Interpretable models are crucial for supporting clinical decision-making, driving advances in their development and application for medical images. However, the nature of 3D volumetric data makes it inherently challenging to visualize and interpret intricate and complex structures like the cerebral cortex. Cortical surface renderings, on the other hand, provide a more accessible and understandable 3D representation of brain anatomy, facilitating visualization and interactive exploration. Motivated by this advantage and the widespread use of surface data for studying neurological disorders, we present the eXplainable Surface Vision Transformer (X-SiT). This is the first inherently interpretable neural network that offers human-understandable predictions based on interpretable cortical features. As part of X-SiT, we introduce a prototypical surface patch decoder for classifying surface patch embeddings, incorporating case-based reasoning with spatially corresponding cortical prototypes. The results demonstrate state-of-the-art performance in detecting Alzheimer's disease and frontotemporal dementia while additionally providing informative prototypes that align with known disease patterns and reveal classification errors.
Foundation models, pre-trained on large image datasets and capable of capturing rich feature representations, have recently shown potential for zero-shot image registration. However, their performance has mostly been tested in the context of rigid or less complex structures, such as the brain or abdominal organs, and it remains unclear whether these models can handle more challenging, deformable anatomy. Breast MRI registration is particularly difficult due to significant anatomical variation between patients, deformation caused by patient positioning, and the presence of thin and complex internal structure of fibroglandular tissue, where accurate alignment is crucial. Whether foundation model-based registration algorithms can address this level of complexity remains an open question. In this study, we provide a comprehensive evaluation of foundation model-based registration algorithms for breast MRI. We assess five pre-trained encoders, including DINO-v2, SAM, MedSAM, SSLSAM, and MedCLIP, across four key breast registration tasks that capture variations in different years and dates, sequences, modalities, and patient disease status (lesion versus no lesion). Our results show that foundation model-based algorithms such as SAM outperform traditional registration baselines for overall breast alignment, especially under large domain shifts, but struggle with capturing fine details of fibroglandular tissue. Interestingly, additional pre-training or fine-tuning on medical or breast-specific images in MedSAM and SSLSAM, does not improve registration performance and may even decrease it in some cases. Further work is needed to understand how domain-specific training influences registration and to explore targeted strategies that improve both global alignment and fine structure accuracy. We also publicly release our code at \href{https://github.com/mazurowski-lab/Foundation-based-reg}{Github}.
Pediatric medical imaging presents unique challenges due to significant anatomical and developmental differences compared to adults. Direct application of segmentation models trained on adult data often yields suboptimal performance, particularly for small or rapidly evolving structures. To address these challenges, several strategies leveraging the nnU-Net framework have been proposed, differing along four key axes: (i) the fingerprint dataset (adult, pediatric, or a combination thereof) from which the Training Plan -including the network architecture-is derived; (ii) the Learning Set (adult, pediatric, or mixed), (iii) Data Augmentation parameters, and (iv) the Transfer learning method (finetuning versus continual learning). In this work, we introduce PSAT (Pediatric Segmentation Approaches via Adult Augmentations and Transfer learning), a systematic study that investigates the impact of these axes on segmentation performance. We benchmark the derived strategies on two pediatric CT datasets and compare them with state-of-theart methods, including a commercial radiotherapy solution. PSAT highlights key pitfalls and provides actionable insights for improving pediatric segmentation. Our experiments reveal that a training plan based on an adult fingerprint dataset is misaligned with pediatric anatomy-resulting in significant performance degradation, especially when segmenting fine structures-and that continual learning strategies mitigate institutional shifts, thus enhancing generalization across diverse pediatric datasets. The code is available at https://github.com/ICANS-Strasbourg/PSAT.
To advance real-world fashion image editing, we analyze existing two-stage pipelines(mask generation followed by diffusion-based editing)which overly prioritize generator optimization while neglecting mask controllability. This results in two critical limitations: I) poor user-defined flexibility (coarse-grained human masks restrict edits to predefined regions like upper torso; fine-grained clothes masks preserve poses but forbid style/length customization). II) weak pose robustness (mask generators fail due to articulated poses and miss rare regions like waist, while human parsers remain limited by predefined categories). To address these gaps, we propose Pose-Star, a framework that dynamically recomposes body structures (e.g., neck, chest, etc.) into anatomy-aware masks (e.g., chest-length) for user-defined edits. In Pose-Star, we calibrate diffusion-derived attention (Star tokens) via skeletal keypoints to enhance rare structure localization in complex poses, suppress noise through phase-aware analysis of attention dynamics (Convergence,Stabilization,Divergence) with threshold masking and sliding-window fusion, and refine edges via cross-self attention merging and Canny alignment. This work bridges controlled benchmarks and open-world demands, pioneering anatomy-aware, pose-robust editing and laying the foundation for industrial fashion image editing.
The clinical utility of deep learning models for medical image segmentation is severely constrained by their inability to generalize to unseen domains. This failure is often rooted in the models learning spurious correlations between anatomical content and domain-specific imaging styles. To overcome this fundamental challenge, we introduce Causal-SAM-LLM, a novel framework that elevates Large Language Models (LLMs) to the role of causal reasoners. Our framework, built upon a frozen Segment Anything Model (SAM) encoder, incorporates two synergistic innovations. First, Linguistic Adversarial Disentanglement (LAD) employs a Vision-Language Model to generate rich, textual descriptions of confounding image styles. By training the segmentation model's features to be contrastively dissimilar to these style descriptions, it learns a representation robustly purged of non-causal information. Second, Test-Time Causal Intervention (TCI) provides an interactive mechanism where an LLM interprets a clinician's natural language command to modulate the segmentation decoder's features in real-time, enabling targeted error correction. We conduct an extensive empirical evaluation on a composite benchmark from four public datasets (BTCV, CHAOS, AMOS, BraTS), assessing generalization under cross-scanner, cross-modality, and cross-anatomy settings. Causal-SAM-LLM establishes a new state of the art in out-of-distribution (OOD) robustness, improving the average Dice score by up to 6.2 points and reducing the Hausdorff Distance by 15.8 mm over the strongest baseline, all while using less than 9% of the full model's trainable parameters. Our work charts a new course for building robust, efficient, and interactively controllable medical AI systems.
X-ray imaging is a rapid and cost-effective tool for visualizing internal human anatomy. While multi-view X-ray imaging provides complementary information that enhances diagnosis, intervention, and education, acquiring images from multiple angles increases radiation exposure and complicates clinical workflows. To address these challenges, we propose a novel view-conditioned diffusion model for synthesizing multi-view X-ray images from a single view. Unlike prior methods, which are limited in angular range, resolution, and image quality, our approach leverages the Diffusion Transformer to preserve fine details and employs a weak-to-strong training strategy for stable high-resolution image generation. Experimental results demonstrate that our method generates higher-resolution outputs with improved control over viewing angles. This capability has significant implications not only for clinical applications but also for medical education and data extension, enabling the creation of diverse, high-quality datasets for training and analysis. Our code is available at GitHub.
Segmenting anatomical structures in medical images plays an important role in the quantitative assessment of various diseases. However, accurate segmentation becomes significantly more challenging in the presence of disease. Disease patterns can alter the appearance of surrounding healthy tissues, introduce ambiguous boundaries, or even obscure critical anatomical structures. As such, segmentation models trained on real-world datasets may struggle to provide good anatomical segmentation, leading to potential misdiagnosis. In this paper, we generate counterfactual (CF) images to simulate how the same anatomy would appear in the absence of disease without altering the underlying structure. We then use these CF images to segment structures of interest, without requiring any changes to the underlying segmentation model. Our experiments on two real-world clinical chest X-ray datasets show that the use of counterfactual images improves anatomical segmentation, thereby aiding downstream clinical decision-making.
Inter reader variability and cross site domain shift challenge the automatic segmentation of prostate anatomy using T2 weighted MRI images. This study investigates whether transformer models can retain precision amid such heterogeneity. We compare the performance of UNETR and SwinUNETR in prostate gland segmentation against our previous 3D UNet model [1], based on 546 MRI (T2weighted) volumes annotated by two independent experts. Three training strategies were analyzed: single cohort dataset, 5 fold cross validated mixed cohort, and gland size based dataset. Hyperparameters were tuned by Optuna. The test set, from an independent population of readers, served as the evaluation endpoint (Dice Similarity Coefficient). In single reader training, SwinUNETR achieved an average dice score of 0.816 for Reader#1 and 0.860 for Reader#2, while UNETR scored 0.8 and 0.833 for Readers #1 and #2, respectively, compared to the baseline UNets 0.825 for Reader #1 and 0.851 for Reader #2. SwinUNETR had an average dice score of 0.8583 for Reader#1 and 0.867 for Reader#2 in cross-validated mixed training. For the gland size-based dataset, SwinUNETR achieved an average dice score of 0.902 for Reader#1 subset and 0.894 for Reader#2, using the five-fold mixed training strategy (Reader#1, n=53; Reader#2, n=87) at larger gland size-based subsets, where UNETR performed poorly. Our findings demonstrate that global and shifted-window self-attention effectively reduces label noise and class imbalance sensitivity, resulting in improvements in the Dice score over CNNs by up to five points while maintaining computational efficiency. This contributes to the high robustness of SwinUNETR for clinical deployment.
Segmenting muscle compartments and measuring their architecture can facilitate movement function assessment, accurate musculoskeletal modeling, and synergy-based electromyogram simulation. Here, we presented a novel method for volumetric segmentation of muscle compartments using in vivo imaging, focusing on the independent compartments for finger control of flexor digitorum superficialis (FDS). Besides, we measured the architectural properties of FDS compartments and validated the segmentation. Specifically, ultrasound and magnetic resonance imaging (MRI) from 10 healthy subjects were used for segmentation and measurement, while electromyography was utilized for validation. A two-step piecewise segmentation was proposed, first annotating compartment regions in the cross-sectional ultrasound image based on compartment movement, and then performing minimum energy matching to register the ultrasound data to the three-dimensional MRI coordinate system. Additionally, the architectural properties were measured in the compartment masks from the segmentation using MRI tractography. Anatomical correctness was verified by comparing known anatomy with reconstructed fiber tracts and measured properties, while segmentation accuracy was quantified as the percentage of finger electromyogram centers falling within their corresponding compartments. Results demonstrated agreement for the fiber orientation between the tractography and cadaveric photographs. Significant differences in architectural properties (P < 0.001) were observed between compartments. The properties of FDS and its compartments were within the physiological ranges (P < 0.01). 95% (38/40) of the electromyogram centers were located within respective compartments, with 2 errors occurring in the index and little fingers. The validated segmentation method and derived architectural properties may advance biomedical applications.
The segmentation of metastatic bone disease (MBD) in whole-body MRI (WB-MRI) is a challenging problem. Due to varying appearances and anatomical locations of lesions, ambiguous boundaries, and severe class imbalance, obtaining reliable segmentations requires large, well-annotated datasets capturing lesion variability. Generating such datasets requires substantial time and expertise, and is prone to error. While self-supervised learning (SSL) can leverage large unlabeled datasets, learned generic representations often fail to capture the nuanced features needed for accurate lesion detection. In this work, we propose a Supervised Anatomical Pretraining (SAP) method that learns from a limited dataset of anatomical labels. First, an MRI-based skeletal segmentation model is developed and trained on WB-MRI scans from healthy individuals for high-quality skeletal delineation. Then, we compare its downstream efficacy in segmenting MBD on a cohort of 44 patients with metastatic prostate cancer, against both a baseline random initialization and a state-of-the-art SSL method. SAP significantly outperforms both the baseline and SSL-pretrained models, achieving a normalized surface Dice of 0.76 and a Dice coefficient of 0.64. The method achieved a lesion detection F2 score of 0.44, improving on 0.24 (baseline) and 0.31 (SSL). When considering only clinically relevant lesions larger than 1~ml, SAP achieves a detection sensitivity of 100% in 28 out of 32 patients. Learning bone morphology from anatomy yields an effective and domain-relevant inductive bias that can be leveraged for the downstream segmentation task of bone lesions. All code and models are made publicly available.
The organization and connectivity of the arcuate fasciculus (AF) in nonhuman primates remain contentious, especially concerning how its anatomy diverges from that of humans. Here, we combined cross-scale single-neuron tracing - using viral-based genetic labeling and fluorescence micro-optical sectioning tomography in macaques (n = 4; age 3 - 11 years) - with whole-brain tractography from 11.7T diffusion MRI. Complemented by spectral embedding analysis of 7.0T MRI in humans, we performed a comparative connectomic analysis of the AF across species. We demonstrate that the macaque AF originates in the temporal-parietal cortex, traverses the auditory cortex and parietal operculum, and projects into prefrontal regions. In contrast, the human AF exhibits greater expansion into the middle temporal gyrus and stronger prefrontal and parietal operculum connectivity - divergences quantified by Kullback-Leibler analysis that likely underpin the evolutionary specialization of human language networks. These interspecies differences - particularly the human AF's broader temporal integration and strengthened frontoparietal linkages - suggest a connectivity-based substrate for the emergence of advanced language processing unique to humans. Furthermore, our findings offer a neuroanatomical framework for understanding AF-related disorders such as aphasia and dyslexia, where aberrant connectivity disrupts language function.
Dental diagnosis relies on two primary imaging modalities: panoramic radiographs (PX) providing 2D oral cavity representations, and Cone-Beam Computed Tomography (CBCT) offering detailed 3D anatomical information. While PX images are cost-effective and accessible, their lack of depth information limits diagnostic accuracy. CBCT addresses this but presents drawbacks including higher costs, increased radiation exposure, and limited accessibility. Existing reconstruction models further complicate the process by requiring CBCT flattening or prior dental arch information, often unavailable clinically. We introduce ViT-NeBLa, a vision transformer-based Neural Beer-Lambert model enabling accurate 3D reconstruction directly from single PX. Our key innovations include: (1) enhancing the NeBLa framework with Vision Transformers for improved reconstruction capabilities without requiring CBCT flattening or prior dental arch information, (2) implementing a novel horseshoe-shaped point sampling strategy with non-intersecting rays that eliminates intermediate density aggregation required by existing models due to intersecting rays, reducing sampling point computations by $52 \%$, (3) replacing CNN-based U-Net with a hybrid ViT-CNN architecture for superior global and local feature extraction, and (4) implementing learnable hash positional encoding for better higher-dimensional representation of 3D sample points compared to existing Fourier-based dense positional encoding. Experiments demonstrate that ViT-NeBLa significantly outperforms prior state-of-the-art methods both quantitatively and qualitatively, offering a cost-effective, radiation-efficient alternative for enhanced dental diagnostics.
Solving inverse problems in cardiovascular modeling is particularly challenging due to the high computational cost of running high-fidelity simulations. In this work, we focus on Bayesian parameter estimation and explore different methods to reduce the computational cost of sampling from the posterior distribution by leveraging low-fidelity approximations. A common approach is to construct a surrogate model for the high-fidelity simulation itself. Another is to build a surrogate for the discrepancy between high- and low-fidelity models. This discrepancy, which is often easier to approximate, is modeled with either a fully connected neural network or a nonlinear dimensionality reduction technique that enables surrogate construction in a lower-dimensional space. A third possible approach is to treat the discrepancy between the high-fidelity and surrogate models as random noise and estimate its distribution using normalizing flows. This allows us to incorporate the approximation error into the Bayesian inverse problem by modifying the likelihood function. We validate five different methods which are variations of the above on analytical test cases by comparing them to posterior distributions derived solely from high-fidelity models, assessing both accuracy and computational cost. Finally, we demonstrate our approaches on two cardiovascular examples of increasing complexity: a lumped-parameter Windkessel model and a patient-specific three-dimensional anatomy.
Widely adopted evaluation metrics for sparse-view CT reconstruction--such as Structural Similarity Index Measure and Peak Signal-to-Noise Ratio--prioritize pixel-wise fidelity but often fail to capture the completeness of critical anatomical structures, particularly small or thin regions that are easily missed. To address this limitation, we propose a suite of novel anatomy-aware evaluation metrics designed to assess structural completeness across anatomical structures, including large organs, small organs, intestines, and vessels. Building on these metrics, we introduce CARE, a Completeness-Aware Reconstruction Enhancement framework that incorporates structural penalties during training to encourage anatomical preservation of significant structures. CARE is model-agnostic and can be seamlessly integrated into analytical, implicit, and generative methods. When applied to these methods, CARE substantially improves structural completeness in CT reconstructions, achieving up to +32% improvement for large organs, +22% for small organs, +40% for intestines, and +36% for vessels.
The diagnosis of prostate cancer increasingly depends on multimodal imaging, particularly magnetic resonance imaging (MRI) and transrectal ultrasound (TRUS). However, accurate registration between these modalities remains a fundamental challenge due to the differences in dimensionality and anatomical representations. In this work, we present a novel framework that addresses these challenges through a two-stage process: TRUS 3D reconstruction followed by cross-modal registration. Unlike existing TRUS 3D reconstruction methods that rely heavily on external probe tracking information, we propose a totally probe-location-independent approach that leverages the natural correlation between sagittal and transverse TRUS views. With the help of our clustering-based feature matching method, we enable the spatial localization of 2D frames without any additional probe tracking information. For the registration stage, we introduce an unsupervised diffusion-based framework guided by modality translation. Unlike existing methods that translate one modality into another, we map both MR and US into a pseudo intermediate modality. This design enables us to customize it to retain only registration-critical features, greatly easing registration. To further enhance anatomical alignment, we incorporate an anatomy-aware registration strategy that prioritizes internal structural coherence while adaptively reducing the influence of boundary inconsistencies. Extensive validation demonstrates that our approach outperforms state-of-the-art methods by achieving superior registration accuracy with physically realistic deformations in a completely unsupervised fashion.
Recent work has shown improved lesion detectability and flexibility to reconstruction hyperparameters (e.g. scanner geometry or dose level) when PET images are reconstructed by leveraging pre-trained diffusion models. Such methods train a diffusion model (without sinogram data) on high-quality, but still noisy, PET images. In this work, we propose a simple method for generating subject-specific PET images from a dataset of multi-subject PET-MR scans, synthesizing "pseudo-PET" images by transforming between different patients' anatomy using image registration. The images we synthesize retain information from the subject's MR scan, leading to higher resolution and the retention of anatomical features compared to the original set of PET images. With simulated and real [$^{18}$F]FDG datasets, we show that pre-training a personalized diffusion model with subject-specific "pseudo-PET" images improves reconstruction accuracy with low-count data. In particular, the method shows promise in combining information from a guidance MR scan without overly imposing anatomical features, demonstrating an improved trade-off between reconstructing PET-unique image features versus features present in both PET and MR. We believe this approach for generating and utilizing synthetic data has further applications to medical imaging tasks, particularly because patient-specific PET images can be generated without resorting to generative deep learning or large training datasets.
Purpose: In high-dose-rate (HDR) prostate brachytherapy procedures, the pattern of needle placement solely relies on physician experience. We investigated the feasibility of using reinforcement learning (RL) to provide needle positions and dwell times based on patient anatomy during pre-planning stage. This approach would reduce procedure time and ensure consistent plan quality. Materials and Methods: We train a RL agent to adjust the position of one selected needle and all the dwell times on it to maximize a pre-defined reward function after observing the environment. After adjusting, the RL agent then moves on to the next needle, until all needles are adjusted. Multiple rounds are played by the agent until the maximum number of rounds is reached. Plan data from 11 prostate HDR boost patients (1 for training, and 10 for testing) treated in our clinic were included in this study. The dosimetric metrics and the number of used needles of RL plan were compared to those of the clinical results (ground truth). Results: On average, RL plans and clinical plans have very similar prostate coverage (Prostate V100) and Rectum D2cc (no statistical significance), while RL plans have less prostate hotspot (Prostate V150) and Urethra D20% plans with statistical significance. Moreover, RL plans use 2 less needles than clinical plan on average. Conclusion: We present the first study demonstrating the feasibility of using reinforcement learning to autonomously generate clinically practical HDR prostate brachytherapy plans. This RL-based method achieved equal or improved plan quality compared to conventional clinical approaches while requiring fewer needles. With minimal data requirements and strong generalizability, this approach has substantial potential to standardize brachytherapy planning, reduce clinical variability, and enhance patient outcomes.
Latent Diffusion Models have shown remarkable results in text-guided image synthesis in recent years. In the domain of natural (RGB) images, recent works have shown that such models can be adapted to various vision-language downstream tasks with little to no supervision involved. On the contrary, text-to-image Latent Diffusion Models remain relatively underexplored in the field of medical imaging, primarily due to limited data availability (e.g., due to privacy concerns). In this work, focusing on the chest X-ray modality, we first demonstrate that a standard text-conditioned Latent Diffusion Model has not learned to align clinically relevant information in free-text radiology reports with the corresponding areas of the given scan. Then, to alleviate this issue, we propose a fine-tuning framework to improve multi-modal alignment in a pre-trained model such that it can be efficiently repurposed for downstream tasks such as phrase grounding. Our method sets a new state-of-the-art on a standard benchmark dataset (MS-CXR), while also exhibiting robust performance on out-of-distribution data (VinDr-CXR). Our code will be made publicly available.
Accurate classification of second-trimester fetal ultrasound images remains challenging due to low image quality, high intra-class variability, and significant class imbalance. In this work, we introduce a simple yet powerful, biologically inspired deep learning ensemble framework that-unlike prior studies focused on only a handful of anatomical targets-simultaneously distinguishes 16 fetal structures. Drawing on the hierarchical, modular organization of biological vision systems, our model stacks two complementary branches (a "shallow" path for coarse, low-resolution cues and a "detailed" path for fine, high-resolution features), concatenating their outputs for final prediction. To our knowledge, no existing method has addressed such a large number of classes with a comparably lightweight architecture. We trained and evaluated on 5,298 routinely acquired clinical images (annotated by three experts and reconciled via Dawid-Skene), reflecting real-world noise and variability rather than a "cleaned" dataset. Despite this complexity, our ensemble (EfficientNet-B0 + EfficientNet-B6 with LDAM-Focal loss) identifies 90% of organs with accuracy > 0.75 and 75% of organs with accuracy > 0.85-performance competitive with more elaborate models applied to far fewer categories. These results demonstrate that biologically inspired modular stacking can yield robust, scalable fetal anatomy recognition in challenging clinical settings.
Cross-subject electromyography (EMG) pattern recognition faces significant challenges due to inter-subject variability in muscle anatomy, electrode placement, and signal characteristics. Traditional methods rely on subject-specific calibration data to adapt models to new users, an approach that is both time-consuming and impractical for large-scale, real-world deployment. This paper presents an approach to eliminate calibration requirements through feature disentanglement, enabling effective cross-subject generalization. We propose an end-to-end dual-branch adversarial neural network that simultaneously performs pattern recognition and individual identification by disentangling EMG features into pattern-specific and subject-specific components. The pattern-specific components facilitate robust pattern recognition for new users without model calibration, while the subject-specific components enable downstream applications such as task-invariant biometric identification. Experimental results demonstrate that the proposed model achieves robust performance on data from unseen users, outperforming various baseline methods in cross-subject scenarios. Overall, this study offers a new perspective for cross-subject EMG pattern recognition without model calibration and highlights the proposed model's potential for broader applications, such as task-independent biometric systems.