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J Neurosci Methods. 2014 Jan 15;221:70-7. doi: 10.1016/j.jneumeth.2013.09.002. Epub 2013 Sep 19.

A perfusion procedure for imaging of the mouse cerebral vasculature by X-ray micro-CT.

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Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 2M9; Mouse Imaging Centre, The Hospital for Sick Children, 25 Orde Street, Toronto, Ontario, Canada M5T 3H7. Electronic address:



Micro-CT is a novel X-ray imaging modality which can provide 3D high resolution images of the vascular network filled with contrast agent. The cerebrovascular system is a complex anatomical structure that can be imaged with contrast enhanced micro-CT. However, the morphology of the cerebrovasculature and many circulatory anastomosis in the brain result in high variations in the extent of contrast agent filling in the blood vessels and as a result, the vasculature of different subjects appear differently in the acquired images. Specifically, the posterior circulation is not consistently perfused with the contrast agent in many brain specimens and thus, many major vessels that perfuse blood to the midbrain and hindbrain are not visible in the micro-CT images acquired from these samples.


In this paper, we present a modified surgical procedure of cerebral vasculature perfusion through the left ventricle with Microfil contrast agent, in order to achieve a more uniform perfusion of blood vessels throughout the brain and as a result, more consistent images of the cerebrovasculature. Our method consists of filling the posterior cerebral circulation with contrast agent, followed by the perfusion of the whole cerebrovasculature.


Our histological results show that over 90% of the vessels in the entire brain, including the cerebellum, were filled with contrast agent.


Our results show that the new technique of sample perfusion decreases the variability of the posterior circulation in the cerebellum in micro-CT images by 6.9%.


This new technique of sample preparation improves the quality of cerebrovascular images.


3D imaging; Brain vasculature; Casting; Contrast agent; Micro-CT; Mouse; Perfusion

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