In computed tomography (CT), achieving high image quality while minimizing radiation exposure remains a key clinical challenge. This paper presents CAPRI-CT, a novel causal-aware deep learning framework for Causal Analysis and Predictive Reasoning for Image Quality Optimization in CT imaging. CAPRI-CT integrates image data with acquisition metadata (such as tube voltage, tube current, and contrast agent types) to model the underlying causal relationships that influence image quality. An ensemble of Variational Autoencoders (VAEs) is employed to extract meaningful features and generate causal representations from observational data, including CT images and associated imaging parameters. These input features are fused to predict the Signal-to-Noise Ratio (SNR) and support counterfactual inference, enabling what-if simulations, such as changes in contrast agents (types and concentrations) or scan parameters. CAPRI-CT is trained and validated using an ensemble learning approach, achieving strong predictive performance. By facilitating both prediction and interpretability, CAPRI-CT provides actionable insights that could help radiologists and technicians design more efficient CT protocols without repeated physical scans. The source code and dataset are publicly available at https://github.com/SnehaGeorge22/capri-ct.

Automated X-ray inspection is crucial for efficient and unobtrusive security screening in various public settings. However, challenges such as object occlusion, variations in the physical properties of items, diversity in X-ray scanning devices, and limited training data hinder accurate and reliable detection of illicit items. Despite the large body of research in the field, reported experimental evaluations are often incomplete, with frequently conflicting outcomes. To shed light on the research landscape and facilitate further research, a systematic, detailed, and thorough comparative evaluation of recent Deep Learning (DL)-based methods for X-ray object detection is conducted. For this, a comprehensive evaluation framework is developed, composed of: a) Six recent, large-scale, and widely used public datasets for X-ray illicit item detection (OPIXray, CLCXray, SIXray, EDS, HiXray, and PIDray), b) Ten different state-of-the-art object detection schemes covering all main categories in the literature, including generic Convolutional Neural Network (CNN), custom CNN, generic transformer, and hybrid CNN-transformer architectures, and c) Various detection (mAP50 and mAP50:95) and time/computational-complexity (inference time (ms), parameter size (M), and computational load (GFLOPS)) metrics. A thorough analysis of the results leads to critical observations and insights, emphasizing key aspects such as: a) Overall behavior of the object detection schemes, b) Object-level detection performance, c) Dataset-specific observations, and d) Time efficiency and computational complexity analysis. To support reproducibility of the reported experimental results, the evaluation code and model weights are made publicly available at https://github.com/jgenc/xray-comparative-evaluation.

Recent advances in deep learning have led to robust automated tools for segmentation of abdominal computed tomography (CT). Meanwhile, segmentation of magnetic resonance imaging (MRI) is substantially more challenging due to the inherent signal variability and the increased effort required for annotating training datasets. Hence, existing approaches are trained on limited sets of MRI sequences, which might limit their generalizability. To characterize the landscape of MRI abdominal segmentation tools, we present here a comprehensive benchmarking of the three state-of-the-art and open-source models: MRSegmentator, MRISegmentator-Abdomen, and TotalSegmentator MRI. Since these models are trained using labor-intensive manual annotation cycles, we also introduce and evaluate ABDSynth, a SynthSeg-based model purely trained on widely available CT segmentations (no real images). More generally, we assess accuracy and generalizability by leveraging three public datasets (not seen by any of the evaluated methods during their training), which span all major manufacturers, five MRI sequences, as well as a variety of subject conditions, voxel resolutions, and fields-of-view. Our results reveal that MRSegmentator achieves the best performance and is most generalizable. In contrast, ABDSynth yields slightly less accurate results, but its relaxed requirements in training data make it an alternative when the annotation budget is limited. The evaluation code and datasets are given for future benchmarking at https://github.com/deepakri201/AbdoBench, along with inference code and weights for ABDSynth.

Pseudo-healthy image inpainting is an essential preprocessing step for analyzing pathological brain MRI scans. Most current inpainting methods favor slice-wise 2D models for their high in-plane fidelity, but their independence across slices produces discontinuities in the volume. Fully 3D models alleviate this issue, but their high model capacity demands extensive training data for reliable, high-fidelity synthesis -- often impractical in medical settings. We address these limitations with a hierarchical diffusion framework by replacing direct 3D modeling with two perpendicular coarse-to-fine 2D stages. An axial diffusion model first yields a coarse, globally consistent inpainting; a coronal diffusion model then refines anatomical details. By combining perpendicular spatial views with adaptive resampling, our method balances data efficiency and volumetric consistency. Our experiments show our approach outperforms state-of-the-art baselines in both realism and volumetric consistency, making it a promising solution for pseudo-healthy image inpainting. Code is available at https://github.com/dou0000/3dMRI-Consistent-Inpaint.

Accurate and efficient medical image segmentation is crucial but challenging due to anatomical variability and high computational demands on volumetric data. Recent hybrid CNN-Transformer architectures achieve state-of-the-art results but add significant complexity. In this paper, we propose MLRU++, a Multiscale Lightweight Residual UNETR++ architecture designed to balance segmentation accuracy and computational efficiency. It introduces two key innovations: a Lightweight Channel and Bottleneck Attention Module (LCBAM) that enhances contextual feature encoding with minimal overhead, and a Multiscale Bottleneck Block (M2B) in the decoder that captures fine-grained details via multi-resolution feature aggregation. Experiments on four publicly available benchmark datasets (Synapse, BTCV, ACDC, and Decathlon Lung) demonstrate that MLRU++ achieves state-of-the-art performance, with average Dice scores of 87.57% (Synapse), 93.00% (ACDC), and 81.12% (Lung). Compared to existing leading models, MLRU++ improves Dice scores by 5.38% and 2.12% on Synapse and ACDC, respectively, while significantly reducing parameter count and computational cost. Ablation studies evaluating LCBAM and M2B further confirm the effectiveness of the proposed architectural components. Results suggest that MLRU++ offers a practical and high-performing solution for 3D medical image segmentation tasks. Source code is available at: https://github.com/1027865/MLRUPP

Accurate and efficient medical image segmentation is crucial but challenging due to anatomical variability and high computational demands on volumetric data. Recent hybrid CNN-Transformer architectures achieve state-of-the-art results but add significant complexity. In this paper, we propose MLRU++, a Multiscale Lightweight Residual UNETR++ architecture designed to balance segmentation accuracy and computational efficiency. It introduces two key innovations: a Lightweight Channel and Bottleneck Attention Module (LCBAM) that enhances contextual feature encoding with minimal overhead, and a Multiscale Bottleneck Block (M2B) in the decoder that captures fine-grained details via multi-resolution feature aggregation. Experiments on four publicly available benchmark datasets (Synapse, BTCV, ACDC, and Decathlon Lung) demonstrate that MLRU++ achieves state-of-the-art performance, with average Dice scores of 87.57% (Synapse), 93.00% (ACDC), and 81.12% (Lung). Compared to existing leading models, MLRU++ improves Dice scores by 5.38% and 2.12% on Synapse and ACDC, respectively, while significantly reducing parameter count and computational cost. Ablation studies evaluating LCBAM and M2B further confirm the effectiveness of the proposed architectural components. Results suggest that MLRU++ offers a practical and high-performing solution for 3D medical image segmentation tasks. Source code is available at: https://github.com/1027865/MLRUPP

MRI is an indispensable clinical tool, offering a rich variety of tissue contrasts to support broad diagnostic and research applications. Clinical exams routinely acquire multiple structural sequences that provide complementary information for differential diagnosis, while research protocols often incorporate advanced functional, diffusion, spectroscopic, and relaxometry sequences to capture multidimensional insights into tissue structure and composition. However, these capabilities come at the cost of prolonged scan times, which reduce patient throughput, increase susceptibility to motion artifacts, and may require trade-offs in image quality or diagnostic scope. Over the last two decades, advances in image reconstruction algorithms--alongside improvements in hardware and pulse sequence design--have made it possible to accelerate acquisitions while preserving diagnostic quality. Central to this progress is the ability to incorporate prior information to regularize the solutions to the reconstruction problem. In this tutorial, we overview the basics of MRI reconstruction and highlight state-of-the-art approaches, beginning with classical methods that rely on explicit hand-crafted priors, and then turning to deep learning methods that leverage a combination of learned and crafted priors to further push the performance envelope. We also explore the translational aspects and eventual clinical implications of these methods. We conclude by discussing future directions to address remaining challenges in MRI reconstruction. The tutorial is accompanied by a Python toolbox (https://github.com/tutorial-MRI-recon/tutorial) to demonstrate select methods discussed in the article.

Existing saliency-guided training approaches improve model generalization by incorporating a loss term that compares the model's class activation map (CAM) for a sample's true-class ({\it i.e.}, correct-label class) against a human reference saliency map. However, prior work has ignored the false-class CAM(s), that is the model's saliency obtained for incorrect-label class. We hypothesize that in binary tasks the true and false CAMs should diverge on the important classification features identified by humans (and reflected in human saliency maps). We use this hypothesis to motivate three new saliency-guided training methods incorporating both true- and false-class model's CAM into the training strategy and a novel post-hoc tool for identifying important features. We evaluate all introduced methods on several diverse binary close-set and open-set classification tasks, including synthetic face detection, biometric presentation attack detection, and classification of anomalies in chest X-ray scans, and find that the proposed methods improve generalization capabilities of deep learning models over traditional (true-class CAM only) saliency-guided training approaches. We offer source codes and model weights\footnote{GitHub repository link removed to preserve anonymity} to support reproducible research.

Faithfulness and interpretability are essential for deploying deep neural networks (DNNs) in safety-critical domains such as medical imaging. B-cos networks offer a promising solution by replacing standard linear layers with a weight-input alignment mechanism, producing inherently interpretable, class-specific explanations without post-hoc methods. While maintaining diagnostic performance competitive with state-of-the-art DNNs, standard B-cos models suffer from severe aliasing artifacts in their explanation maps, making them unsuitable for clinical use where clarity is essential. Additionally, the original B-cos formulation is limited to multi-class settings, whereas chest X-ray analysis often requires multi-label classification due to co-occurring abnormalities. In this work, we address both limitations: (1) we introduce anti-aliasing strategies using FLCPooling (FLC) and BlurPool (BP) to significantly improve explanation quality, and (2) we extend B-cos networks to support multi-label classification. Our experiments on chest X-ray datasets demonstrate that the modified $\text{B-cos}_\text{FLC}$ and $\text{B-cos}_\text{BP}$ preserve strong predictive performance while providing faithful and artifact-free explanations suitable for clinical application in multi-label settings. Code available at: $\href{https://github.com/mkleinma/B-cos-medical-paper}{GitHub repository}$.

Deep learning models for medical image segmentation often struggle with task-specific characteristics, limiting their generalization to unseen tasks with new anatomies, labels, or modalities. Retraining or fine-tuning these models requires substantial human effort and computational resources. To address this, in-context learning (ICL) has emerged as a promising paradigm, enabling query image segmentation by conditioning on example image-mask pairs provided as prompts. Unlike previous approaches that rely on implicit modeling or non-end-to-end pipelines, we redefine the core interaction mechanism in ICL as an explicit retrieval process, termed E-ICL, benefiting from the emergence of vision foundation models (VFMs). E-ICL captures dense correspondences between queries and prompts at minimal learning cost and leverages them to dynamically weight multi-class prompt masks. Built upon E-ICL, we propose EICSeg, the first end-to-end ICL framework that integrates complementary VFMs for universal medical image segmentation. Specifically, we introduce a lightweight SD-Adapter to bridge the distinct functionalities of the VFMs, enabling more accurate segmentation predictions. To fully exploit the potential of EICSeg, we further design a scalable self-prompt training strategy and an adaptive token-to-image prompt selection mechanism, facilitating both efficient training and inference. EICSeg is trained on 47 datasets covering diverse modalities and segmentation targets. Experiments on nine unseen datasets demonstrate its strong few-shot generalization ability, achieving an average Dice score of 74.0%, outperforming existing in-context and few-shot methods by 4.5%, and reducing the gap to task-specific models to 10.8%. Even with a single prompt, EICSeg achieves a competitive average Dice score of 60.1%. Notably, it performs automatic segmentation without manual prompt engineering, delivering results comparable to interactive models while requiring minimal labeled data. Source code will be available at https://github.com/ zerone-fg/EICSeg.