Remember that the Optical Fractionator probe requires tissue thick enough so you can focus on several distinct focal planes. This is dependent on the post-processing tissue thickness. Your thickly cut sections may shrink so much during post-processing that distinguishing several focal planes is difficult—if not impossible.
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!