Accurate segmentation of lung tumors is essential for advancing personalized medicine in non-small cell lung cancer (NSCLC). However, stage IV NSCLC presents significant challenges due to heterogeneous tumor morphology and the presence of associated conditions including infection, atelectasis and pleural effusion. The complexity of multicentric datasets further complicates robust segmentation across diverse clinical settings. In this study, we evaluate deep-learning-based approaches for automated segmentation of advanced-stage lung tumors using 3D architectures on 387 CT scans from the Deep-Lung-IV study. Through comprehensive experiments, we assess the impact of model design, HU windowing, and dataset size on delineation performance, providing practical guidelines for robust implementation. Additionally, we propose a confidence score using deep ensembles to quantify prediction uncertainty and automate the identification of complex cases that require further review. Our results demonstrate the potential of attention-based architectures and specific preprocessing strategies to improve segmentation quality in such a challenging clinical scenario, while emphasizing the importance of uncertainty estimation to build trustworthy AI systems in medical imaging. Code is available at: https://github.com/Sacha-Dedeken/SegStageIVNSCLC.

Accurately and efficiently estimating the cortical thickness from magnetic resonance images (MRIs) is crucial for neuroscientific studies and clinical applications with various large-scale datasets. Diffeomorphic registration-based cortical thickness estimation (DiReCT) is a prominent traditional method of calculating such measures directly from original MRIs by applying diffeomorphic registration on segmented tissues. However, it suffers from prolonged computational time and limited reproducibility, impediments to its application in large-scale studies or real-time environments. This paper proposes a framework for cortical thickness estimation using deep learning-based anatomy segmentation and diffeomorphic registration. The framework begins by applying a convolutional neural network (CNN) segmentation model to the original image, generating a segmentation map that accurately delineates the cortical boundaries. Subsequently, a pair of distance maps generated from the segmentation map is injected into an unsupervised learning-based registration network for fast and diffeomorphic registration. A novel algorithm based on diffeomorphisms of different time points is proposed to calculate the final thickness map. We systematically evaluated and compared our method with surface-based measures from FreeSurfer on two distinct datasets. The experimental results demonstrated a superior performance of the proposed method, surpassing the performance of DiReCT and DL+DiReCT in terms of time efficiency and consistency with FreeSurfer. Our code and pre-trained models are publicly available at: https://github.com/wujiong-hub/DL-CTE.git.

Inhalation injuries face a challenge in clinical diagnosis and grading due to the limitations of traditional methods, such as Abbreviated Injury Score (AIS), which rely on subjective assessments and show weak correlations with clinical outcomes. This study introduces a novel deep learning-based framework for grading inhalation injuries using bronchoscopy images with the duration of mechanical ventilation as an objective metric. To address the scarcity of medical imaging data, we propose enhanced StarGAN, a generative model that integrates Patch Loss and SSIM Loss to improve synthetic images' quality and clinical relevance. The augmented dataset generated by enhanced StarGAN significantly improved classification performance when evaluated using the Swin Transformer, achieving an accuracy of 77.78%, an 11.11% improvement over the original dataset. Image quality was assessed using the Fr\'echet Inception Distance (FID), where Enhanced StarGAN achieved the lowest FID of 30.06, outperforming baseline models. Burn surgeons confirmed the realism and clinical relevance of the generated images, particularly the preservation of bronchial structures and color distribution. These results highlight the potential of enhanced StarGAN in addressing data limitations and improving classification accuracy for inhalation injury grading.

AO_SCPLOWBSTRACTC_SCPLOWThe quantification of the Ki-67 labeling index (LI) is critical for assessing tumor proliferation and prognosis in tumors, yet manual scoring remains a common practice. This study presents an automated workflow for Ki-67 scoring in whole slide images (WSIs) using an Apache Groovy code script for QuPath, complemented by a Python-based post-processing script, providing cell density maps and summary tables. The tissue and cell segmentation are performed using StarDist, a deep learning model, and adaptive thresholding to classify Ki-67 positive and negative nuclei. The pipeline was applied to a cohort of 632 pediatric brain tumor cases with 734 Ki-67-stained WSIs from the Childrens Brain Tumor Network. Medulloblastoma showed the highest Ki-67 LI (median: 19.84), followed by atypical teratoid rhabdoid tumor (median: 19.36). Moderate values were observed in brainstem glioma-diffuse intrinsic pontine glioma (median: 11.50), high-grade glioma (grades 3 & 4) (median: 9.50), and ependymoma (median: 5.88). Lower indices were found in meningioma (median: 1.84), while the lowest were seen in low-grade glioma (grades 1 & 2) (median: 0.85), dysembryoplastic neuroepithelial tumor (median: 0.63), and ganglioglioma (median: 0.50). The results aligned with the consensus of the oncology, demonstrating a significant correlation in Ki-67 LI across most of the tumor families/types, with high malignancy tumors showing the highest proliferation indices and lower malignancy tumors exhibiting lower Ki-67 LI. The automated approach facilitates the assessment of large amounts of Ki-67 WSIs in research settings.

Accurate multi-modal medical image translation requires ha-rmonizing global anatomical semantics and local structural fidelity, a challenge complicated by intermodality information loss and structural distortion. We propose ABS-Mamba, a novel architecture integrating the Segment Anything Model 2 (SAM2) for organ-aware semantic representation, specialized convolutional neural networks (CNNs) for preserving modality-specific edge and texture details, and Mamba's selective state-space modeling for efficient long- and short-range feature dependencies. Structurally, our dual-resolution framework leverages SAM2's image encoder to capture organ-scale semantics from high-resolution inputs, while a parallel CNNs branch extracts fine-grained local features. The Robust Feature Fusion Network (RFFN) integrates these epresentations, and the Bidirectional Mamba Residual Network (BMRN) models spatial dependencies using spiral scanning and bidirectional state-space dynamics. A three-stage skip fusion decoder enhances edge and texture fidelity. We employ Efficient Low-Rank Adaptation (LoRA+) fine-tuning to enable precise domain specialization while maintaining the foundational capabilities of the pre-trained components. Extensive experimental validation on the SynthRAD2023 and BraTS2019 datasets demonstrates that ABS-Mamba outperforms state-of-the-art methods, delivering high-fidelity cross-modal synthesis that preserves anatomical semantics and structural details to enhance diagnostic accuracy in clinical applications. The code is available at https://github.com/gatina-yone/ABS-Mamba

We developed and tested a deep-learning-based algorithm for the approximation of contrast agent dosage based on computed tomography (CT) scout images. We prospectively enrolled 817 patients undergoing clinically indicated CT imaging, predominantly of the thorax and/or abdomen. Patient weight was collected by study staff prior to the examination 1) with a weight scale and 2) as self-reported. Based on the scout images, we developed an EfficientNet convolutional neural network pipeline to estimate the optimal contrast agent dose based on patient weight and provide a browser-based user interface as a versatile open-source tool to account for different contrast agent compounds. We additionally analyzed the body-weight-informative CT features by synthesizing representative examples for different weights using in-context learning and dataset distillation. The cohort consisted of 533 thoracic, 70 abdominal and 229 thoracic-abdominal CT scout scans. Self-reported patient weight was statistically significantly lower than manual measurements (75.13 kg vs. 77.06 kg; p < 10-5, Wilcoxon signed-rank test). Our pipeline predicted patient weight with a mean absolute error of 3.90 {+/-} 0.20 kg (corresponding to a roughly 4.48 - 11.70 ml difference in contrast agent depending on the agent) in 5-fold cross-validation and is publicly available at https://tinyurl.com/ct-scout-weight. Interpretability analysis revealed that both larger anatomical shape and higher overall attenuation were predictive of body weight. Our open-source deep learning pipeline allows for the automatic estimation of accurate contrast agent dosing based on scout images in routine CT imaging studies. This approach has the potential to streamline contrast agent dosing workflows, improve efficiency, and enhance patient safety by providing quick and accurate weight estimates without additional measurements or reliance on potentially outdated records. The models performance may vary depending on patient positioning and scout image quality and the approach requires validation on larger patient cohorts and other clinical centers. Author SummaryAutomation of medical workflows using AI has the potential to increase reproducibility while saving costs and time. Here, we investigated automating the estimation of the required contrast agent dosage for CT examinations. We trained a deep neural network to predict the body weight from the initial 2D CT Scout images that are required prior to the actual CT examination. The predicted weight is then converted to a contrast agent dosage based on contrast-agent-specific conversion factors. To facilitate application in clinical routine, we developed a user-friendly browser-based user interface that allows clinicians to select a contrast agent or input a custom conversion factor to receive dosage suggestions, with local data processing in the browser. We also investigate what image characteristics predict body weight and find plausible relationships such as higher attenuation and larger anatomical shapes correlating with higher body weights. Our work goes beyond prior work by implementing a single model for a variety of anatomical regions, providing an accessible user interface and investigating the predictive characteristics of the images.

Late gadolinium enhancement (LGE) cardiac magnetic resonance (CMR) imaging is considered the in vivo reference standard for assessing infarct size (IS) and microvascular obstruction (MVO) in ST-elevation myocardial infarction (STEMI) patients. However, the exact quantification of those markers of myocardial infarct severity remains challenging and very time-consuming. As LGE distribution patterns can be quite complex and hard to delineate from the blood pool or epicardial fat, automatic segmentation of LGE CMR images is challenging. In this work, we propose a cascaded framework of two-dimensional and three-dimensional convolutional neural networks (CNNs) which enables to calculate the extent of myocardial infarction in a fully automated way. By artificially generating segmentation errors which are characteristic for 2D CNNs during training of the cascaded framework we are enforcing the detection and correction of 2D segmentation errors and hence improve the segmentation accuracy of the entire method. The proposed method was trained and evaluated on two publicly available datasets. We perform comparative experiments where we show that our framework outperforms state-of-the-art reference methods in segmentation of myocardial infarction. Furthermore, in extensive ablation studies we show the advantages that come with the proposed error correcting cascaded method. The code of this project is publicly available at https://github.com/matthi99/EcorC.git.

This paper proposes batch augmentation with unimodal fine-tuning to detect the fetus's organs from ultrasound images and associated clinical textual information. We also prescribe pre-training initial layers with investigated medical data before the multimodal training. At first, we apply a transferred initialization with the unimodal image portion of the dataset with batch augmentation. This step adjusts the initial layer weights for medical data. Then, we apply neural networks (NNs) with fine-tuned initial layers to images in batches with batch augmentation to obtain features. We also extract information from descriptions of images. We combine this information with features obtained from images to train the head layer. We write a dataloader script to load the multimodal data and use existing unimodal image augmentation techniques with batch augmentation for the multimodal data. The dataloader brings a new random augmentation for each batch to get a good generalization. We investigate the FPU23 ultrasound and UPMC Food-101 multimodal datasets. The multimodal large language model (LLM) with the proposed training provides the best results among the investigated methods. We receive near state-of-the-art (SOTA) performance on the UPMC Food-101 dataset. We share the scripts of the proposed method with traditional counterparts at the following repository: github.com/dipuk0506/multimodal

Interest has grown in combining radiology, pathology, genomic, and clinical data to improve the accuracy of diagnostic and prognostic predictions toward precision health. However, most existing works choose their datasets and modeling approaches empirically and in an ad hoc manner. A prior study proposed four partial information decomposition (PID)-based metrics to provide a theoretical understanding of multimodal data interactions: redundancy, uniqueness of each modality, and synergy. However, these metrics have only been evaluated in a limited collection of biomedical data, and the existing work does not elucidate the effect of parameter selection when calculating the PID metrics. In this work, we evaluate PID metrics on a wider range of biomedical data, including clinical, radiology, pathology, and genomic data, and propose potential improvements to the PID metrics. We apply the PID metrics to seven different modality pairs across four distinct cohorts (datasets). We compare and interpret trends in the resulting PID metrics and downstream model performance in these multimodal cohorts. The downstream tasks being evaluated include predicting the prognosis (either overall survival or recurrence) of patients with non-small cell lung cancer, prostate cancer, and glioblastoma. We found that, while PID metrics are informative, solely relying on these metrics to decide on a fusion approach does not always yield a machine learning model with optimal performance. Of the seven different modality pairs, three had poor (0%), three had moderate (66%-89%), and only one had perfect (100%) consistency between the PID values and model performance. We propose two improvements to the PID metrics (determining the optimal parameters and uncertainty estimation) and identified areas where PID metrics could be further improved. The current PID metrics are not accurate enough for estimating the multimodal data interactions and need to be improved before they can serve as a reliable tool. We propose improvements and provide suggestions for future work. Code: https://github.com/zhtyolivia/pid-multimodal.

Deformable registration is a fundamental task in medical image processing, aiming to achieve precise alignment by establishing nonlinear correspondences between images. Traditional methods offer good adaptability and interpretability but are limited by computational efficiency. Although deep learning approaches have significantly improved registration speed and accuracy, they often lack flexibility and generalizability across different datasets and tasks. In recent years, foundation models have emerged as a promising direction, leveraging large and diverse datasets to learn universal features and transformation patterns for image registration, thus demonstrating strong cross-task transferability. However, these models still face challenges in generalization and robustness when encountering novel anatomical structures, varying imaging conditions, or unseen modalities. To address these limitations, this paper incorporates Sharpness-Aware Minimization (SAM) into foundation models to enhance their generalization and robustness in medical image registration. By optimizing the flatness of the loss landscape, SAM improves model stability across diverse data distributions and strengthens its ability to handle complex clinical scenarios. Experimental results show that foundation models integrated with SAM achieve significant improvements in cross-dataset registration performance, offering new insights for the advancement of medical image registration technology. Our code is available at https://github.com/Promise13/fm_sam}{https://github.com/Promise13/fm\_sam.