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Unprecedented visual details of biological structures are being revealed by subcellular-resolution whole-brain 3D microscopy data, enabled by recent advances in intact tissue processing and light-sheet fluorescence microscopy (LSFM). These…

Recently, it has become progressively more evident that classic diagnostic labels are unable to reliably describe the complexity and variability of several clinical phenotypes. This is particularly true for a broad range of neuropsychiatric…

Electroanatomical mapping is a technique used in cardiology to create a detailed 3D map of the electrical activity in the heart. It is useful for diagnosis, treatment planning and real time guidance in cardiac ablation procedures to treat…

Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most…

We describe a diffeomorphic registration algorithm that allows groups of images to be accurately aligned to a common space, which we intend to incorporate into the SPM software. The idea is to perform inference in a probabilistic graphical…

Deep learning has shown promising results in medical image analysis, however, the lack of very large annotated datasets confines its full potential. Although transfer learning with ImageNet pre-trained classification models can alleviate…

We propose a novel machine learning strategy for studying neuroanatomical shape variation. Our model works with volumetric binary segmentation images, and requires no pre-processing such as the extraction of surface points or a mesh. The…

Generative adversarial networks (GANs) have provided promising data enrichment solutions by synthesizing high-fidelity images. However, generating large sets of labeled images with new anatomical variations remains unexplored. We propose a…

In the medical field, landmark detection in MRI plays an important role in reducing medical technician efforts in tasks like scan planning, image registration, etc. First, 88 landmarks spread across the brain anatomy in the three respective…

Image-based computer simulation of cardiac function can be used to probe the mechanisms of (patho)physiology, and guide diagnosis and personalized treatment of cardiac diseases. This paradigm requires constructing simulation-ready meshes of…

The segmentation of organs in volumetric medical images plays an important role in computer-aided diagnosis and treatment/surgery planning. Conventional 2D convolutional neural networks (CNNs) can hardly exploit the spatial correlation of…

Automated fetal brain extraction from full-uterus MRI is a challenging task due to variable head sizes, orientations, complex anatomy, and prevalent artifacts. While deep-learning (DL) models trained on synthetic images have been successful…

Direct automatic segmentation of objects from 3D medical imaging, such as magnetic resonance (MR) imaging, is challenging as it often involves accurately identifying a number of individual objects with complex geometries within a large…

The task of automatically segmenting 3-D surfaces representing boundaries of objects is important for quantitative analysis of volumetric images, and plays a vital role in biomedical image analysis. Recently, graph-based methods with a…

Semantic segmentation of medical images is pivotal in applications like disease diagnosis and treatment planning. While deep learning has excelled in automating this task, a major hurdle is the need for numerous annotated segmentation…

Foundation models such as Segment Anything Model 2 (SAM 2) exhibit strong generalization on natural images and videos but perform poorly on medical data due to differences in appearance statistics, imaging physics, and three-dimensional…

Accurate 3D face reconstruction from 2D images is an enabling technology with applications in healthcare, security, and creative industries. However, current state-of-the-art methods either rely on supervised training with very limited 3D…

Automated image processing approaches are indispensable for many biomedical experiments and help to cope with the increasing amount of microscopy image data in a fast and reproducible way. Especially state-of-the-art deep learning-based…

Convolutional neural networks are state-of-the-art for various segmentation tasks. While for 2D images these networks are also computationally efficient, 3D convolutions have huge storage requirements and therefore, end-to-end training is…

Vision foundation models (FMs) achieve state-of-the-art performance in medical imaging. However, they encode information in abstract latent representations that clinicians cannot interrogate or verify. The goal of this study is to…