Small molecules are low molecular weight (How are Small Molecules Utilized in Histological Techniques? In histology, small molecules are often used as stains or dyes to highlight specific cellular components. For example, hematoxylin and eosin (H&E) staining uses small molecules to differentiate between various tissue types. Hematoxylin stains the cell nuclei blue, while eosin stains the cytoplasm and extracellular matrix pink.