IHC guide v3 952x200px

Counterstains and special stains for immunohistochemistry

​​Histology stains, fluorescent stains and special stains are used to stain specific cell and tissue structures, and also to stain microorganisms to help identify the location of primary antibody staining.

​​Find information below about

​​This page is part of our IHC application guide: download it or read it online.

​​Tis page is part of our IHC application guide: download it or read it online.
Iron stain kit


Example of the use of special stains and counterstains. Prussian blue iron stain kit staining iron (blue) in liver tissue. Nuclei and background were counterstained with nuclear fast red.

​​Chromogenic counterstains

Chromogenic counterstains are used when the primary antibody is visualized using HRP or alkaline phospatase combined with DAB, AEC, or similar enzyme substrates. The traditional combination is HRP/DAB with hematoxylin to stain nuclei. Eosin, for cytoplasmic staining, is often used in combination with hematoyxolin.   

Mayers HematoxylinNucleiBlue to violetab220365

Nuclear fast red(Kernechtrot)

Nucleic acidsRed
Methyl greenNucleic acidsGreen

Fluorescent counterstains

Fluorescent counterstains are used when the primary antibody staining is visualized with a fluorescent dye either directly conjugated to the primary antibody, or to a secondary antibody. Avoid using a counterstain with an overlapping emission spectra to the dye used for  primary antibody visualization.

DAPI is traditionally the most popular fluorescent nuclear counterstain.

DRAQ5™Nucleic acidsRedab108410

Nucleic acids

Nuclear yellow (Hoechst S769121)Nucleic acidsYellow/Blue*ab138903
Nuclear Green DCS1Nucleic acidsGreenab138905
Hoechst stainNucleic acidsBlue-
4', 6-diamino-2-pheylindole (DAPI)Nucleic acidsBlue-
Propidium iodideNucleic acidsRedab14083

*Emission is blue/violet under acidic conditions and yellow under neutral pH conditions

Special stains

Special stains are used to stain certain cell types, microorganisms, and specific proteins, carbohydrates and metabolites found in the tissue matrix and within cells. 

Whilst simple to use once established, special stains are often time consuming to set up and optimize. Optimized special stain kits provide a convenient alternative to setting up a stain yourself, and they are often faster to use than the traditional staining methods.

Special stain



Acid Fast Bacteria (AFB) Stain

Stains microoganisms - specifically acid-fast bacteria and Tubercle bacilli


Alcian Blue (pH 1.0) Stain

Stains mucins - acidic mucosubstances stained blue, nuclei pink to red and cytoplasm pale pink (for visualization of strongly sulfated mucosubstances)


Alcian Blue (pH 2.5) Stain

Stains mucins - acidic mucosubstances stained blue, nuclei pink to red and cytoplasm pale pink


Alizarin Red Stain

Stains calcium - may not-specifically stain magnesium, manganese, barium, strontium or iron depending on concentration


Amyloid Stain (Congo Red)

Stains amyloid deposits


Colloidal Iron Stain

Stains mucins


Combined Eosionphil-Mast Cell Stain

Stains mucins - simultaneously visualize eosinophils and mast cells


Copper Stain

Staining copper deposits


Elastic Stain (Modified Verhoff's)

Stains connective tissue (eg elastin)


Fite's Stain

Stains microorganisms (eg Mycobacterium leprae)


Fontana-Masson Stain

Stains melanin and argetaffin granules black


Giemsa Stain (May-Grunwald)

Hematologic stain for visualizing cells in hematopoietic tissues and some microorganisms


Hydroxystilbamidine   (also known as Fluoro-Gold™)

Fluoresent label that can be used as a retrograde enhancer to label neurons (Ex/Em: 385/536 nm)


Modified Gomori Methenamine-Silver (GMS) Nitrate Stain

Stains fungi, basement membranes and some opportunistic organisms (eg Pneumocystis carinii)


Golgi Cox Stain

Stains neuronal dendrites and dendritic spines


Gram Stain

Stains microorganisms - differentiates between Gram-positive and Gram-negative bacteria


H. pylori Rapid Stain

Stains Helicobacter pylori


Prussian Blue Iron Stain

Stains iron - highly sensitive stain, stains ferric ions in tissue bright blue


Luxol Fast Blue Stain

Stains myelinated axons in brain and spinal cord tissue blue, neurons violet and myelin and phospholipids blue/green


Methyl Green Pyronin (pH 4.8) Stain

Stains DNA, RNA and mast cell granules


Mucicarmine Stain

Stains mucin


Nissl Stain

Stains Nissl body in cytoplasm of neurons


Oil Red O Stain

Stains lipids and fat


Papanicolaou (PAP) Red Stain

Cytology stain - allows differentiation of a variety of cell types in bodily secretions such as gynecological smears


Periodic Acid Schiff (PAS) Stain

Stains mucin - stains glycogen, mucin and fungi magenta and nuclei black/blue


Picro Sirius Red Stain

Stains connective tissue - specifically collagen


Pneumocystis Stain

Stains Pneumoscystis carinii


Phosphotungstic Acid Hematoxylin (PTAH) Stain

Staining connective tissue - specifically collagen, striate muscle and glial fibers


Reticulum Stain

Stains reticular fibers in connective tissue


Safranin O Stain

Stains mucin, cartilage and mast cell granules


Steiner Stain

Stains fungi, H.pylori, L. pneumophila and spirochete-infected tissue


Sudan Black

Stains lipids and fat blue/black and nuclei red


Toluidine Blue Stain

Stains nucleic acids blue and polysaccharides purple.  Mast cells are stained dark blue/red purple


Trichome Stain (Modified Masson's)

Stains connective tissue


Calcium Stain (Modified Von Kossa)

Stains calcium grey to black in histology sections


Warthin-Starry Stain

Stains spirochetes, H. pylori, L. pneumophila and cat scratch fever bacteria


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