Preparing Tissue

Sections in the same orientation: Try to have all sections mounted in the same Z orientation (right side up); it is much easier to flip the occasional upside-down section than to re-orient all of your sections in Neurolucida.
Have sections mounted in order on slides: The bottom of one section is aligned with the top of the next section to facilitate continuity of tracing.
Mount every section when applicable. While this is not necessary for 3D reconstruction of large anatomical regions, you cannot fully reconstruct neurons if sections are missing.
Keep track of any missing sections in your notebook. It can be very frustrating to search for the ‘next’ section during neuron reconstruction if it is not there.
Don’t try to mount too many sections per slide and don’t try to mount them too close to the edges of the slide (especially the left and right edges); you may not be able to trace all the way to the edge of the slide without the condenser cap hitting the bottom of the stage.