Although the transparency of Nereis embryos makes them ideal for studying internal development, it also makes cell outlines and other features difficult to distinguish. Especially in the later stages that Wilson studied, the smaller size and increased number of cells makes that task particularly difficult. To address this issue, he used diluted dyes to make the embryos as a whole more visible. For live specimens, Wilson used a diluted solution of the histological stain methyl-blue to make the cell outlines more distinct (Wilson 1892). With the fixed embryos, he used carmine to dye the cytoplasm red and make the nuclei, cell outlines, and mitotic spindles clearly visible (Wilson 1892). Although it likely does not display exactly what Wilson saw through his microscope, a view through a modern light microscope demonstrates the necessity of this step (see below).
Although his figures show individual cells marked with different colors, Wilson did not differentially stain or mark cells so that he could more easily follow them throughout development. The colors, he states, were added later for the benefit of the reader even though “the effect of the drawings is injured by it.” (Wilson 1892). It is likely that Wilson followed individual cells by comparing several camera lucida sketches and live specimens at different stages of development. Although Wilson was able to obtain remarkable results with his methods, there was a limit to what he was able to do. In Cell-Lineage he states: “The record is without a gap up to the fifty-eight-celled stage. Beyond this point the development of the embryo as a whole cannot be fully represented in the diagram, on account of increasing variations in the order of division of the individual cells.” (Wilson 1892, p. 383) Looking at his figures, it is clear that in the later stages, Wilson is less concerned with depicting all the details of every specimen. Instead he shows only those details relevant to the argument he is making and blurs out the rest of the embryo.
Unlike Wilson’s works, modern cell-lineage studies take advantage of a number of different tools available for labeling individual cells. For example, intracellular dyes can be injected directly into individual cells using microinjection rigs, allowing the lineage of each cell to be easily followed (see below). Although the dye becomes more dilute with every cell division, it remains strong enough to be detected through to the larval stages. (Seaver 2014). Other methods involve marking nuclei, cell membranes, proteins, or RNA with fluorescent labels or dyes, which can then be visualized with certain kinds of microscopes.