Interactive 3D Analysis of Blood Vessel Trees and Collateral Vessel Volumes in Magnetic Resonance Angiograms in the Mouse Ischemic Hindlimb Model

Peter C. Marks, Marilena Preda, Terry Henderson, Lucy Liaw, Volkhard Lindner, Robert E. Friesel, Ilka M. Pinz*
Maine Medical Center Research Institute, 81 Research Drive, Scarborough, ME 04074

© 2013 Marks et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Small Animal Imaging Core, Center for Molecular Medicine, Maine Medical Center Research Institute , 81 Research Drive, Scarborough, ME 04074, Tel: 207 396 8280, Fax: 207 396 8179, E-mail:


The quantitative analysis of blood vessel volumes from magnetic resonance angiograms (MRA) or μCT images is difficult and time-consuming. This fact, when combined with a study that involves multiple scans of multiple subjects, can represent a significant portion of research time. In order to enhance analysis options and to provide an automated and fast analysis method, we developed a software plugin for the ImageJ and Fiji image processing frameworks that enables the quick and reproducible volume quantification of blood vessel segments. The novel plugin named Volume Calculator (VolCal), accepts any binary (thresholded) image and produces a three-dimensional schematic representation of the vasculature that can be directly manipulated by the investigator.

Using MRAs of the mouse hindlimb ischemia model, we demonstrate quick and reproducible blood vessel volume calculations with 95 – 98% accuracy. In clinical settings this software may enhance image interpretation and the speed of data analysis and thus enhance intervention decisions for example in peripheral vascular disease or aneurysms.

In summary, we provide a novel, fast and interactive quantification of blood vessel volumes for single blood vessels or sets of vessel segments with particular focus on collateral formation after an ischemic insult.

Keywords: Magnetic resonance angiogram, blood vessel volume analysis, 3D analysis, mouse hindlimb ischemia.