Artificial intelligence (AI) has introduced numerous opportunities for human assistance and task automation in medicine. However, it suffers from poor generalization in the presence of shifts in the data distribution. In the context of AI-based computed tomography (CT) analysis, significant data distribution shifts can be caused by changes in scanner manufacturer, reconstruction technique or dose. AI harmonization techniques can address this problem by reducing distribution shifts caused by various acquisition settings. This paper presents an open-source benchmark dataset containing CT scans of an anthropomorphic phantom acquired with various scanners and settings, which purpose is to foster the development of AI harmonization techniques. Using a phantom allows fixing variations attributed to inter- and intra-patient variations. The dataset includes 1378 image series acquired with 13 scanners from 4 manufacturers across 8 institutions using a harmonized protocol as well as several acquisition doses. Additionally, we present a methodology, baseline results and open-source code to assess image- and feature-level stability and liver tissue classification, promoting the development of AI harmonization strategies.

PanTS is a large-scale, multi-institutional dataset curated to advance research in pancreatic CT analysis. It contains 36,390 CT scans from 145 medical centers, with expert-validated, voxel-wise annotations of over 993,000 anatomical structures, covering pancreatic tumors, pancreas head, body, and tail, and 24 surrounding anatomical structures such as vascular/skeletal structures and abdominal/thoracic organs. Each scan includes metadata such as patient age, sex, diagnosis, contrast phase, in-plane spacing, slice thickness, etc. AI models trained on PanTS achieve significantly better performance in pancreatic tumor detection, localization, and segmentation compared to those trained on existing public datasets. Our analysis indicates that these gains are directly attributable to the 16x larger-scale tumor annotations and indirectly supported by the 24 additional surrounding anatomical structures. As the largest and most comprehensive resource of its kind, PanTS offers a new benchmark for developing and evaluating AI models in pancreatic CT analysis.

Low-dose computed tomography (LDCT) imaging employed in lung cancer screening (LCS) programs is increasing in uptake worldwide. LCS programs herald a generational opportunity to simultaneously detect cancer and non-cancer-related early-stage lung disease. Yet these efforts are hampered by a shortage of radiologists to interpret scans at scale. Here, we present TANGERINE, a computationally frugal, open-source vision foundation model for volumetric LDCT analysis. Designed for broad accessibility and rapid adaptation, TANGERINE can be fine-tuned off the shelf for a wide range of disease-specific tasks with limited computational resources and training data. Relative to models trained from scratch, TANGERINE demonstrates fast convergence during fine-tuning, thereby requiring significantly fewer GPU hours, and displays strong label efficiency, achieving comparable or superior performance with a fraction of fine-tuning data. Pretrained using self-supervised learning on over 98,000 thoracic LDCTs, including the UK's largest LCS initiative to date and 27 public datasets, TANGERINE achieves state-of-the-art performance across 14 disease classification tasks, including lung cancer and multiple respiratory diseases, while generalising robustly across diverse clinical centres. By extending a masked autoencoder framework to 3D imaging, TANGERINE offers a scalable solution for LDCT analysis, departing from recent closed, resource-intensive models by combining architectural simplicity, public availability, and modest computational requirements. Its accessible, open-source lightweight design lays the foundation for rapid integration into next-generation medical imaging tools that could transform LCS initiatives, allowing them to pivot from a singular focus on lung cancer detection to comprehensive respiratory disease management in high-risk populations.

Vision transformers (ViTs) have rapidly gained prominence in medical imaging tasks such as disease classification, segmentation, and detection due to their superior accuracy compared to conventional deep learning models. However, due to their size and complex interactions via the self-attention mechanism, they are not well understood. In particular, it is unclear whether the representations produced by such models are semantically meaningful. In this paper, using a projected gradient-based algorithm, we show that their representations are not semantically meaningful and they are inherently vulnerable to small changes. Images with imperceptible differences can have very different representations; on the other hand, images that should belong to different semantic classes can have nearly identical representations. Such vulnerability can lead to unreliable classification results; for example, unnoticeable changes cause the classification accuracy to be reduced by over 60\%. %. To the best of our knowledge, this is the first work to systematically demonstrate this fundamental lack of semantic meaningfulness in ViT representations for medical image classification, revealing a critical challenge for their deployment in safety-critical systems.

Vision Transformers (ViTs) have gained significant popularity in the natural image domain but have been less successful in 3D medical image segmentation. Nevertheless, 3D ViTs are particularly interesting for large medical imaging volumes due to their efficient self-supervised training within the masked autoencoder (MAE) framework, which enables the use of imaging data without the need for expensive manual annotations. intracranial arterial calcification (IAC) is an imaging biomarker visible on routinely acquired CT scans linked to neurovascular diseases such as stroke and dementia, and automated IAC quantification could enable their large-scale risk assessment. We pre-train ViTs with MAE and fine-tune them for IAC segmentation for the first time. To develop our models, we use highly heterogeneous data from a large clinical trial, the third International Stroke Trial (IST-3). We evaluate key aspects of MAE pre-trained ViTs in IAC segmentation, and analyse the clinical implications. We show: 1) our calibrated self-supervised ViT beats a strong supervised nnU-Net baseline by 3.2 Dice points, 2) low patch sizes are crucial for ViTs for IAC segmentation and interpolation upsampling with regular convolutions is preferable to transposed convolutions for ViT-based models, and 3) our ViTs increase robustness to higher slice thicknesses and improve risk group classification in a clinical scenario by 46%. Our code is available online.

Estimating brain age from structural MRI has emerged as a powerful tool for characterizing normative and pathological aging. In this work, we explore contrastive learning as a scalable and robust alternative to supervised approaches for brain age estimation. We introduce a novel contrastive loss function, $\mathcal{L}^{exp}$, and evaluate it across multiple public neuroimaging datasets comprising over 20,000 scans. Our experiments reveal four key findings. First, scaling pre-training on diverse, multi-site data consistently improves generalization performance, cutting external mean absolute error (MAE) nearly in half. Second, $\mathcal{L}^{exp}$ is robust to site-related confounds, maintaining low scanner-predictability as training size increases. Third, contrastive models reliably capture accelerated aging in patients with cognitive impairment and Alzheimer's disease, as shown through brain age gap analysis, ROC curves, and longitudinal trends. Lastly, unlike supervised baselines, $\mathcal{L}^{exp}$ maintains a strong correlation between brain age accuracy and downstream diagnostic performance, supporting its potential as a foundation model for neuroimaging. These results position contrastive learning as a promising direction for building generalizable and clinically meaningful brain representations.

We present our solution for the Multi-Source COVID-19 Detection Challenge, which classifies chest CT scans from four distinct medical centers. To address multi-source variability, we employ the Spatial-Slice Feature Learning (SSFL) framework with Kernel-Density-based Slice Sampling (KDS). Our preprocessing pipeline combines lung region extraction, quality control, and adaptive slice sampling to select eight representative slices per scan. We compare EfficientNet and Swin Transformer architectures on the validation set. The EfficientNet model achieves an F1-score of 94.68%, compared to the Swin Transformer's 93.34%. The results demonstrate the effectiveness of our KDS-based pipeline on multi-source data and highlight the importance of dataset balance in multi-institutional medical imaging evaluation.

The limited availability of bronchoscopy images makes image synthesis particularly interesting for training deep learning models. Robust image translation across different domains -- virtual bronchoscopy, phantom as well as in-vivo and ex-vivo image data -- is pivotal for clinical applications. This paper proposes BronchoGAN introducing anatomical constraints for image-to-image translation being integrated into a conditional GAN. In particular, we force bronchial orifices to match across input and output images. We further propose to use foundation model-generated depth images as intermediate representation ensuring robustness across a variety of input domains establishing models with substantially less reliance on individual training datasets. Moreover our intermediate depth image representation allows to easily construct paired image data for training. Our experiments showed that input images from different domains (e.g. virtual bronchoscopy, phantoms) can be successfully translated to images mimicking realistic human airway appearance. We demonstrated that anatomical settings (i.e. bronchial orifices) can be robustly preserved with our approach which is shown qualitatively and quantitatively by means of improved FID, SSIM and dice coefficients scores. Our anatomical constraints enabled an improvement in the Dice coefficient of up to 0.43 for synthetic images. Through foundation models for intermediate depth representations, bronchial orifice segmentation integrated as anatomical constraints into conditional GANs we are able to robustly translate images from different bronchoscopy input domains. BronchoGAN allows to incorporate public CT scan data (virtual bronchoscopy) in order to generate large-scale bronchoscopy image datasets with realistic appearance. BronchoGAN enables to bridge the gap of missing public bronchoscopy images.

The use of deep learning (DL) in medical image analysis has significantly improved the ability to predict lung cancer. In this study, we introduce a novel deep convolutional neural network (CNN) model, named ResNet+, which is based on the established ResNet framework. This model is specifically designed to improve the prediction of lung cancer and diseases using the images. To address the challenge of missing feature information that occurs during the downsampling process in CNNs, we integrate the ResNet-D module, a variant designed to enhance feature extraction capabilities by modifying the downsampling layers, into the traditional ResNet model. Furthermore, a convolutional attention module was incorporated into the bottleneck layers to enhance model generalization by allowing the network to focus on relevant regions of the input images. We evaluated the proposed model using five public datasets, comprising lung cancer (LC2500 $n$=3183, IQ-OTH/NCCD $n$=1336, and LCC $n$=25000 images) and lung disease (ChestXray $n$=5856, and COVIDx-CT $n$=425024 images). To address class imbalance, we used data augmentation techniques to artificially increase the representation of underrepresented classes in the training dataset. The experimental results show that ResNet+ model demonstrated remarkable accuracy/F1, reaching 98.14/98.14\% on the LC25000 dataset and 99.25/99.13\% on the IQ-OTH/NCCD dataset. Furthermore, the ResNet+ model saved computational cost compared to the original ResNet series in predicting lung cancer images. The proposed model outperformed the baseline models on publicly available datasets, achieving better performance metrics. Our codes are publicly available at https://github.com/AIPMLab/Graduation-2024/tree/main/Peng.

Accurate segmentation of brain tumors in MRI scans is essential for reliable clinical diagnosis and effective treatment planning. Recently, diffusion models have demonstrated remarkable effectiveness in image generation and segmentation tasks. This paper introduces a novel approach to corrective segmentation based on diffusion models. We propose DMCIE (Diffusion Model with Concatenation of Inputs and Errors), a novel framework for accurate brain tumor segmentation in multi-modal MRI scans. We employ a 3D U-Net to generate an initial segmentation mask, from which an error map is generated by identifying the differences between the prediction and the ground truth. The error map, concatenated with the original MRI images, are used to guide a diffusion model. Using multimodal MRI inputs (T1, T1ce, T2, FLAIR), DMCIE effectively enhances segmentation accuracy by focusing on misclassified regions, guided by the original inputs. Evaluated on the BraTS2020 dataset, DMCIE outperforms several state-of-the-art diffusion-based segmentation methods, achieving a Dice Score of 93.46 and an HD95 of 5.94 mm. These results highlight the effectiveness of error-guided diffusion in producing precise and reliable brain tumor segmentations.