Two novel sample preparation procedures have been developed to visualize morphological structures in embryonic and fetal tissues. In the first, optimization of the sample preparation allows for the visualization of embryos with a thickness in excess of 500 microns. The morphology of the internal structures in these embryos is observed by optical sectioning. The general sample preparation procedures included paraformaldehyde fixation, methanol dehydration and clearing with either benzyl alcohol/benzyl benzoate or methyl salicylate. The dyes (i.e. LysoTracker Red, YoPro) are incorporated into living or fixed embryos to indicate a specific biological function or embryo morphology. Using these stained embryos, the detection of apoptosis and its subsequent quantification were made in addition to the observation of morphology.

In the second technique, the confocal microscope has been adapted to produce images similar to those generated by a scanning electron microscope. For this application, the embryos are coated with a dilute solution of acridine orange resulting in opaque surface fluorescence.