Kyphosis is a prevalent spinal condition where the spine curves in the sagittal plane, resulting in spine deformities. Curvature estimation provides a powerful index to assess the deformation severity of scoliosis. In current clinical diagnosis, the standard curvature estimation method for quantitatively assessing the curvature is performed by measuring the vertebral angle, which is the angle between two lines, drawn perpendicular to the upper and lower endplates of the involved vertebra. However, manual Cobb angle measurement requires considerable time and effort, along with associated problems such as interobserver and intraobserver variations. Hence, in this study, we propose UNet-based Attention Network for Thoracolumbar Vertebral Compression Fracture Angle (UANV), a vertebra angle measuring model using lateral spinal X-ray based on a deep convolutional neural network (CNN). Specifically, we considered the detailed shape of each vertebral body with an attention mechanism and then recorded each edge of each vertebra to calculate vertebrae angles.

We extend the Hybrid Unet Transformer (HUT) foundation model, which combines the advantages of the CNN and Transformer architectures with a noisy self-supervised approach, and demonstrate it in an ischemic stroke lesion segmentation task. We introduce a self-supervised approach using a noise anchor and show that it can perform better than a supervised approach under a limited amount of annotated data. We supplement our pre-training process with an additional unannotated CT perfusion dataset to validate our approach. Compared to the supervised version, the noisy self-supervised HUT (HUT-NSS) outperforms its counterpart by a margin of 2.4% in terms of dice score. HUT-NSS, on average, gained a further margin of 7.2% dice score and 28.1% Hausdorff Distance score over the state-of-the-art network USSLNet on the CT perfusion scans of the Ischemic Stroke Lesion Segmentation (ISLES2018) dataset. In limited annotated data sets, we show that HUT-NSS gained 7.87% of the dice score over USSLNet when we used 50% of the annotated data sets for training. HUT-NSS gained 7.47% of the dice score over USSLNet when we used 10% of the annotated datasets, and HUT-NSS gained 5.34% of the dice score over USSLNet when we used 1% of the annotated datasets for training. The code is available at https://github.com/vicsohntu/HUTNSS_CT .

To facilitate implementation of plan-of-the-day (POTD) selection for treating locally advanced cervical cancer (LACC), we developed a POTD assessment tool for CBCT-guided radiotherapy (RT). A female pelvis segmentation model (U-Seg3) is combined with a quantitative standard operating procedure (qSOP) to identify optimal and acceptable plans. 

Approach: The planning CT[i], corresponding structure set[ii], and manually contoured CBCTs[iii] (n=226) from 39 LACC patients treated with POTD (n=11) or non-adaptive RT (n=28) were used to develop U-Seg3, an algorithm incorporating deep-learning and deformable image registration techniques to segment the low-risk clinical target volume (LR-CTV), high-risk CTV (HR-CTV), bladder, rectum, and bowel bag. A single-channel input model (iii only, U-Seg1) was also developed. Contoured CBCTs from the POTD patients were (a) reserved for U-Seg3 validation/testing, (b) audited to determine optimal and acceptable plans, and (c) used to empirically derive a qSOP that maximised classification accuracy. 

Main Results: The median [interquartile range] DSC between manual and U-Seg3 contours was 0.83 [0.80], 0.78 [0.13], 0.94 [0.05], 0.86[0.09], and 0.90 [0.05] for the LR-CTV, HR-CTV, bladder, rectum, and bowel bag. These were significantly higher than U-Seg1 in all structures but bladder. The qSOP classified plans as acceptable if they met target coverage thresholds (LR-CTV≧99%, HR-CTV≧99.8%), with lower LR-CTV coverage (≧95%) sometimes allowed. The acceptable plan minimising bowel irradiation was considered optimal unless substantial bladder sparing could be achieved. With U-Seg3 embedded in the qSOP, optimal and acceptable plans were identified in 46/60 and 57/60 cases. 

Significance: U-Seg3 outperforms U-Seg1 and all known CBCT-based female pelvis segmentation models. The tool combining U-Seg3 and the qSOP identifies optimal plans with equivalent accuracy as two observers. In an implementation strategy whereby this tool serves as the second observer, plan selection confidence and decision-making time could be improved whilst simultaneously reducing the required number of POTD-trained radiographers by 50%.

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Accurate segmentation of mammographic mass is very important as shape characteristics of these masses play a significant role for radiologist to diagnose benign and malignant cases. Recently, various deep learning segmentation algorithms have become popular for segmentation tasks. In the present work, rigorous performance analysis of ten semantic-segmentation models has been performed with 518 images taken from DDSM dataset (digital database for screening mammography) with 208 mass images ϵ BIRAD3, 150 mass images ϵ BIRAD4 and 160 mass images ϵ BIRAD5 classes, respectively. These models are (1) simple convolution series models namely- VGG16/VGG19, (2) simple convolution DAG (directed acyclic graph) models namely- U-Net (3) dilated convolution DAG models namely ResNet18/ResNet50/ShuffleNet/XceptionNet/InceptionV2/MobileNetV2 and (4) hybrid model, i.e. hybrid U-Net. On the basis of exhaustive experimentation, it was observed that dilated convolution DAG models namely- ResNet50, ShuffleNet and MobileNetV2 outperform other network models yielding cumulative JI and F1 score values of 0.87 and 0.92, 0.85 and 91, 0.84 and 0.90, respectively. The segmented images obtained by best performing models were subjectively analyzed by participating radiologist in terms of (a) size (b) margins and (c) shape characteristics. From objective and subjective analysis it was concluded that ResNet50 is the optimal model for segmentation of difficult to delineate breast masses with dense background and masses where both masses and micro-calcifications are simultaneously present. The result of the study indicates that ResNet50 model can be used in routine clinical environment for segmentation of mammographic masses.

The two-dimensional computed tomography measurement of the consolidation tumor ratio (2D-CTR) has limitations in the prognostic evaluation of early-stage lung adenocarcinoma: the measurement is subject to inter-observer variability and lacks spatial information, which undermines its reliability as a prognostic tool. This study aims to investigate the value of the three-dimensional volume-based CTR (3D-CTR) in preoperative prognosis prediction for pathological Stage IA lung adenocarcinoma, and compare its predictive performance with that of 2D-CTR. A retrospective cohort of 980 patients with pathological Stage IA lung adenocarcinoma who underwent surgery was included. Preoperative thin-section CT images were processed using artificial intelligence (AI) software for 3D segmentation. Tumor solid component volume was quantified using different density thresholds (-300 to -150 HU, in 50 HU intervals), and 3D-CTR was calculated. The optimal threshold associated with prognosis was selected using multivariate Cox regression. The predictive performance of 3D-CTR and 2D-CTR for recurrence-free survival (RFS) post-surgery was compared using receiver operating characteristic (ROC) curves, and the best cutoff value was determined. The integrated discrimination improvement (IDI) was utilized to assess the enhancement in predictive efficacy of 3D-CTR relative to 2D-CTR. Among traditional preoperative factors, 2D-CTR (cutoff value 0.54, HR=1.044, P=0.001) and carcinoembryonic antigen (CEA) were identified as independent prognostic factors for RFS. In 3D analysis, -150 HU was determined as the optimal threshold for distinguishing solid components from ground-glass opacity (GGO) components. The corresponding 3D-CTR (cutoff value 0.41, HR=1.033, P<0.001) was an independent risk factor for RFS. The predictive performance of 3D-CTR was significantly superior to that of 2D-CTR (AUC: 0.867 vs. 0.840, P=0.006), with a substantial enhancement in predictive capacity, as evidenced by an IDI of 0.038 (95% CI: 0.021-0.055, P<0.001). Kaplan-Meier analysis revealed that the 5-year RFS rate for the 3D-CTR >0.41 group was significantly lower than that of the ≤0.41 group (68.5% vs. 96.7%, P<0.001). The 3D-CTR based on a -150 HU density threshold provides a more accurate prediction of postoperative recurrence risk in pathological Stage IA lung adenocarcinoma, demonstrating superior performance compared to traditional 2D-CTR.

Universal medical image segmentation using the Segment Anything Model (SAM) remains challenging due to its limited adaptability to medical domains. Existing adaptations, such as MedSAM, enhance SAM's performance in medical imaging but at the cost of reduced generalization to unseen data. Therefore, in this paper, we propose SAM-aware Test-Time Adaptation (SAM-TTA), a fundamentally different pipeline that preserves the generalization of SAM while improving its segmentation performance in medical imaging via a test-time framework. SAM-TTA tackles two key challenges: (1) input-level discrepancies caused by differences in image acquisition between natural and medical images and (2) semantic-level discrepancies due to fundamental differences in object definition between natural and medical domains (e.g., clear boundaries vs. ambiguous structures). Specifically, our SAM-TTA framework comprises (1) Self-adaptive Bezier Curve-based Transformation (SBCT), which adaptively converts single-channel medical images into three-channel SAM-compatible inputs while maintaining structural integrity, to mitigate the input gap between medical and natural images, and (2) Dual-scale Uncertainty-driven Mean Teacher adaptation (DUMT), which employs consistency learning to align SAM's internal representations to medical semantics, enabling efficient adaptation without auxiliary supervision or expensive retraining. Extensive experiments on five public datasets demonstrate that our SAM-TTA outperforms existing TTA approaches and even surpasses fully fine-tuned models such as MedSAM in certain scenarios, establishing a new paradigm for universal medical image segmentation. Code can be found at https://github.com/JianghaoWu/SAM-TTA.

Computed tomography (CT) analysis of lung morphology has significantly advanced our understanding of acute respiratory distress syndrome (ARDS). During the Coronavirus Disease 2019 (COVID-19) pandemic, CT imaging was widely utilized to evaluate lung injury and was suggested as a tool for predicting patient outcomes. However, data specifically focused on patients with ARDS admitted to intensive care units (ICUs) remain limited. This retrospective study analyzed patients admitted to ICUs between March 2020 and November 2022 with moderate to severe COVID-19 ARDS. All CT scans performed within 48 h of ICU admission were independently reviewed by three experts. Lung injury severity was quantified using the CT Severity Score (CT-SS; range 0-25). Patients were categorized as having severe disease (CT-SS ≥ 18) or non-severe disease (CT-SS < 18). The primary outcome was all-cause mortality at 90 days. Secondary outcomes included ICU mortality and medical complications during the ICU stay. Additionally, we evaluated a computer-assisted CT-score assessment using artificial intelligence software (CT Pneumonia Analysis^®, SIEMENS Healthcare) to explore the feasibility of automated measurement and routine implementation. A total of 215 patients with moderate to severe COVID-19 ARDS were included. The median CT-SS at admission was 18/25 [interquartile range, 15-21]. Among them, 120 patients (56%) had a severe CT-SS (≥ 18), while 95 patients (44%) had a non-severe CT-SS (< 18). The 90-day mortality rates were 20.8% for the severe group and 15.8% for the non-severe group (p = 0.35). No significant association was observed between CT-SS severity and patient outcomes. In patients with moderate to severe COVID-19 ARDS, systematic CT assessment of lung parenchymal injury was not a reliable predictor of 90-day mortality or ICU-related complications.

To develop a deep learning model to automatically measure the curvature-related sagittal parameters on cervical spinal X-ray images. This retrospective study collected a total of 700 lateral cervical spine X-ray images from three hospitals, consisting of 500 training sets, 100 internal test sets, and 100 external test sets. 6 measured parameters and 34 landmarks were measured and labeled by two doctors and averaged as the gold standard. A Convolutional neural network (CNN) model was built by training on 500 images and testing on 200 images. Statistical analysis is used to evaluate labeling differences and model performance. The percentages of the difference in distance between landmarks within 4 mm were 96.90% (Dr. A vs. Dr. B), 98.47% (Dr. A vs. model), and 97.31% (Dr. B vs. model); within 3 mm were 94.88% (Dr. A vs. Dr. B), 96.43% (Dr. A vs. model), and 94.16% (Dr. B vs. model). The mean difference of the algorithmic model in labeling landmarks was 1.17 ± 1.14 mm. The mean absolute error (MAE) of the algorithmic model for the Borden method, Cervical curvature index (CCI), Vertebral centroid measurement cervical lordosis (CCL), C₀-C₇ Cobb, C₁-C₇ Cobb, C₂-C₇ Cobb in the test sets are 1.67 mm, 2.01%, 3.22°, 2.37°, 2.49°, 2.81°, respectively; symmetric mean absolute percentage error (SMAPE) was 20.06%, 21.68%, 20.02%, 6.68%, 5.28%, 20.46%, respectively. Also, the algorithmic model of the six cervical sagittal parameters is in good agreement with the gold standard (intraclass correlation efficiency was 0.983; p < 0.001). Our deep learning algorithmic model had high accuracy in recognizing the landmarks of the cervical spine and automatically measuring cervical spine-related parameters, which can help radiologists improve their diagnostic efficiency.

To assess the suitability of Transformer-based architectures for medical image segmentation and investigate the potential advantages of Graph Neural Networks (GNNs) in this domain. We analyze the limitations of the Transformer, which models medical images as sequences of image patches, limiting its flexibility in capturing complex and irregular tumor structures. To address it, we propose U-GNN, a pure GNN-based U-shaped architecture designed for medical image segmentation. U-GNN retains the U-Net-inspired inductive bias while leveraging GNNs' topological modeling capabilities. The architecture consists of Vision GNN blocks stacked into a U-shaped structure. Additionally, we introduce the concept of multi-order similarity and propose a zero-computation-cost approach to incorporate higher-order similarity in graph construction. Each Vision GNN block segments the image into patch nodes, constructs multi-order similarity graphs, and aggregates node features via multi-order node information aggregation. Experimental evaluations on multi-organ and cardiac segmentation datasets demonstrate that U-GNN significantly outperforms existing CNN- and Transformer-based models. U-GNN achieves a 6% improvement in Dice Similarity Coefficient (DSC) and an 18% reduction in Hausdorff Distance (HD) compared to state-of-the-art methods. The source code will be released upon paper acceptance.

Although genetic variant effects often interact nonadditively, strategies to uncover epistasis remain in their infancy. Here we develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy, using deep learning-derived left ventricular mass estimates from 29,661 UK Biobank cardiac magnetic resonance images. We report epistatic variants near CCDC141, IGF1R, TTN and TNKS, identifying loci deemed insignificant in genome-wide association studies. Functional genomic and integrative enrichment analyses reveal that genes mapped from these loci share biological process gene ontologies and myogenic regulatory factors. Transcriptomic network analyses using 313 human hearts demonstrate strong co-expression correlations among these genes in healthy hearts, with significantly reduced connectivity in failing hearts. To assess causality, RNA silencing in human induced pluripotent stem cell-derived cardiomyocytes, combined with novel microfluidic single-cell morphology analysis, confirms that cardiomyocyte hypertrophy is nonadditively modifiable by interactions between CCDC141, TTN and IGF1R. Our results expand the scope of cardiac genetic regulation to epistasis.