Counterstains and special stains for immunohistochemistry
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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.
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This page is part of our IHC application guide: download it or read it online.
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 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.
| Dye | Target | Color | Product |
| Mayers Hematoxylin | Nuclei | Blue to violet | ab220365 |
Nuclear fast red(Kernechtrot) | Nucleic acids | Red | |
| Methyl green | Nucleic acids | Green |
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.
| Dye | Target | Color | Product |
| DRAQ5™ | Nucleic acids | Red | ab108410 |
DRAQ7™ | Nucleic acids | Red | ab109202 |
| Nuclear yellow (Hoechst S769121) | Nucleic acids | Yellow/Blue* | ab138903 |
| Nuclear Green DCS1 | Nucleic acids | Green | ab138905 |
| Hoechst stain | Nucleic acids | Blue | - |
| 4', 6-diamino-2-pheylindole (DAPI) | Nucleic acids | Blue | - |
| Propidium iodide | Nucleic acids | Red | ab14083 |
*Emission is blue/violet under acidic conditions and yellow under neutral pH conditions
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 | Description | Product |
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) | |
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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