Usually, within a group, there is no need to change sampling parameters; in other words, the biological variability between the subjects of the same group is not enough to warrant changing section interval or area sub-fraction among the members of that group.
It may be that the experimental manipulation causes a change that does indicate different parameters between groups. In order to help stay blind, you can opt to use the more stringent parameters on both groups.
The parameters for a region in a single subject must not change; all sections for a region within a subject should be analyzed with the same parameters.
This FAQ comes from stereology.info, our curated collection of information and references regarding the use of stereology in the biological sciences. Feel free to review the other FAQs there as well. We hope this thread will spark some in-depth discussion on stereology!