Brain microinfarcts are prevalent in humans, however due to the inherent difficulty of identifying and localizing individual microinfarcts, brain-wide quantification is impractical. In mice, microinfarcts have been created by surgically introducing microemboli into the brain, but a major limitation of this model is the absence of automated methods to identify and localize individual occlusions. We present a novel and semi-automated workflow to identify the anatomical location of fluorescent emboli (microspheres) within the mouse brain through histological processing and atlas registration. By incorporating vibratome block-face imaging with the QuickNII brain registration tool, we show that the anatomical location of microspheres can be accurately registered to brain structures within the Allen mouse brain (AMB) atlas (e.g. somatomotor areas, hippocampal region, visual areas, etc.). Compared to registering images of slide mounted sections to the AMB atlas, microsphere location was more accurately determined when block-face images were utilized. As a proof of principle, using this workflow we compared the distribution of microspheres within the brains of mice that were either perfused or immersion fixed. No significant effect of perfusion on total microsphere number or location was detected. In general, microspheres were distributed brain-wide, with the largest density found in the thalamus. In sum, our block-face imaging workflow, enables efficient characterization of the widespread distribution of fluorescent microemboli, facilitating future investigation into the impact of microinfarct load and location on brain health. Significance StatementCerebral microemboli are small materials, such as a blood clot or atherosclerotic plaque, that pass through the circulation until being lodged within downstream vasculature and occasionally resulting in localized cell death (microinfarction). The largest limitation of microemboli models of microinfarction in rodents is the lack of efficient methods for accurately quantifying the brainwide distribution of occlusions in individual subjects. Compared to traditional histology, incorporating our block-face imaging workflow significantly reduces the time required to register all emboli from a single brain (from days to hours). Going forward, this workflow will allow researchers to more efficiently characterize the global distribution of microemboli in mice and facilitate the stratification of mice based on microsphere load or location.