| Cerebellar vermis |
For parasagittal slices, cut coronally in front of the cerebellum to separate it from the forebrain. Cut transversely below the cerebellum to separate it from the brainstem. Cut sagittally, as parallel to the midline of the cerebellum as possible, on either side of the cerebellar vermis. Glue either surface to a flat slicing stage (the first cut is usually more parallel to the midline). |
| Hippocampus |
Make a longitudinal cut to separate the brain into two hemispheres. Place the brain on the cut (medial) surface and use a scalpel to cut a few millimeters (adult rat) off the dorsal surface of the cortex. This cut surface should then be glued down for slicing. The first few slices must be discarded before reaching the ventral hippocampus. As the vibratome blade is moved downward, each slice is obtained from a progressively more dorsal region of the hippocampus. With this procedure, optimal orientation of dendrites occurs in the dorsal hippocampus. To optimize dendritic orientation in the mid or ventral hippocampus, the angle at which the dorsal surface of the cortex is cut must be adjusted to tilt the hippocampus accordingly. |
| Neocortex |
For slices from the S1/M1 border, cut the cerebral cortices apart sagittally, along the midline. Glue the medial surface to a slicing stage angled at 10-151 (sloping towards the slicer blade) with the dorsal cortex facing the blade. Slice off a 3000 mm section and discard it. Cut a 1000 mm thick slice half way through the tissue; separate this with a scalpel cut across the slicer’s blade. Cut ~ 1800 μm worth of 300 μm slices, detaching each slice from the brain block with a scalpel cut. Lay them out in order in the slice incubation chamber. Each slice should be inspected for dendrites that run parallel to the surface of the slice; these dendrites are typically found in slices number 3 and/or 4 (where slice surfaces face each other). |
| Substantia nigra |
For coronal slices, make two coronal cuts in front of the cerebellum and behind the somatosensory cortex. Glue the block onto its caudal surface with the ventral surface of the brain facing the blade. Cut slices down to the subthalamic nucleus, and then carefully select only slices containing substantia nigra. |
