PT  - JOURNAL ARTICLE
AU  - Matthew W. McDonald
AU  - Matthew S. Jeffers
AU  - Melissa Filadelfi
AU  - Andrea Vicencio
AU  - Gavin Heidenreich
AU  - Junzheng Wu
AU  - Gergely Silasi
TI  - Localizing Microemboli within the Rodent Brain through Block-Face Imaging and Atlas Registration
AID  - 10.1523/ENEURO.0216-21.2021
DP  - 2021 Jul 01
TA  - eneuro
PG  - ENEURO.0216-21.2021
VI  - 8
IP  - 4
4099  - http://www.eneuro.org/content/8/4/ENEURO.0216-21.2021.short
4100  - http://www.eneuro.org/content/8/4/ENEURO.0216-21.2021.full
SO  - eNeuro2021 Jul 01; 8
AB  - Brain microinfarcts are prevalent in humans, however because of 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 anatomic location of fluorescent emboli (microspheres) within the mouse brain through histologic processing and atlas registration. By incorporating vibratome block-face imaging with the QuickNII brain registration tool, we show that the anatomic 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 with registering images of slide mounted sections to the AMB atlas, microsphere location was more accurately determined when block-face images were used. 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.