Internal testing and external validation compare it with conventional fusion strategies and reference classifiers. The FiLM model achieves an area under the receiver operating characteristic curve (AUC) of 0.804 internally and 0.854 externally, with the highest mean AUC among the evaluated RenalCLIP fusion strategies in both cohorts. Pathway ablations examine the contributions of conditional modulation and the direct radiomics residual, while feature permutation highlights the role of tumour texture. These findings support radiomics as a useful complement to RenalCLIP in a small labelled cohort and identify FiLM as an effective approach to integrating their representations for robust renal tumour classification.

Abstract: Recent advances in Artificial Intelligence (AI)-powered Computer-Aided Diagnosis (CAD) systems have substantially improved breast cancer screening, diagnosis, and prognosis. Comparatively, postradiotherapy outcome prediction using paired longitudinal mammograms has received considerably less attention. This is largely due to the limited availability of well-annotated longitudinal datasets. Longitudinal mammograms, coupled with paired pre- and post-treatment information, provide a unique opportunity to characterize treatment-induced breast tissue changes following radiotherapy. The resulting learned representations can serve as a valuable asset for advancing personalized radiotherapy planning and post-treatment management. In this context, we propose Mammo-LIFE, a patient-level multimodal framework for post-radiotherapy outcome prediction that combines longitudinal mammographic features with patient-level clinical variables. The imaging branch processes paired pre- and post-treatment mammograms acquired from the four standard views using a mammography-specific encoder adapted via Low-Rank Adaptation (LoRA). Within each view, preand post-treatment representations are explicitly compared through a longitudinal comparison module to capture treatment-related changes. The resulting view-level embeddings are then aggregated using learned view-attention pooling to form a unified patient-level mammographic representation. Selected clinical variables are subsequently combined with the image-derived prediction probability through a late-fusion strategy. To evaluate the effectiveness of combining paired longitudinal mammograms with clinical information, experiments were conducted on an in-house clinical cohort using patient-level stratified five-fold cross-validation.

Abstract: Medical image interpretation is high-volume and time-consuming, and while AI interpretation can reduce workload, fully autonomous deployment carries potential safety concerns and low specificity may in practice lead to increased clinician workload. Learning to Defer (L2D) addresses this by selectively routing cases between autonomous prediction and human experts by learning from input features and AI model and human performance. While theoretical guarantees have been proven for L2D, its performance has not been validated on real-world medical datasets with human reader annotations. We evaluate the predictor-rejector formulation of two-stage L2D, where the AI predictor model is fixed and separate from the trainable routing or rejector model, on Collab-CXR, a multilabel chest X-ray dataset with multiple human annotations per case. This is the first work to look at L2D in the context of real-world medical imaging data with human annotations. We further introduce a new setup, L2D with Guidance, where the decision space is extended to three choices: predict autonomously, defer to a human expert, or defer to a human expert and provide AI guidance. We compare multiple rejector architectures and loss functions, and different input feature availabilities. This is reproduced on two larger datasets, VinDr-CXR and CheXpert. Our results show that two-stage L2D with Guidance outperforms classic two-stage learning to defer, as well as human-alone, AI-alone and AI-guided human baselines. Notably, this performance is achieved with simpler loss functions compared to formally defined L2D surrogate loss functions in current literature.

Abstract: Interactive segmentation of 3D medical images supports quantitative analysis of anatomical structures and disease while allowing users to specify and refine their targets. Despite substantial progress by nnInteractive and VISTA3D, reliable segmentation across diverse clinical targets remains challenging, particularly for complex anatomical structures and the heterogeneous, long-tailed spectrum of pathology. We present SAMI3D-DW V1 (hereafter SAMI3D-DW), an interactive 3D segmentation model trained on Deepwise's large-scale proprietary medical image datasets. We evaluate the model under simulated user interactions on a CT/MR benchmark comprising 4,326 cases from 219 source datasets, spanning 107 anatomical and pathological categories, organized by a medical taxonomy and evaluated with a category-balanced DSC score. SAMI3D-DW achieves the highest category-macro Dice among evaluated methods in both interaction modes. With one point, it scores 0.5764 versus 0.5315 for nnInteractive, the strongest baseline, rising to 0.7771 versus 0.7494 with five points. With bounding-box initialization, the scores are 0.7130 versus 0.6530. After five corrective clicks, SAMI3D-DW reaches 0.8002 versus 0.7868, making it the only evaluated box-compatible model to exceed 0.80. For radiologists and clinicians, SAMI3D-DW enables segmentation of complex anatomical structures, including intracranial vessel trees on CT and MR angiography, with a few clicks. In a preliminary in-house comparison involving neurofibromatosis type 1 (NF1), SAMI3D-DW-assisted tumor annotation took minutes per case and approximately one-fifteenth of the time required for manual annotation, highlighting its potential to support volumetric treatment-response assessment.

Abstract: Accurately isolating disease-related features from confounding covariates (e.g., age, gender, site) and individual variations remains a fundamental challenge in medical image classification. Traditional regression-based approaches may ignore non-linear relations between image features and true covariates. To overcome this issue, we present a generalized Medical Imaging Disentanglement Learning (MedIDL) framework. MedIDL maps image features into three mutually orthogonal latent spaces through specialized disentanglement heads: a disease classification head guided by a supervised loss, a covariate-alignment head constrained by cross-subject similarity matching, and a Gaussian head absorbing individual variations. We evaluated our framework across 7 datasets encompassing diverse imaging modalities. MedIDL outperforms state-of-the-art supervised and self-supervised classification methods in accuracy across all datasets. Association analyses demonstrate that MedIDL successfully isolates target-specific latent representations. Gradient-based interpretability mappings localize pathognomonic patterns aligning with established clinical literature.

Abstract: Mitotic figure (MF) analysis supports tumor grading and prognostic assessment, but automated models remain sensitive to differences in tissue type and image acquisition. We present MiTHras, a task-specific pretraining framework that combines pseudo-label-guided image- and token-level contrastive learning with masked reconstruction. We construct TCGA-MF-Pseudo, a corpus of 1.8 million cell-centered images from 14 TCGA cohorts spanning 11 organ sites. Comprehensive evaluation on MF classification, detection, count-based survival prediction, and subtype classification demonstrates the efficacy of MiTHras. It achieves the highest mean F1 on all three MF classification benchmarks and both subtype benchmarks. MiTHras also outperforms general-purpose and pathology foundation encoders by a larger margin under frozen-encoder linear probing than under full fine-tuning. Although detection gains are modest due to a shared candidate-detection stage, ablations confirm that token-level supervision improves typical-versus-atypical classification and linear probing. These findings establish that MiTHras yields robust, transferable representations for automated mitotic activity assessment.

Abstract: Head-and-neck anatomy changes over a six-to-seven-week proton course, and the anatomy of a later week cannot be imaged when the plan is made. We present a digital-twin framework that forecasts a patient's treatment-day anatomy as an ensemble of predicted CTs with propagated contours and quantifies the uncertainty of the forecast contours. The twin is a library of previously treated patients with planning and weekly quality-assurance CTs (QACTs), made patient-specific by a two-step foundation-model deformable registration: a cross-patient field carries each library patient onto the current patient, and a longitudinal field, estimated in the current patient's frame, carries that patient's planning-to-QACT change onto the current patient's own planning CT. A library of 302 observations from 88 patients yields about 300 replicates per patient, each a deformation that occurred in a treated patient. The dispersion of the propagated contours, resolved by outward normal, is six-direction contour uncertainty in millimeters. This is uncertainty in the input to the forecast, which library patient the current patient follows, rather than in model parameters, and it is unchanged when the registration engine is exchanged. On ten patients with clinician contours on two QACTs, the library alone fixes the anisotropic shape of the uncertainty (4.5 to 6.2 mm); the first QACT narrows it by a factor of 3.2 to 3.6 without a contour being drawn; an approved contour improves the center but not the width. The estimate orders directions correctly but is not Gaussian-calibrated. A clinical target volume expansion is worked out as one application.

Abstract: Multimodal large language models (MLLMs) are increasingly explored as interfaces for scientific image analysis, where a visual question-answering (VQA) response may be paired with a spatial output that guides a downstream stage. A supervisor reads the language answer, while a downstream workflow such as segmentation or region review consumes the point-set output. We call this transition from inspecting the answer to relying on its point action the language-to-action hand-off. A silent failure occurs when the answer is correct while the paired action misses annotated objects needed downstream, so answer-based oversight clears a region whose action is unreliable. We introduce Spatial Action Review, a visual analytics dashboard for auditing this failure mode in electron microscopy (EM) mitochondria analysis. It links paired answer-action records through an answer-action ledger, a task-by-dataset risk map, and an image-region audit view, connecting aggregate patterns to image evidence while an adjustable action-reliability gate supports re-audit. The review ends in a human-AI hand-off, where a supervisor records whether the action is accepted, escalated, held under a stricter gate, or flagged for model revision. Across 541 image regions from an EM-adapted Qwen3-VL case-study run, point actions fail the gate in 54.4% of records with a correct VQA response, and 27.4% of all records are silent failures. A correct answer is associated with only a 5.8-percentage-point higher probability of a reliable action, with a bootstrap interval spanning zero; the point-biserial correlation between answer correctness and object coverage is 0.061. This weak coupling persists across five model conditions on 753 matched image regions. Spatial Action Review makes answer-action mismatches visible and ties them to image evidence and a recorded decision before MLLM outputs enter autonomous scientific workflows.

Abstract: Medical image interpretation is central to diagnosis and care, yet adapting general-purpose multimodal large language models (MLLMs) often requires resource-intensive domain-specific fine-tuning. Here we introduce representation-guided in-context learning (RG-ICL), a training-free inference framework that retrieves query-aligned demonstrations using frozen encoders, without task-specific parameter updates. Across eight datasets spanning histopathology, radiology and retinal fundoscopy, RG-ICL improved classification (mean gain 20 percentage points) and visual question answering (VQA) (mean gain 13 percentage points) over no-context and conventional ICL, approaching or exceeding training-based comparators. Which cases were retrieved mattered more than how many: 6 query-aligned cases outperformed up to 32 randomly selected ones, whereas fixed or random cases often reduced accuracy below baseline. For VQA, aligning reference cases with both image content and question intent produced further gains. These findings indicate that for medical image interpretation, curating which reference cases an MLLM sees is a practical alternative to retraining it.

Abstract: We consider a nonlinear model motivated by polychromatic computed tomography (CT). Here, $W$ distinct $d$-dimensional signals $x^*_1, \ldots, x^*_W \in \mathbb{R}^d$ must be recovered from $n$ measurements $(a_i, y_i)_{i = 1}^n$ that obey the nonlinear model $\mathbb{E}[y_i|a_i] = h(\langle a_i, x^*_1 \rangle, \ldots, \langle a_i, x^*_W \rangle)$, where $h: \mathbb{R}^W \to \mathbb{R}$ is a known nonlinearity that models a certain type of exponential attenuation law. Even when there is no noise in the measurements, the sample size $n$ (for any measurement ensemble $\{a_i\}_{i = 1}^n$) must exceed the number of unknowns $Wd$ to guarantee that the underlying signals are identifiable. We construct a measurement ensemble that ensures perfect signal recovery almost surely provided $n \geq Wd + W - 1$, thereby isolating the injectivity threshold up to an additive factor $W - 1$. We also study computational complexity of signal recovery in this model with a general measurement ensemble $\{a_i\}$. We show that if $W \geq 2$, then there is a measurement ensemble for which deciding whether there exist signals consistent with the measurements is NP-hard. In particular, this implies that polychromatic, multimaterial CT reconstruction is NP-hard in general. This finding stands in sharp contrast to the single-material setting, for which a polynomial-time algorithm can provably perform signal recovery for any measurement ensemble.

Abstract: Soma instance segmentation, i.e., identifying and delineating individual cell somas as distinct instances, is crucial for cellular analysis and connectomic reconstruction. Three-dimensional electron microscopy (3D EM) provides nanometer-scale resolution for capturing fine-grained soma morphology. However, dense instance-level manual annotation is prohibitively costly, limiting the scalability of fully supervised methods. To address this challenge, we propose SomaNet, a weakly supervised framework for 3D EM soma instance segmentation under partial annotation constraints. SomaNet adopts a teacher--student learning paradigm tailored to partial labels. The teacher is trained using partially annotated data to generate pseudo-labels, while the student jointly learns from the partial ground-truth annotations and the generated pseudo-labels, progressively recovering dense instance segmentations. To accurately delineate cell somas under limited supervision with varying instance counts, SomaNet incorporates affinity learning, which encourages high similarity within instances and low similarity across instance boundaries. Semantic-guided affinity decoding and 2D-to-3D reconstruction then produce volumetrically consistent 3D soma instances while preserving the large receptive fields of 2D backbones. The framework is architecture-flexible and supports diverse backbones, including vision transformers and foundation models, enabling direct transfer of pretrained visual representations to volumetric EM segmentation. Experiments on 3D EM brain datasets demonstrate that SomaNet achieves accurate and robust soma instance segmentation across regions with diverse soma morphologies under partial annotation. Code is available at https://github.com/mkhateri/SomaNet.

Abstract: Surgical instrument segmentation (SIS) plays a critical role in robotic assistance and surgical workflow analysis. However, most existing SIS methods formulate segmentation as a category-driven localization problem, limiting their ability to capture procedural context and task-dependent semantics in surgical workflows. We introduce Reasoning-Aware Surgical Instrument Segmentation (RA-SIS), a task formulation that frames segmentation as query-conditioned inference under surgical context. To benchmark this setting, we construct SurgRS, a surgical reasoning segmentation dataset consisting of 41,000 image-text pairs, which aligns instance-level masks with structured query-answer supervision to enable semantic grounding at the pixel level. Based on SurgRS, we propose Surgical Instrument Reasoning and Segmentation Assistant (SIRA), a multimodal framework that disentangles target-level and query-level semantics and integrates them with visual features through query-anchored dual alignment. By aligning query semantics with spatial features and segmentation prompts, SIRA enhances semantic-visual consistency in mask prediction. Extensive experiments on SurgRS demonstrate improvements over existing reasoning-aware baselines. Code is available at https://github.com/linxir226/SIRA.

Abstract: Sparse longitudinal CT follow-up limits lesion-size forecasting when only a few prior observations are available. We constructed a five-visit DLT-derived same-lesion trajectory benchmark from DeepLesion and Deep Lesion Tracker (DLT), yielding 205 trajectories from 129 patients. We compared an exploratory conventional sparse-to-final analysis with a primary fixed visit-index horizon design predicting the common log change from T3 to T4 while progressively adding earlier observations, evaluating predictive accuracy, uncertainty reliability, post-hoc conformal interval calibration, subgroup performance, and Gompertz-inspired trajectory regularization. The evaluated methods showed partially overlapping point-prediction accuracy but distinct uncertainty behavior. Mean held-out RMSE across ten training seeds was 0.4726, 0.4305, 0.4499, and 0.4513 for m = 1, 2, 3, 4, indicating the lowest mean RMSE at m = 2; additional history did not improve RMSE. At m = 4, raw Cohort-Level Feature GP coverage was near the 95% nominal level, whereas MC Dropout, Deep Ensemble, and residual-scale intervals were conservative. Patient-level conformal calibration generally produced near-nominal or conservative coverage at the cost of wider intervals. Patient-grouped development cross-validation selected lambda* = 0 for the Gompertz-inspired term. A global population reference frequently opposed lesion-level change directions, and prediction difficulty varied across anatomical subgroups. Overall, additional historical observations provided limited predictive benefit once the prediction horizon was controlled, while predictive accuracy, uncertainty reliability, and trajectory consistency did not necessarily improve together, and should be evaluated jointly in sparse longitudinal imaging.

Abstract: Clinical decision-making for coronary intervention relies mainly on angiography and fractional flow reserve (FFR). However, angiography is two-dimensional and lacks depth information for 3D lesion characterization, while FFR provides only a single functional index, offering limited hemodynamic insight. Among existing methods, numerical analysis is computationally expensive, whereas learning-based approaches require extensive supervision and often lack physical consistency. To address these limitations, we propose physics-informed hemodynamic modeling, an integrated deep learning framework for 3D coronary blood flow analysis from dual-view angiography. First, an attention-enhanced CNN reconstructs coronary geometry from angiography. The resulting point clouds are then mapped to a reference domain and Fourier-encoded for joint representation. A decoupled network separately predicts velocity and pressure fields, with embedded physical priors enabling efficient transfer across physiological conditions. Across 32 clinical patients evaluated under four flow conditions, the trans-stenotic pressure-drop mean absolute percentage error was 2.02%, while the velocity and pressure relative-L2 errors were 0.054 and 0.023, respectively. Validation against hospital-measured FFR further achieved 93.8% diagnostic accuracy (30/32; exact 95% CI, 79.2%-99.2%). The framework also supports illustrative revascularization comparisons and sparse-data assimilation, with the full angiography-to-hemodynamics pipeline completed within 20 minutes per patient.

Abstract: Reliability under sparse and heterogeneous failures remains a fundamental challenge for medical image segmentation. High average accuracy can conceal a small set of structurally distinct and clinically consequential errors. Existing post-hoc correction methods alleviate this problem, but typically estimate false-positive and false-negative corrections from the same fixed prediction. This ignores the dynamic evolution of error states and limits the correction of complex cases. Inspired by iterative error feedback in structured prediction, we propose Failure-Aware Progressive Repair (FAPR). FAPR represents the current segmentation mask as a dynamic failure state and models each repair operation as a state-transition operator. Each accepted correction forms a new prediction state for subsequent error diagnosis and repair, enabling later operations to adapt to preceding changes. Conditional routing selectively activates necessary state transitions, while failure replay exposes the model to rare error states. By keeping the base segmentor frozen, FAPR preserves its established segmentation capability while improving difficult cases. Across three public ultrasound lesion segmentation benchmarks, FAPR improves mean DSC by 1.52%. On the very-hard subsets of BUSI and TN3K, the average gain reaches 13.77%.

Abstract: Background Non-invasive presurgical diagnosis of brain tumor types from Magnetic Resonance Imaging (MRI) is essential but challenging due to overlapping imaging features across tumor types, inter-observer variability, and the extensive training required for expertise. We aimed to develop an MRI-based Artificial Intelligence (AI) model for automatic and reliable brain tumor classification with diagnostic uncertainty quantification and radiology reports generation. Methods We developed BrainVLM to classify all 12 World Health Organization (WHO) 2021 brain tumor types. BrainVLM integrates an uncertainty quantification strategy to indicate prediction reliability and a module for generating radiology reports to elucidate the clinical rationale. BrainVLM was trained on multi-modal data (MRI scans, demographics, and radiology reports) from 40,043 individuals. It was validated on 5,211 patients with pathologically confirmed brain tumors, including 3,877 held-out patients from the primary hospital and 1,334 patients from 11 independent hospitals. We further conducted two proof-of-concept studies to validate its clinical utility in AI-clinician workflows: 1) a blinded multi-reader study where 12 neuroradiologists across varying experience levels interpreted 248 retrospective cases with or without AI assistance, and 2) a real-world prospective study in which 1,009 patients were independently and blindly assessed by BrainVLM and radiologists before surgery. Additionally, we demonstrated BrainVLM's utility in preoperative molecular subgroup prediction for adult-type diffuse gliomas, using a multi-center cohort of 632 patients.

Abstract: Breast histopathology analysis increasingly relies on distributed learning because direct data pooling across institutions is often restricted by privacy, governance, and communication constraints. This study compares server-based Federated Averaging (FedAvg), fully decentralized gossip learning, and Hybrid Gossip-FedAvg for invasive ductal carcinoma (IDC) patch classification. Experiments used 277,524 color image patches with patient-disjoint training, validation, and test partitions and a workload-balanced, Dirichlet-guided allocation across six nodes. Ring, random degree-3, and fully connected gossip topologies were evaluated together with sensitivity analyses for statistical heterogeneity, mixing coefficient, learning rate, model drift, prediction disagreement, calibration, clinically motivated operating points, communication payload, and patient-level IDC burden, together with auxiliary backbone robustness analyses. In the principal alpha=0.3 experiment, Hybrid Gossip-FedAvg achieved a test area under the receiver operating characteristic curve (ROC-AUC) of 0.8811, closely followed by FedAvg at 0.8801 and fully connected gossip at 0.8751. Across three independent patient-level repetitions, FedAvg and Hybrid Gossip-FedAvg obtained the same mean ROC-AUC of 0.9082, with standard deviations of 0.0037 and 0.0043, respectively. Hybrid achieved the highest mean area under the precision-recall curve of 0.8240, whereas FedAvg produced the lowest mean Brier score of 0.1335. Denser gossip graphs improved discrimination but increased theoretical model payload, while ring gossip remained sensitive to learning rate and mixing strength. Overall, FedAvg provided the most consistently reliable server-based baseline, topology-aware gossip offered a viable decentralized alternative, and Hybrid Gossip-FedAvg provided a balanced compromise between peer-to-peer diffusion and periodic global coordination.

Abstract: Multimodal image registration is a key component of many clinical workflows, yet it remains challenging because corresponding anatomical structures often exhibit substantially different image intensities across modalities. In this work, we present a comprehensive benchmark of intra-patient 3D multimodal deformable registration methods across three datasets covering different anatomical regions and difficulty levels, including both synthetic deformation recovery and real clinical scenarios. We evaluate classical optimization-based approaches and modern learning-based methods, including recent deep learning and foundation models, using complementary metrics: Average Dice similarity coefficient (DSC), average 95th-percentile Hausdorff distance (HD95), and a modality-independent structural similarity measure based on the MIND self-similarity context (MIND-SSC). Results show high variability across datasets, with learning-based methods demonstrating superior performance on large synthetic benchmarks, while only limited improvements are observed in real pelvic registration. A key finding of this study is the consistent disagreement between geometric metrics (DSC, HD95) and image-based similarity metrics (MIND-SSC), highlighting that improved overlap does not necessarily imply better global multimodal correspondence. Furthermore, anatomy-guided approaches achieve the highest overlap scores but exhibit degraded performance outside of segmented regions, revealing a trade-off between label-driven alignment and global structural coherence. Overall, our results indicate that no current method achieves robust performance across anatomies and modalities. We demonstrate that intra-patient 3D multimodal registration requires multi-criteria evaluation, including deformation-based metrics, and remains an open problem.

Abstract: Pseudo-labeling is a strong paradigm for semi-supervised medical image segmentation, yet its effectiveness is highly sensitive to confidence thresholding. In abdominal multi-organ segmentation, a fixed global threshold is particularly suboptimal because organ classes differ substantially in size, appearance, and learning difficulty. In this work, we propose ThreshGuide, a class-aware threshold adaptation framework that uses labeled data to guide pseudo-label selection on unlabeled data. Built upon a standard teacher-student architecture, the teacher model evaluates labeled samples during training to estimate class-aware threshold targets by maximizing an error-aware F\b{eta} criterion that balances precision and coverage. These targets are then smoothed with an exponential moving average (EMA) and used to filter unlabeled voxels in a class-dependent manner. Experiments on FLARE2022 and AMOS2022 show that ThreshGuide performs competitively overall, yielding clear improvements specifically on hard-to-learn organs.

Abstract: Accurate sperm detection is essential for computer-assisted semen analysis, yet it remains challenging in microscopic images due to dense distributions, visually similar artifacts, and sperm-like impurities. In this paper, we propose SpermYOLO, a coordinated and compact YOLOv11-derived framework for joint sperm and impurity detection in microscopic images. SpermYOLO introduces four architectural improvements: C3k2-IDB for channel-wise discriminative feature extraction, D2SEM for spatial--spectral semantic enhancement, MFM for adaptive multi-scale feature fusion, and the DESD Head for detail-enhanced shared prediction. Experiments on the SVIA semen microscopic imaging benchmark show that SpermYOLO achieves 97.2\% sperm AP and 75.4\% impurity AP, outperforming generic detectors, dedicated sperm detection models, and improved YOLO variants. Compared with the baseline model, SpermYOLO improves sperm AP, impurity AP, $\mathrm{mAP}_{50}$, and $\mathrm{mAP}_{50:95}$ by 1.6, 10.0, 5.8, and 2.7 percentage points, respectively, while preserving a lightweight model scale. Cross-scene evaluation on the SDTB testicular-biopsy microscopy benchmark shows that SpermYOLO remains effective with extremely small sperm targets and complex tissue backgrounds, achieving the highest $\mathrm{mAP}_{50}$ and $\mathrm{mAP}_{50:95}$ of 74.8\% and 31.2\%, respectively. Ablation studies and qualitative analyses further support these improvements by demonstrating the contributions of the proposed modules and showing more focused feature response patterns than the baseline model. These findings suggest that SpermYOLO is an effective and efficient approach for sperm detection in challenging microscopic imaging scenarios.

Abstract: We present CirrGuide, a deep cascaded framework for cirrhotic liver segmentation and severity classification. Cirrhosis causes progressive structural changes in the liver and can lead to serious clinical complications, making severity assessment important for disease monitoring and treatment planning. However, severity classification is challenging because imaging patterns are often subtle, spatially variable, and similar across adjacent stages. CirrGuide addresses this by explicitly linking localization with classification. A ResNet50 encoder with an Attention U-Net decoder first predicts a soft cirrhotic liver mask, which is then used as an anatomical prior in a ResNet50-based classification branch. This branch combines global multi-scale features with mask-guided attention-pooled regional features to classify Mild, Moderate, and Severe cirrhosis. On the official CirrMRI600+ T2-weighted (T2W) 2D split, CirrGuide achieves 89.83% Dice and 84.14% mIoU for segmentation, 69.58% accuracy and 61.55% macro F1-score for severity classification. Compared with segmentation-only, classification-only, and multi-task baselines, CirrGuide improves both localization and severity classification, demonstrating the benefit of using predicted cirrhotic liver masks as anatomical priors for cirrhosis analysis.

Abstract: Computed tomography (CT) and positron emission tomography (PET) provide complementary anatomical and functional information for cancer diagnosis and treatment planning. However, the widespread use of PET is limited by high radiation exposure, elevated costs, and restricted availability. To address these limitations, deep learning-based CT-to-PET translation has emerged as a promising approach for synthesizing PET-like information directly from CT images, although accurately modeling the large cross-modal gap remains challenging. In this work, we propose a 3D CT-to-PET translation framework based on latent Brownian Bridge Diffusion (BBDM). The method consists of two stages. First, a Variational Autoencoder (VAE) is trained on paired CT-PET patches, integrating contrastive learning to improve latent alignment between anatomical and metabolic representations. Second, a BBDM is trained in the latent space to translate CT latent representations into their corresponding PET counterparts. The translated PET latents are then decoded and stitched to reconstruct the final 3D PET volume. We evaluate the proposed approach on two publicly available datasets. Quantitative results based on image fidelity and lesion-level PET-specific metrics demonstrate improved performance compared with competing methods. In particular, the proposed approach improves PET signal fidelity, better preserves clinically relevant uptake patterns, and shows improved performance in preserving small-lesion metabolic activation, paving the way for virtual imaging applications.

Abstract: Bone-marrow cytology is inherently structured: each cell belongs to a hematopoietic lineage, and many cell types lie on ordered maturation trajectories. Standard flat classifiers ignore this structure, treating a mild same-lineage confusion the same as a severe cross-lineage mistake and predicting only discrete labels. We propose HemaHier, an ordinal-hierarchical prediction head for a frozen or lightly adapted cytology foundation model. Its central component is a chain-conditioned maturity score that reads a single maturity value under a per-chain query, supervised only on biologically valid healthy chains, while dysplastic and off-chain cell types remain classes but are excluded from maturity supervision. Fine and lineage predictions are coupled through a shared posterior that guarantees hierarchical consistency, and a staged objective first stabilizes recognition, then adds lineage and maturity supervision. On three bone-marrow datasets under a shared ontology, HemaHier achieves competitive recognition while reducing biologically severe errors and adding a within-lineage maturity ordering that flat classifiers lack. Code is available at https://github.com/xmindflow/HemaHier.

Abstract: Cervical cancer is a major global health challenge, with disease burden falling disproportionately on low- and middle-income countries (LMICs) due to a shortage of trained specialists and the subjective nature of colposcopy-based screening. To address this challenge, we propose a novel deep learning framework for the automated grading of Cervical Intraepithelial Neoplasia (CIN) and the prediction of clinical Swede scores. We also introduce the BUET Multi-Center Colposcopy Dataset, a novel, multi-center cohort designed and annotated for Swede score prediction and CIN grading. Our proposed dual-stream cross-attention architecture mimics the visual reasoning of an expert colposcopist by explicitly fusing paired multimodal cervigrams to evaluate comparative tissue responses. Furthermore, we introduce a custom composite loss function to address severe class imbalances and scoring inconsistencies across the five Swede score components. The proposed framework achieved 71.85% accuracy and an 86.23% AUC-ROC for three-class CIN grading, outperforming existing methods. For Swede score component prediction, the architecture achieved AUC-ROC values ranging from 75.7% to 88.4%, with the composite loss function yielding consistent F1-score improvements. Finally, the total predicted Swede Score, which ranges between 0 and 10, shows a Mean Absolute Error (MAE) of 1.489. The results show that the proposed method can pave the way towards developing AI-assisted colposcopy screening tools to support risk-based triage in resource-limited healthcare settings. The dataset and source code are publicly available(url: https://github.com/mHealthBuet/BUET-colposcopy)

Abstract: Vision-Language Models such as CLIP enable effective few-shot medical anomaly detection (AD) via strong image-text semantic alignment. However, their globally contrastive pretraining lacks explicit spatial supervision, limiting precise lesion localization. In contrast, Vision Foundation Models (VFMs) such as DINO learn spatially coherent patch representations via self-distillation and local-to-global consistency, better capturing fine-grained anatomical structures. Leveraging this complementarity, we propose Spatial-FAD, a spatial-aware few-shot medical AD framework that improves lesion localization by combining VFM spatial priors with CLIP semantics. Specifically, we introduce a VFM-enhanced adapter that injects a structural affinity prior derived from DINO into CLIP features. This structure-guided refinement encourages visual embeddings to better adhere to lesion boundaries while maintaining semantic alignment. To address the loss of spatial detail from patchification and the limited input resolution of CLIP, we adopt a sliding-window aggregation strategy. This generates high-resolution, spatially dense embeddings to further enhance localization granularity. Moreover, we introduce a prototype-enhanced support memory scheme to efficiently exploit the few-shot support set. This module stores compact prototypes for normal and abnormal patterns, reducing memory costs while boosting performance by fusing patch-to-prototype and image-text similarities. Extensive experiments on three benchmark datasets, including Liver CT, Retinal OCT, and Brain MRI, demonstrate that Spatial-FAD significantly outperforms state-of-the-art methods, especially in lesion segmentation. Notably, in the 4-shot scenario, our method achieves an average improvement of over 11.4% in Dice score and 1.8% in AUC. Code is available at: https://github.com/JuzhengMiao/Spatial-FAD.

Abstract: Perineural invasion (PNI) is an adverse histopathologic marker in intrahepatic cholangiocarcinoma (ICC), but it is usually confirmed only after resection. Preoperative T2-weighted MRI may provide noninvasive imaging cues predictive of PNI, although labels are available only at the patient level without slice- or voxel-level annotations. We propose Order-Aware Slab Multiple Instance Learning (OAS-MIL), a weakly supervised framework for patient-level PNI prediction. Each tumor-centered MRI crop is represented as an ordered sequence of overlapping 2.5D slabs formed from contiguous axial slices. A shared encoder extracts slab-level features, which are aggregated by a permutation-invariant set-attention branch and a bidirectional sequence-attention branch. Using five-fold label-stratified cross-validation at the patient level, OAS-MIL achieved a mean AUROC of 0.770, outperforming the evaluated volumetric and MIL baselines. These results suggest that axial order provides a useful inductive bias for weakly supervised PNI prediction from MRI.

Abstract: All-in-One medical image restoration (MedIR) aims to address diverse tasks across modalities and degradation types using a single universal model. Existing methods typically prioritize modeling inter-task heterogeneity (e.g., distinct data distributions and degradation types). However, they largely neglect the inherent homogeneity present in medical images, such as widely shared anatomical structures within and across modalities, which can be leveraged to ease model training and improve generalization. To this end, we propose UniH3, a novel framework that Unifies Hierarchical Homogeneity and Heterogeneity for all-in-one medical image restoration. Specifically, to comprehensively exploit homogeneity, we introduce a Hierarchical Homogeneity Memory (H2M) module that progressively distills intra- and inter-task homogeneity priors from high-quality images during training, and adaptively retrieves the most relevant priors tailored to the input for guided restoration. These retrieved priors are then injected into the restoration pipeline via an efficient Homogeneity-Guided Attention (HGA) mechanism. Furthermore, to comprehensively address heterogeneity, we design a Hierarchical Heterogeneity Balancer (H2B) that mitigates both inter- and intra-task conflicts during optimization, facilitating balanced and effective multi-task learning. Extensive experiments on two large-scale benchmarks, MedIR-2D-500K and MedIR-3D-3K, demonstrate that UniH3 achieves state-of-the-art performance on both all-in-one and single-task medical image restoration. We hope this work establishes a strong benchmark and advances the development of general-purpose medical image restoration models. Code is available at https://github.com/Yaziwel/UniH3.

Abstract: Label-free virtual staining offers a compelling, non-destructive alternative to standard histopathology; however, its clinical adoption is hindered by the computational bottlenecks inherent to processing gigapixel Whole Slide Images (WSIs). Current deep learning approaches require patch-based inference to avoid memory constraints, which disrupts global tissue continuity and introduces tiling artifacts--displaying visible seams and color shifts. To address this, we introduce the Consistency Memory Bank (COMB), a novel label-free virtual staining framework that enforces spatial and channel consistency across tiles without memory bottlenecks. COMB decouples context storage from computation, utilizing a dynamic retrieval mechanism to fetch feature representations from adjacent tiles. This enables a retrieval-based context integration strategy that adopts local padding to resolve spatial discontinuities and neighbor-aware channel attention to stabilize statistical drift. Further optimized with a sliding window schedule to ensure minimal memory overhead, our method demonstrates superior performance over state-of-the-art baselines, achieving significant improvements in both perceptual fidelity and tiling consistency, while suggesting its downstream utility in tumor segmentation. Code is available at https://github.com/dou0000/COMB.

Abstract: Detecting brain metastases in magnetic resonance imaging (MRI) remains challenging because lesions vary widely in size and appearance, with very small metastases occupying only a minute fraction of a three-dimensional input. We investigate whether combining different spatial fields of view (FOVs) improves lesion detection in multimodal MRI and present a scale-aware 3D deep-learning framework. The method uses independently trained $96^3$ and $64^3$ 3D U-Nets whose whole-volume probability maps are combined by weighted late fusion. This design allows us to study the effect of spatial context separately from image resolution and modality choice. On a 97-patient development cohort, cross-FOV fusion improved lesion-level precision and F1 while substantially reducing false positives relative to the individual models. A same-FOV ensemble control showed that these gains were not explained solely by averaging independently trained networks, supporting a contribution from complementary spatial context. An exploratory cross-FOV agreement filter reduced false positives but did not improve overall F1. These results support cross-FOV probability fusion as a simple and computationally practical strategy for improving the precision-false-positive trade-off in 3D brain-metastasis detection.

Abstract: Few-shot medical image segmentation (FSMIS) seeks to delineate unseen structures from a small support set, but its standard formulation fixes task-defining evidence before inference. This assumption is fragile when query cases exhibit acquisition shift, atypical pathology, ambiguous boundaries, or poor image quality. Prototype learning, cross-domain matching, interactive segmentation, uncertainty estimation, test-time adaptation, and promptable foundation models address parts of this problem, yet have not been jointly evaluated under a common model of expert attention and clinical risk. This Perspective reframes FSMIS as a sequential clinician-model decision problem with a static support budget $K$ and a distinct interaction budget $B$. At each step, a system accepts the current segmentation, requests feedback, or defers to full expert review. Queries vary in location and modality and are selected by response-conditioned net expected value of information; clinician-provided feedback informs bounded adaptation only after prespecified provenance, consistency, and safety gates. The framework separates distributional atypicality from predicted clinical failure and treats clinician responses as informative but fallible observations. We synthesize the transition from few-shot and cross-domain segmentation to interactive and selective adaptation, delineate the integration gap, and define four research directions with falsifiable hypotheses. Evaluation spans external-domain calibration, quality-effort trade-offs, reader studies, and prospective workflow assessment. The central claim is not that interaction alone resolves domain shift, but that scarce expert attention should be allocated only when it is expected to reduce clinically relevant risk.

Abstract: Reconstructing volumetric Computed Tomography (CT) from a single 2D chest radiograph (CXR) is an ill-posed inverse problem, further complicated by the scarcity of paired CXR-CT training data. Prior approaches address this by training on Digitally Reconstructed Radiographs (DRRs), which are synthetic projections derived from CT volumes. However, the domain gap between DRRs and real CXRs limits generalization, often resulting in coarse or anatomically inconsistent reconstructions when applied to clinical images. To address this challenging problem, this study introduces a Multi-Pass Multi-View Blended Learning framework for synthesizing high-fidelity volumetric CT directly from real chest X-ray (CXR) images. The proposed approach progressively decomposes the synthesis task into two distinct, complementary learning stages. Stage 1 is an unsupervised CXR-to-DRR Domain Adaptation, while Stage 2 includes three passes, namely, (a) supervised DRR-to-CT Transformation, (b) unsupervised Multi-View Slice Refinement, followed by (c) Progressive Transfer Learning (PTL). With such a blended learning paradigm, the proposed approach mitigates the synthetic-to-real domain gap while enhancing both the structural integrity and anatomical detail of the final output. On the LIDC-IDRI dataset, where paired DRR-CT ground truth is available for quantitative evaluation, the proposed method improves upon prior methods by up to 14% in PSNR and 7.6% in SSIM. The framework successfully generates structurally consistent and anatomically realistic high-fidelity CT volumes from real CXRs, marking a significant advancement toward clinical viability of CT reconstruction from standard radiographic images.

Abstract: Real-time MRI (rtMRI) captures the dynamics of the entire vocal tract during speech, but labeled data are scarce and the modality - single-slice, grayscale, low-resolution - differs substantially from the natural videos that video foundation models are trained on. We introduce Arti-JEPA, a joint embedding predictive architecture to model vocal tract rtMRI by continuing its self-supervised objective on about 62h of unlabelled vocal-tract videos, and evaluate the frozen representation on three tasks: cross-domain phoneme prediction (on typical speakers), fluent-vs-disfluent classification (a corpus containing stuttered speech), and characterizing pre/post-operative transfer (after partial glossectomy). Three key findings emerge. (1) A temporal video prior decisively outperforms per-frame image encoders, and latent prediction (V-JEPA) is at least as strong as pixel reconstruction (VideoMAE), with the edge on fine-grained phonemes. (2) Domain adaptation is \emph{task-dependent}: it roughly doubles cross-domain phoneme prediction $κ$ (to 0.352) but does not help binary stuttering classification. (3) Arti-JEPA was able to recover phoneme signal from pre/post glossectomy speech --- an in-domain probe decodes patients at least as well as a typical speaker, indicating that the residual transfer gap is cross-speaker/domain misalignment, not surgical signal loss, and post-operative decoding does not fall below performance on pre-operative speech. Together, these position a frozen, domain-adapted rtMRI encoder as a reusable measurement tool for articulatory and clinical speech science.

Abstract: Large networks and ensembles often lead medical image segmentation challenges, but their storage and inference demands complicate deployment. We present LightMedSeg-ISLES, a 1.26-million-parameter pipeline for T1-weighted stroke lesion segmentation in ISLES'26. On a 146-case held-out cohort, flip test-time augmentation produces 0.618 mean Dice and 0.599 lesion-wise F1. A 102.35-million-parameter nnU-Net ResEnc-L produces 0.634 Dice and 0.544 lesion-wise F1 after size filtering. LightMedSeg therefore retains 97.5\% of nnU-Net's Dice with 81.4$\times$ fewer parameters while improving lesion-wise F1 by 0.055. Its four-pass TTA operating point requires 4.7$\times$ fewer FLOPs per standardized patch than nnU-Net. It also slightly exceeds filtered UNETR++ and nnFormer. Longer training and stronger augmentation add 0.0358 Dice without increasing capacity, establishing a strong single-checkpoint alternative to much larger models.

Abstract: Delineating lung tumours on computed tomography (CT) takes a considerable share of the time spent on radiotherapy planning, and a contour proposed by a model can be refined interactively by the clinician. Promptable foundation models such as SAM 3 support this workflow by writing each correction into a session memory that conditions the remaining slices, while the model weights stay fixed. On 690 test cases from five public CT cohorts, fine-tuning SAM 3 on lung tumours raises the Dice obtained from a single point prompt from 0.298 to 0.757, and seven rounds of corrections raise it further to 0.765, but under memory conditioning alone the accuracy on slices the annotator has not touched stops improving after six rounds. We therefore treat each correction as a training signal and propose LeCor, which performs test-time training on a small set of case adapters that are reset for every case and meta-learned such that a single gradient step driven by a click improves the slices that were not clicked. On the 133 test cases that span at least eight slices, LeCor raises the Dice reached after seven correction rounds from 0.787 with the fine-tuned model to 0.827, reduces the number of cases that never reach a Dice of 0.80 from 47 to 27, and reaches in three correction rounds the accuracy that the fine-tuned model attains in seven.

Abstract: Longitudinal characterization of multiple sclerosis (MS) lesions remains constrained by the lack of frameworks capable of establishing consistent instance-level correspondences across time. Conventional segmentation approaches produce semantic lesion masks at each visit and therefore fail to capture the complex instance temporal patterns associated with lesion appearance, disappearance, splitting, or merging. This study presents a comparative evaluation of five strategies for automated tracking of spinal cord MS lesions in longitudinal MRI data from a multi-site cohort. The investigated strategies rely either on deformable registration or on a spinal anatomical reference system, and encompass overlap-based matching, coordinate-based Hungarian algorithm, gradient-boosted classification, and Siamese model classification. Tracking accuracy is quantified using instance-level true positives, false positives, and false negatives, allowing to assess the presence of one-to-many and many-to-one associations. Results show best performance for the registration-based overlap method. This study provides the first systematic analysis of lesion-instance correspondence in the spinal cord and outlines the strengths and limitations of registration-based and registration-free paradigms for longitudinal MS assessment. The code is available at http://github.com/ivadomed/longitudinal-sc-ms-lesion-tracking .

Abstract: In proton therapy, plans are typically optimized on a single planning CT, making robustness evaluation essential under anatomical changes. However, current scenarios often rely on simplified perturbations that poorly capture complex, patient-specific variability. We propose SynthRCT, a scalable conditional generative framework for 3D anatomical deformation synthesis. Based on a conditional variational autoencoder, SynthRCT learns a latent deformation space and decodes sampled latent codes into local stationary velocity fields conditioned on an input anatomy. Local fields are assembled into coherent full-volume transformations, enabling memory-scalable generation for large field-of-view CT data. We validate the approach on respiratory 4DCT data with multiple breathing-phase anatomies per subject. SynthRCT enables patient-specific sampling of plausible anatomical transformations beyond predefined robustness scenarios. Code available at: https://github.com/TomasGuija/SynthRCT.

Abstract: Purpose: Accurate CT protocol selection is critical for diagnostic quality and patient safety, yet the current process is manual, time-consuming, and prone to inconsistencies. Prior Machine Learning methods using keywords or bag-of-words lack contextual understanding and perform poorly on rare protocols. We propose a decision support system using large language model (LLM) features to recommend protocols from free-text clinical indications, capturing clinical nuance and phrasing variation for more consistent, efficient selection. Methods: In this REB-approved retrospective study, 285,123 chest CT imaging requests from a large academic medical center (2017-2024) were split into training (228,099, 80%) and held-out test (57,024, 20%) sets. Each request included procedure names, clinical indication, HIS comments, and the selected protocol. Clinical text was embedded using a fine-tuned LLM, Meta's LLaMA-3.1-70B; these features input a logistic regression classifier predicting 18 protocol labels (e.g., PE, LDCT). Results: The pipeline achieved a weighted precision of 0.84, weighted F1-score of 0.81, and overall accuracy of 79% across 18 CT protocols. On 300 independent cases with expert consensus, the LLM reached an overall accuracy of 80% versus 83% for radiologists, with no significant difference (p = 0.263). Performance was comparable across most classes, with the LLM exceeding radiologists for some challenging categories, and entropy analyses indicated more balanced protocol use, suggesting reduced variability. Conclusion: An LLM-based recommendation system can leverage general knowledge from a large natural-text corpus to accurately assign chest CT protocols from free-text imaging requests, and may serve as a viable foundation for protocol recommendation tools where inputs require language understanding.

Abstract: Cranial nerves (CNs) play essential roles in sensory, motor, and autonomic functions. Accurate CN parcellation from multimodal magnetic resonance imaging (MRI) is crucial for neuroanatomical analysis and neurosurgical planning. However, accurate CN parcellation remains extremely challenging because CNs are very small, exhibit low image contrast, and have slender tubular morphologies and complex anatomical trajectories. Moreover, the lack of publicly available, expert-annotated datasets has impeded the development and fair benchmarking of learning-based CN analysis methods. In this work, we introduce CNsEMD, an expert-annotated multimodal dataset for CN parcellation. It comprises data from 202 subjects acquired on 3T, 5T, and 7T MRI scanners. We further propose the projective hyperspherical manifold network (PHM-Net), which learns cross-modal representations by capturing angular relationships in a shared hyperspherical embedding space. Rather than performing multimodal fusion in Euclidean space, the proposed Hyperspherical cross-modal interaction (HCI) module enables bidirectional feature exchange between T1-weighted (T1w) and direction-encoded color (DEC) representations on a unit hypersphere. The Magnitude-preserving projective hyperspherical orientation representation (PHOR) captures the axial nature of DEC orientations while preserving diffusion magnitude. The hyperspherical prototype segmentation head (HPSH) further extends angular similarity to voxel-wise classification using normalized voxel embeddings and learnable class prototypes. Extensive experimental results on the CNsEMD dataset demonstrate the effectiveness of our PHM-Net against state-of-the-art methods. CNsEMD establishes a reproducible benchmark for multimodal CN imaging, while PHM-Net provides a geometry-consistent solution for CN parcellation across diverse MRI acquisitions.

Abstract: Invasive coronary angiography (CAG) is the gold standard for diagnosing coronary artery disease, but interpretation varies substantially among observers. Existing AI systems can improve consistency but lack auditable decision processes and are limited in comprehensive open-ended assessment, undermining clinician trust and clinical adoption readiness. We developed CARDEA, a unified large vision-language model that serves as the inference core of a CAG pipeline. It was trained solely on public datasets and closed-ended tasks in three stages: visual feature alignment, a self-distilled Chain-of-Box (CoB) cold start, and reinforcement learning with verifiable rewards (RLVR) with a CoB reward encouraging bounding-box use in the reasoning trace. We assessed its two study-level diagnoses, dominance classification and complexity assessment, against a dedicated classifier and two interventional cardiologists. Report generation was excluded from training and evaluated zero-shot across stages on an external cohort using vessel-severity macro-$F_1$. CARDEA trailed the classifier on in-distribution dominance but drew level under domain shift (accuracy, 0.91 [95% confidence interval (CI), 0.86 to 0.95]) and was comparable to the cardiologists on complexity assessment (accuracy, 0.90 [CI, 0.82 to 0.97]). Only RLVR improved zero-shot report generation, raising its vessel-severity macro-$F_1$ (0.686 [CI, 0.664 to 0.707]) above the untuned base model (0.513) and over twice the always-normal floor (0.312). CARDEA runs an end-to-end CAG pipeline from raw multi-view videos through keyframe selection to study-level diagnosis while exposing auditable spatial evidence behind its conclusions. RLVR on verifiable closed-ended tasks surfaced open-ended reporting ability that supervised imitation did not. Clinical use requires prospective validation against expert cardiologists.