Neuroscientists at MBF Bioscience have developed user-friendly software programs for performing detailed quantitative analysis of microvessel anatomy. Vesselucida and Vesselucida 360 provide automated and manual vessel tracing tools in an interactive 3D modelling environment for efficiently navigating through tissue layers. Automatic vessel reconstruction can provide validation of manual vessel tracings, adding credibility to measurements and the statistical analyses submitted for publication. As with all MBF Bioscience products the vessel reconstruction programs are continuously being updated with new features based on the feedback obtained from scientists actively using the software, saving researchers the cost and time of hiring a software developer for individual projects. We developed Vesselucida and Vesselucida 360 as tools to allow scientists to quickly and reliably obtain quantifiable measurements of vasculature with minimal training and expense. The Neuroscientists at MBF Bioscience use Vesselucida in their own research projects and are available to assist academic and institutional researchers with their investigations at any step in the research process from image acquisition to publication.