Comparison of different quantification methods to determine hippocampal damage after cerebral ischemia.

•The number of NeuN and Fluoro-Jade B positive cells in CA1 is dependent on localization within CA1.•Mean cell number does not change significantly over time from day 3 to 28.•Variations within groups often become smaller resulting in lower SD and higher effect size at 28 days post insult.•Number of Fluoro-Jade B positive cells does not decrease over time between 3 and 28 days post insult, suggesting that this staining is not labeling dying cells.•Placement of counting windows has a major influence on extent of differences between moderate and severe ischemic brain damage.