The above image is taken during acquisition of a poorly prepared sample. Damage, particularly in the top right brain, will impair registration to the Allen atlas template. These brains have not been perfused, as evidenced by the bright white vessels. This can cause cutting issues and interfere with automated analysis pipelines. The bottom right brain in particular is highly rotated. Rotation of this degree can cause automated registration to the Allen template to fail, and necessitate manual de-rotation of the raw data.