This study aims to develop and validate a deep learning radiomics signature (DLRS) that integrates radiomics and deep learning features for the non-invasive prediction of microvascular invasion (MVI) in patients with colon cancer (CC). Furthermore, the study explores the potential association between DLRS and tumor immune heterogeneity. This study is a multi-center retrospective study that included a total of 1007 patients with colon cancer (CC) from three medical centers and The Cancer Genome Atlas (TCGA-COAD) database. Patients from Medical Centers 1 and 2 were divided into a training cohort (n = 592) and an internal validation cohort (n = 255) in a 7:3 ratio. Medical Center 3 (n = 135) and the TCGA-COAD database (n = 25) were used as external validation cohorts. Radiomics and deep learning features were extracted from contrast-enhanced venous-phase CT images. Feature selection was performed using machine learning algorithms, and three predictive models were developed: a radiomics model, a deep learning (DL) model, and a combined deep learning radiomics (DLR) model. The predictive performance of each model was evaluated using multiple metrics, including the area under the curve (AUC), sensitivity, and specificity. Additionally, differential gene expression analysis was conducted on RNA-seq data from the TCGA-COAD dataset to explore the association between the DLRS and tumor immune heterogeneity within the tumor microenvironment. Compared to the standalone radiomics and deep learning models, DLR fusion model demonstrated superior predictive performance. The AUC for the internal validation cohort was 0.883 (95% CI: 0.828-0.937), while the AUC for the external validation cohort reached 0.855 (95% CI: 0.775-0.935). Furthermore, stratifying patients from the TCGA-COAD dataset into high-risk and low-risk groups based on the DLRS revealed significant differences in immune cell infiltration and immune checkpoint expression between the two groups (P < 0.05). The contrast-enhanced CT-based DLR fusion model developed in this study effectively predicts the MVI status in patients with CC. This model serves as a non-invasive preoperative assessment tool and reveals a potential association between the DLRS and immune heterogeneity within the tumor microenvironment, providing insights to optimize individualized treatment strategies.

End-stage renal disease is characterized by an irreversible decline in kidney function. Despite a risk of chronic dysfunction of the transplanted kidney, renal transplantation is considered the most effective solution among available treatment options. Clinical attributes of graft survival prediction, such as allocation variables or results of pathological examinations, have been widely studied. Nevertheless, medical imaging is clinically used only to assess current transplant status. This study investigated the use of unsupervised deep learning-based algorithms to identify rich radiomic features that may be linked to graft survival from early dynamic contrast-enhanced magnetic resonance imaging data of renal transplants. A retrospective cohort of 108 transplanted patients (mean age 50 +/- 15, 67 men) undergoing systematic magnetic resonance imaging follow-up examinations (2013 to 2015) was used to train deep convolutional neural network models based on an unsupervised contrastive learning approach. 5-year graft survival analysis was performed from the obtained artificial intelligence radiomics features using penalized Cox models and Kaplan-Meier estimates. Using a validation set of 48 patients (mean age 54 +/- 13, 30 men) having 1-month post-transplantation magnetic resonance imaging examinations, the proposed approach demonstrated promising 5-year graft survival capability with a 72.7% concordance index from the artificial intelligence radiomics features. Unsupervised clustering of these radiomics features enabled statistically significant stratification of patients (p=0.029). This proof-of-concept study exposed the promising capability of artificial intelligence algorithms to extract relevant radiomics features that enable renal transplant survival prediction. Further studies are needed to demonstrate the robustness of this technique, and to identify appropriate procedures for integration of such an approach into multimodal and clinical settings.

We present a fully automated, anatomically guided deep learning pipeline for prostate cancer (PCa) risk stratification using routine MRI. The pipeline integrates three key components: an nnU-Net module for segmenting the prostate gland and its zones on axial T2-weighted MRI; a classification module based on the UMedPT Swin Transformer foundation model, fine-tuned on 3D patches with optional anatomical priors and clinical data; and a VAE-GAN framework for generating counterfactual heatmaps that localize decision-driving image regions. The system was developed using 1,500 PI-CAI cases for segmentation and 617 biparametric MRIs with metadata from the CHAIMELEON challenge for classification (split into 70% training, 10% validation, and 20% testing). Segmentation achieved mean Dice scores of 0.95 (gland), 0.94 (peripheral zone), and 0.92 (transition zone). Incorporating gland priors improved AUC from 0.69 to 0.72, with a three-scale ensemble achieving top performance (AUC = 0.79, composite score = 0.76), outperforming the 2024 CHAIMELEON challenge winners. Counterfactual heatmaps reliably highlighted lesions within segmented regions, enhancing model interpretability. In a prospective multi-center in-silico trial with 20 clinicians, AI assistance increased diagnostic accuracy from 0.72 to 0.77 and Cohen's kappa from 0.43 to 0.53, while reducing review time per case by 40%. These results demonstrate that anatomy-aware foundation models with counterfactual explainability can enable accurate, interpretable, and efficient PCa risk assessment, supporting their potential use as virtual biopsies in clinical practice.

Purpose: To evaluate the impact of harmonization and multi-region CT image feature integration on survival prediction in non-small cell lung cancer (NSCLC) patients, using handcrafted radiomics, pretrained foundation model (FM) features, and clinical data from a multicenter dataset. Methods: We analyzed CT scans and clinical data from 876 NSCLC patients (604 training, 272 test) across five centers. Features were extracted from the whole lung, tumor, mediastinal nodes, coronary arteries, and coronary artery calcium (CAC). Handcrafted radiomics and FM deep features were harmonized using ComBat, reconstruction kernel normalization (RKN), and RKN+ComBat. Regularized Cox models predicted overall survival; performance was assessed using the concordance index (C-index), 5-year time-dependent area under the curve (t-AUC), and hazard ratio (HR). SHapley Additive exPlanations (SHAP) values explained feature contributions. A consensus model used agreement across top region of interest (ROI) models to stratify patient risk. Results: TNM staging showed prognostic utility (C-index = 0.67; HR = 2.70; t-AUC = 0.85). The clinical + tumor radiomics model with ComBat achieved a C-index of 0.7552 and t-AUC of 0.8820. FM features (50-voxel cubes) combined with clinical data yielded the highest performance (C-index = 0.7616; t-AUC = 0.8866). An ensemble of all ROIs and FM features reached a C-index of 0.7142 and t-AUC of 0.7885. The consensus model, covering 78% of valid test cases, achieved a t-AUC of 0.92, sensitivity of 97.6%, and specificity of 66.7%. Conclusion: Harmonization and multi-region feature integration improve survival prediction in multicenter NSCLC data. Combining interpretable radiomics, FM features, and consensus modeling enables robust risk stratification across imaging centers.

Background: Accurate MRI-based identification of extramural vascular invasion (EVI) and mesorectal fascia invasion (MFI) is pivotal for risk-stratified management of rectal cancer, yet visual assessment is subjective and vulnerable to inter-institutional variability. Purpose: To develop and externally evaluate a multicenter, foundation-model-driven framework that automatically classifies EVI and MFI on axial and sagittal T2-weighted MRI. Methods: This retrospective study used 331 pre-treatment rectal cancer MRI examinations from three European hospitals. After TotalSegmentator-guided rectal patch extraction, a self-supervised frequency-domain harmonization pipeline was trained to minimize scanner-related contrast shifts. Four classifiers were compared: ResNet50, SeResNet, the universal biomedical pretrained transformer (UMedPT) with a lightweight MLP head, and a logistic-regression variant using frozen UMedPT features (UMedPT_LR). Results: UMedPT_LR achieved the best EVI detection when axial and sagittal features were fused (AUC = 0.82; sensitivity = 0.75; F1 score = 0.73), surpassing the Chaimeleon Grand-Challenge winner (AUC = 0.74). The highest MFI performance was attained by UMedPT on axial harmonized images (AUC = 0.77), surpassing the Chaimeleon Grand-Challenge winner (AUC = 0.75). Frequency-domain harmonization improved MFI classification but variably affected EVI performance. Conventional CNNs (ResNet50, SeResNet) underperformed, especially in F1 score and balanced accuracy. Conclusion: These findings demonstrate that combining foundation model features, harmonization, and multi-view fusion significantly enhances diagnostic performance in rectal MRI.

Medical image segmentation is vital for clinical diagnosis, yet current deep learning methods often demand extensive expert effort, i.e., either through annotating large training datasets or providing prompts at inference time for each new case. This paper introduces a zero-shot and automatic segmentation pipeline that combines off-the-shelf vision-language and segmentation foundation models. Given a medical image and a task definition (e.g., "segment the optic disc in an eye fundus image"), our method uses a grounding model to generate an initial bounding box, followed by a visual prompt boosting module that enhance the prompts, which are then processed by a promptable segmentation model to produce the final mask. To address the challenges of domain gap and result verification, we introduce a test-time adaptation framework featuring a set of learnable adaptors that align the medical inputs with foundation model representations. Its hyperparameters are optimized via Bayesian Optimization, guided by a proxy validation model without requiring ground-truth labels. Our pipeline offers an annotation-efficient and scalable solution for zero-shot medical image segmentation across diverse tasks. Our pipeline is evaluated on seven diverse medical imaging datasets and shows promising results. By proper decomposition and test-time adaptation, our fully automatic pipeline performs competitively with weakly-prompted interactive foundation models.

Human epidermal growth factor receptor 2 (HER2) is a crucial determinant of breast cancer prognosis and treatment options. The study aimed to establish an MRI-based habitat model to quantify intratumoral heterogeneity (ITH) and evaluate its potential in predicting HER2 expression status. Data from 340 patients with pathologically confirmed invasive breast cancer were retrospectively analyzed. Two tasks were designed for this study: Task 1 distinguished between HER2-positive and HER2-negative breast cancer. Task 2 distinguished between HER2-low and HER2-zero breast cancer. We developed the ITH, deep learning (DL), and radiomics signatures based on the features extracted from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). Clinical independent predictors were determined by multivariable logistic regression. Finally, a combined model was constructed by integrating the clinical independent predictors, ITH signature, and DL signature. The area under the receiver operating characteristic curve (AUC) served as the standard for assessing the performance of models. In task 1, the ITH signature performed well in the training set (AUC = 0.855) and the validation set (AUC = 0.842). In task 2, the AUCs of the ITH signature were 0.844 and 0.840, respectively, which still showed good prediction performance. In the validation sets of both tasks, the combined model exhibited the best prediction performance, with AUCs of 0.912 and 0.917 respectively, making it the optimal model. A combined model integrating clinical independent predictors, ITH signature, and DL signature can predict HER2 expression status preoperatively and noninvasively.

Substantial gaps exist in the neuroprognostication of cardiac arrest patients who remain comatose after the restoration of spontaneous circulation. Most studies focus on predicting survival, a measure confounded by the withdrawal of life-sustaining treatment decisions. Severe cerebral edema (SCE) may serve as an objective proximal imaging-based surrogate of neurologic injury. We retrospectively analyzed data from 288 patients to automate SCE detection with machine learning (ML) and to test the hypothesis that the quantitative values produced by these algorithms (ML_SCE) can improve predictions of neurologic outcomes. Ground-truth SCE (GT_SCE) classification was based on radiology reports. The model attained a cross-validated testing accuracy of 87% [95% CI: 84%, 89%] for detecting SCE. Attention maps explaining SCE classification focused on cisternal regions (p<0.05). Multivariable analyses showed that older age (p<0.001), non-shockable initial cardiac rhythm (p=0.004), and greater ML_SCE values (p<0.001) were significant predictors of poor neurologic outcomes, with GT_SCE (p=0.064) as a non-significant covariate. Our results support the feasibility of automated SCE detection. Future prospective studies with standardized neurologic assessments are needed to substantiate the utility of quantitative ML_SCE values to improve neuroprognostication.

Magnetic resonance (MR) tagging is an imaging technique for noninvasively tracking tissue motion in vivo by creating a visible pattern of magnetization saturation (tags) that deforms with the tissue. Due to longitudinal relaxation and progression to steady-state, the tags and tissue brightnesses change over time, which makes tracking with optical flow methods error-prone. Although Fourier methods can alleviate these problems, they are also sensitive to brightness changes as well as spectral spreading due to motion. To address these problems, we introduce the brightness-invariant tracking estimation (BRITE) technique for tagged MRI. BRITE disentangles the anatomy from the tag pattern in the observed tagged image sequence and simultaneously estimates the Lagrangian motion. The inherent ill-posedness of this problem is addressed by leveraging the expressive power of denoising diffusion probabilistic models to represent the probabilistic distribution of the underlying anatomy and the flexibility of physics-informed neural networks to estimate biologically-plausible motion. A set of tagged MR images of a gel phantom was acquired with various tag periods and imaging flip angles to demonstrate the impact of brightness variations and to validate our method. The results show that BRITE achieves more accurate motion and strain estimates as compared to other state of the art methods, while also being resistant to tag fading.

This paper presents a novel method for monocular patient-to-image intraoperative registration, specifically designed to operate without any external hardware tracking equipment or fiducial point markers. Leveraging a synthetic microscopy surgical scene dataset with a wide range of transformations, our approach directly maps preoperative CT scans to 2D intraoperative surgical frames through a lightweight neural network for real-time cochlear implant surgery guidance via a zero-shot learning approach. Unlike traditional methods, our framework seamlessly integrates with monocular surgical microscopes, making it highly practical for clinical use without additional hardware dependencies and requirements. Our method estimates camera poses, which include a rotation matrix and a translation vector, by learning from the synthetic dataset, enabling accurate and efficient intraoperative registration. The proposed framework was evaluated on nine clinical cases using a patient-specific and cross-patient validation strategy. Our results suggest that our approach achieves clinically relevant accuracy in predicting 6D camera poses for registering 3D preoperative CT scans to 2D surgical scenes with an angular error within 10 degrees in most cases, while also addressing limitations of traditional methods, such as reliance on external tracking systems or fiducial markers.