Vessel network extraction and analysis of mouse pulmonary vasculature via X-ray micro-computed tomographic imaging

In this work, non-invasive high-spatial resolution three-dimensional (3D) X-ray micro-computed tomography (mu CT) of healthy mouse lung vasculature is performed. Methodologies are presented for filtering, segmenting, and skeletonizing the collected 3D images. Novel methods for the removal of spurious branch artefacts from the skeletonized 3D image are introduced, and these novel methods involve a combination of distance transform gradients, diameter-length ratios, and the fast marching method (FMM). These new techniques of spurious branch removal result in the consistent removal of spurious branches without compromising the connectivity of the pulmonary circuit. Analysis of the filtered, skeletonized, and segmented 3D images is performed using a newly developed Vessel Network Extraction algorithm to fully characterize the morphology of the mouse pulmonary circuit. The removal of spurious branches from the skeletonized image results in an accurate representation of the pulmonary circuit with significantly less variability in vessel diameter and vessel length in each generation. The branching morphology of a full pulmonary circuit is characterized by the mean diameter per generation and number of vessels per generation. The methods presented in this paper lead to a significant improvement in the characterization of 3D vasculature imaging, allow for automatic separation of arteries and veins, and for the characterization of generations containing capillaries and intrapulmonary arteriovenous anastomoses (IPAVA). Author summary Chronic pulmonary diseases are a leading cause of death responsible for 4 million deaths per year worldwide. Pulmonary diseases attack both the airways and vasculature of the lungs, restricting the oxidation of blood delivered to the rest of the body. For studying disease treatments, the vasculature is of particular importance as it is used as the pathway for drugs as well as nutrients for the case of regenerative medicine. Imaging techniques can be effective tools for studying the effectiveness of such treatments by providing a three-dimensional map of the vasculature before, during, and after treatment. Lung vasculature is incredibly complex and therefore requires great care in the imaging acquisition and analysis phases. Therefore, we have developed a detailed methodology for extracting the vasculature as a network of connected cylinders with accurately estimated measurements and connectivity of the entire vasculature network. The net