Brilliant Blue G is triphenylmethane dye that was developed for use in the textile industry but is now commonly used for staining proteins in analytical biochemistry. The Bradford assay is a standard, rapid dye-binding assay that uses Brilliant Blue G to quantify the amount of protein in a solution. Brilliant Blue G also acts as a selective inhibitor of the P2X purinoceptor channel P2X7 (IC50s = 10.1 and 265 nM for rat and human P2X7, respectively). In mice, it inhibits interleukin-1β expression and reduces neurological injury secondary to traumatic brain injury. Brilliant Blue G was used to prepare the protein reagent for the determination of protein content of the collagenase enzyme isolated from fish waste. It may be employed as a stain for the internal limiting membrane (ILM) for the macular hole (MH) and epiretinal membrane (ERM) surgery.

Trypan blue (trade name MembraneBlue, VisionBlue) is a vital stain used to selectively color dead tissues or cells blue. Live cells or tissues with intact cell membranes are not colored. Since cells are very selective in the compounds that pass through the membrane, in a viable cell trypan blue is not absorbed; however, it traverses the membrane in a dead cell. Hence, dead cells are shown as a distinctive blue color under a microscope. Since live cells are excluded from staining, this staining method is also described as a dye exclusion method. This dye may be a cause of certain birth defects such as encephalocele. Trypan blue is commonly used in microscopy (for cell counting) and in laboratory mice for assessment of tissue viability. The method cannot distinguish between necrotic and apoptotic cells. Trypan blue is also used in ophthalmic cataract surgery to stain the anterior capsule in the presence of a mature cataract, to aid in visualization, before creating the continuous curvilinear capsulorhexis.

Methylene blue, also known as methylthioninium chloride, is a medication from WHO's list of essential medicines. Upon administration, methylene blue is converted to leukomethylene blue by erythrocyte methemoblobin reductase in the presence of NADPH. Leukomethylene blue than reduces methemoglobin to oxyhemoglobin, thus restoring oxygen carrying capacity of the blood. Methylene blue is also used as a dye for various diagnostic procedures, for treatment of ifosfamide toxicity and for in vitro staining. Historically, it was used as a photosensitizer for photodynamic therapy for topical treatment of dermatologic or mucocutaneous infections, as an antidote for cyanide poisoning, but these applications are no longer approved. Methylene blue is investigated in clinical trials for treatment of septic shock and Alzheimer's disease.

Thiazolyl Blue is a membrane-permeable yellow dye that is reduced by mitochondrial reductases in living cells to form the dark blue product. The net positive charge on Thiazolyl Blue appears to be the predominant factor involved in their cellular uptake via the plasma membrane potential. Thiazolyl Blue is used as a direct indicator of cytotoxicity (such as for screening cancer drugs), proliferation and apoptosis. Thiazolyl Blue is also an electron acceptor used for studying NADP-dependent dehydrogenases. Thiazolyl Blue reduction is associated not only with mitochondria, but also with the cytoplasm and with nonmitochondrial membranes including the endosome/lysosome compartment and the plasma membrane. Biological Applications: cell viability assay; microbial growth assays; DNA quantification assays; tissue viability assays; detecting enzymes; measuring membrane potential; treating Alzheimer’s disease, asthma, cancer. Because Thiazolyl Blue forms an insoluble formazan it has usually been applied in endpoint assays.