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.

Isosulfan Blue is a synthetic visual lymphatic imaging agent. Injected into the periphery of the tumor site, isosulfan blue localizes to the lymphatic system and aids in the surgical identification of tumor sentinel nodes which stain blue. The chemical name of isosulfan blue is N-[4-[[4-(diethylamino)phenyl] (2,5-disulfophenyl) methylene]-2,5-cyclohexadien-1-ylidene]-N-ethylethanaminium hydroxide, inner salt, sodium salt. Isosulfan blue is a greenish blue color hygroscopic powder. Isosulfan blue injection 1% is a contrast agent for the delineation of lymphatic vessels. Isosulfan blue injection 1% upon subcutaneous administration, delineates lymphatic vessels draining the region of injection. It is an adjunct to lymphography in: primary and secondary lymphedema of the extremities; chyluria, chylous ascites or chylothorax; lymph node involvement by primary or secondary neoplasm; and lymph node response to therapeutic modalities.

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.

Toluidine Blue (also known as tolonium chloride or Toluidine blue O) is metachromatic dye used for a variety of histological staining, it selectively stains acidic tissue components (sulfates, carboxylates, and phosphate radicals. Toluidine blue has an affinity for nucleic acids, and therefore binds to nuclear material of tissues with a high DNA and RNA content. It was evaluated the toluidine blue staining in premalignancies, and superficial oral ulceration suggesting malignancy. The study showed 100% sensitivity in the detection of in situ and invasive carcinoma and no false-negative results occurred. The lesions that were diagnosed as dysplasia did not retain stain, and thus gave false-negative results. The reasons could be that the exact mechanisms by which the dye differentially stains malignant or dysplastic tissues remain unknown.

Pinacyanol iodide is a fluorescent cationic cyanine dye used to stain biological specimens. It is the obstetric diagnostic aid. The mechanism of tracing with pinacyanol iodide dyes is based on their lipid solubility. Pinacyanol iodide dyes are more efficacious than classical tracing methodologies especially during early stages of development and consequently have been used to reveal the spatiotemporal patterns of axonal development in different species. The unique properties of the pinacyanol iodide dye tracing method have opened up new avenues for tracing connections in human postmortem specimens. Pinacyanol iodide dye tracing is incompatible with alcohol fixation and paraffin embedding of tissue.