Sections were analyzed under bright-field through a slide scanner (FSX-100 Inverted Microscope, Olympus). To refine our scope, sections were first non-quantitatively analyzed to identify regions with notable changes in c-Fos expression. Noradrenergic regions and areas with unambiguous c-Fos expression were then manually counted with observers blinded to the treatment. A cell was considered c-Fos+ if a cell expressed a black nucleus and excluded cells that expressed nuclei that were light/medium brown (which may or may not be c-Fos+). This level of stringency ensured that we only identified c-Fos+ cells and thereby excluded the possibility of identifying false positive cells. Regions of interest were identified using the rat brain atlas12 and counted using ImageJ. Three representative sections were taken across the rostral/caudal axis for each region per animal, and this sampling strategy is based on a recent study that showed that the distribution of LC projections had no specific organization across anterior/posterior or medial/lateral axes13 (link).
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