Fluorescent microsphere technique to measure cerebral blood flow in the rat

The present protocol describes a method for parallel measurement of cerebral blood flow (CBF) using fluorescent microspheres and structural assessment of the same material. The method is based on the standard microsphere technique, embolizing capillaries proportional to the blood flow, but requires dissolution of the tissue to retrieve the microspheres. To link the blood flow to the tissue morphology we modified the technique to fluorescent microspheres, which are quantified in cryo- or vibratome sections, allowing structural analysis by, for example, immunohistochemistry or standard histology. The protocol takes 8 h 50 min, without pauses, to complete, but additional flow measurements or specific protocols can increase the time needed.