Anatomical trees are critical for clinical diagnosis and treatment planning, yet their complex and diverse geometry make accurate representation a significant challenge. Motivated by the latest advances in large language models, we introduce an autoregressive method for synthesizing anatomical trees. Our approach first embeds vessel structures into a learned discrete vocabulary using a VQ-VAE architecture, then models their generation autoregressively with a GPT-2 model. This method effectively captures intricate geometries and branching patterns, enabling realistic vascular tree synthesis. Comprehensive qualitative and quantitative evaluations reveal that our technique achieves high-fidelity tree reconstruction with compact discrete representations. Moreover, our B-spline representation of vessel cross-sections preserves critical morphological details that are often overlooked in previous' methods parameterizations. To the best of our knowledge, this work is the first to generate blood vessels in an autoregressive manner. Code is available at https://github.com/LIA-DiTella/VesselGPT-MICCAI.

Surgical assessment of liver cancer patients requires identification of the vessel trees from medical images. Specifically, the venous trees - the portal (perfusing) and the hepatic (draining) trees are important for understanding the liver anatomy and disease state, and perform surgery planning. This research aims to improve the 3D segmentation, skeletonization, and subsequent analysis of vessel trees, by creating an automatic pipeline based on deep learning and image processing techniques. The first part of this work explores the impact of differentiable skeletonization methods such as ClDice and morphological skeletonization loss, on the overall liver vessel segmentation performance. To this aim, it studies how to improve vessel tree connectivity. The second part of this study converts a single class vessel segmentation into multi-class ones, separating the two venous trees. It builds on the previous two-class vessel segmentation model, which vessel tree outputs might be entangled, and on connected components and skeleton analyses of the trees. After providing sub-labeling of the specific anatomical branches of each venous tree, these algorithms also enable a morphometric analysis of the vessel trees by extracting various geometrical markers. In conclusion, we propose a method that successfully improves current skeletonization methods, for extensive vascular trees that contain vessels of different calibers. The separation algorithm creates a clean multi-class segmentation of the vessels, validated by surgeons to provide low error. A new, publicly shared high-quality liver vessel dataset of 77 cases is thus created. Finally a method to annotate vessel trees according to anatomy is provided, enabling a unique liver vessel morphometry analysis.

Precise localization of coronary arteries in Computed Tomography (CT) scans is critical from the perspective of medical assessment of coronary artery disease. Although various methods exist that offer high-quality segmentation of coronary arteries in cardiac contrast-enhanced CT scans, the potential of less invasive, non-contrast CT in this area is still not fully exploited. Since such fine anatomical structures are hardly visible in this type of medical images, the existing methods are characterized by high recall and low precision, and are used mainly for filtering of atherosclerotic plaques in the context of calcium scoring. In this paper, we address this research gap and introduce a deep learning algorithm for segmenting coronary arteries in multi-vendor ECG-gated non-contrast cardiac CT images which benefits from a novel framework for semi-automatic generation of Ground Truth (GT) via image registration. We hypothesize that the proposed GT generation process is much more efficient in this case than manual segmentation, since it allows for a fast generation of large volumes of diverse data, which leads to well-generalizing models. To investigate and thoroughly evaluate the segmentation quality based on such an approach, we propose a novel method for manual mesh-to-image registration, which is used to create our test-GT. The experimental study shows that the trained model has significantly higher accuracy than the GT used for training, and leads to the Dice and clDice metrics close to the interrater variability.

The morphology and hierarchy of the vascular systems are essential for perfusion in supporting metabolism. In human retina, one of the most energy-demanding organs, retinal circulation nourishes the entire inner retina by an intricate vasculature emerging and remerging at the optic nerve head (ONH). Thus, tracing the vascular branching from ONH through the vascular tree can illustrate vascular hierarchy and allow detailed morphological quantification, and yet remains a challenging task. Here, we presented a novel approach for a robust semi-automatic vessel tracing algorithm on human fundus images by an instance segmentation neural network (InSegNN). Distinct from semantic segmentation, InSegNN separates and labels different vascular trees individually and therefore enable tracing each tree throughout its branching. We have built-in three strategies to improve robustness and accuracy with temporal learning, spatial multi-sampling, and dynamic probability map. We achieved 83% specificity, and 50% improvement in Symmetric Best Dice (SBD) compared to literature, and outperformed baseline U-net. We have demonstrated tracing individual vessel trees from fundus images, and simultaneously retain the vessel hierarchy information. InSegNN paves a way for any subsequent morphological analysis of vascular morphology in relation to retinal diseases.

Patient-specific hemodynamics assessment could support diagnosis and treatment of neurovascular diseases. Currently, conventional medical imaging modalities are not able to accurately acquire high-resolution hemodynamic information that would be required to assess complex neurovascular pathologies. Therefore, computational fluid dynamics (CFD) simulations can be applied to tomographic reconstructions to obtain clinically relevant information. However, three-dimensional (3D) CFD simulations require enormous computational resources and simulation-related expert knowledge that are usually not available in clinical environments. Recently, deep-learning-based methods have been proposed as CFD surrogates to improve computational efficiency. Nevertheless, the prediction of high-resolution transient CFD simulations for complex vascular geometries poses a challenge to conventional deep learning models. In this work, we present an architecture that is tailored to predict high-resolution (spatial and temporal) velocity fields for complex synthetic vascular geometries. For this, an octree-based spatial discretization is combined with an implicit neural function representation to efficiently handle the prediction of the 3D velocity field for each time step. The presented method is evaluated for the task of cerebral hemodynamics prediction before and during the injection of contrast agent in the internal carotid artery (ICA). Compared to CFD simulations, the velocity field can be estimated with a mean absolute error of 0.024 m/s, whereas the run time reduces from several hours on a high-performance cluster to a few seconds on a consumer graphical processing unit.

Synthesizing images of the eye fundus is a challenging task that has been previously approached by formulating complex models of the anatomy of the eye. New images can then be generated by sampling a suitable parameter space. In this work, we propose a method that learns to synthesize eye fundus images directly from data. For that, we pair true eye fundus images with their respective vessel trees, by means of a vessel segmentation technique. These pairs are then used to learn a mapping from a binary vessel tree to a new retinal image. For this purpose, we use a recent image-to-image translation technique, based on the idea of adversarial learning. Experimental results show that the original and the generated images are visually different in terms of their global appearance, in spite of sharing the same vessel tree. Additionally, a quantitative quality analysis of the synthetic retinal images confirms that the produced images retain a high proportion of the true image set quality.