The parameters must be constant within a subject, and almost always are kept constant within a group. The disector height is one of these parameters. The one parameter that will be allowed to change within an animal/region is section height (section thickness). This should be measured with a frequency to account for variance in the section thickness.
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!