An image analysis toolbox for 3D vascular tracing and network topology

Proper vascular structure and function is critical to maintain healthy tissue. Vascular dysfunction is a hallmark in a number of diseases including but not limited to Alzheimer's disease, diabetes, hypertension, and the normal process of aging. It has become clear than an early biomarker for these disparate diseases is dysfunction in retinal vascular structure and function. There is a growing computational toolbox for the analysis of vascular networks yet there are few easy to use graphical-user-interfaces that bring these tools to mere biologists. Here we present a suite of graphical-user-interfaces for the tracing, curation, and analysis of retinal vascular networks from 3D imaging datasets. The goal of these tools is to provide the needed link between continual advances in computational analysis with easy to use graphical-user-interfaces that will allow ground-truth results. We present an analysis of optical coherence tomography angiography (OCTA) images acquired in mice in vivo.