Brilliant Green is a stain for differentiating E. coli from S. typhosa. It is also used in bacteriological media.

Bromocresol Green sodium salt is a tracking dye for RNA gels with a pH range of 3.8 (yellow) to 5.4 (blue).

Crystal violet is used in the classification of bacteria and is the active ingredient in Gram stain.

Eosin Y is a popular dye used in cosmetics and pharmaceuticals as well as a tissue and vital stain. It is used as a counterstain to hematoxylin in haematoxylin and eosin (H&E) staining, one of the principal stains in histology for cancer diagnosis. It stains proteins in the cytoplasm along with collagen and muscle fibers. In other applications, when combined with silica nanoparticles it can be part of a fluorophore for a peroxyoxalate chemiluminescence system.

Fluoresceinamine Isomer I is a fluorescent molecule used for staining procedures. For tissue staining it was combined with albumin to form a useful stain for tissues of malignant brain tumors. Fluoresceinamine Isomer I is also used as a label for detection of synthesis of DNA in vivo and labeling of other nucleosides, nucleotides and oligonucleotides.

Neutral red dye is a dark brown to dark green power used to stain nuclei red, in cell viability tests, and as a pH indicator (transition of pH indicator: pH 6.8-8.0, red to yellow). Additionally, it is used to prepare neutral red paper and as a histological stain for lysozymes.

TrueBlack™ is a new alternative to Sudan Black B for the quenching of lipofuscin autofluorescence in tissue sections for immunofluorescence staining. Lipofuscin consists of highly autofluorescent granules of oxidized proteins and lipids that build up in the lysosomes of aging cells. Lipofuscin granules fluoresce brightly in all channels used for fluorescence microscopy and accumulate in a variety of cell and tissue types with age. It’s necessary to quench or mask lipofuscin fluorescence in certain adult human tissues or aged animal tissues in order to properly image specific immunofluorescence signals.

Sudan Black B has traditionally been used to quench lipofuscin autofluorescence by incubating tissue sections with the dye after immunofluorescence staining. However it also introduces uniform, non-specific background fluorescence in the red and far-red channels, limiting the use of fluorescent dyes in those wavelengths.