Do you dissect the region first, or use another method?
Array Tomography is a technique for excellent axial resolution imaging by using ultrathin sections for fluorescent microscopy. it also permits repeated staining and imaging of the same sections
Our lab dissects the region first before embedding, then prepares the arrays. On occasion, I'll also taken semi-thin (500 nm) sections after embedding but before taking arrays and stain with toluidine blue to verify location. Then, when we image, we use DAPI to verify and locate the cell bodies.