Haematoxylin and Eosin Stain (H&E)
The H&E stain is probably the most widely used histological stain. Its popularity is based on its comparative simplicity and ability to demonstrate clearly an enormous number of different tissues.

Gills haematoxylin and Eosin is the standard method I the lab but other stains; like Ehirlichs and Weigert’s haematoxylin for nuclei are also available.

Nuclei stain blue, other elements shades of pink/red.

Connective Tissue Stains
Connective tissue’s major function is to connect together and support the other tissue of the body. It usually consists of a cellular portion in an enveloping framework of non-cellular substances; there are many techniques available for the demonstration of the different connective tissues.

Masson Trichrome
Nuclei: Black
Collagen: Green / Blue
Muscle: Red
Fibrin: Red
Reticulin: Green
Elastic: Red

Van Gieson
Nuclei: Black
Collagen: Red
Muscle: Yellow

MSB
Fibrin: Red
Collagen: Blue
Muscle: Pale Red
Erythrocytes: Yellow
Nuclei: Blue

Elastic Van Gieson (EVG)
Elastic: Blue/Black
Nuclei: Blue
Collagen: Red
Muscle: Yellow

Gordon & Sweet’s Stain for Reticulin Fibres
Reticulin: Black
Collagen: Brown (if untoned)

Safranin O
Nuclei: Black
Cytoplasm: Grey/Green
Mucus, cartilage, mast cell granules: Red
Muscle: Green

Nucleic Acids
Nucleoproteins are combinations of basic proteins (protamines and histones) and nucleic acids. The two nucleic acids are DNA which is found in the nucleus of the cell and RNA which is located in the cytoplasm of cells, mainly in ribosomes. Both DNA and RNA molecules consist of alternate sugar and phosphate groups with a nitrogenous base being attached to each sugar group. The sugar in DNA is the 5-carbon sugar deoxyribose; in RNA it is ribose.

Feulgen Stain
DNA: Red-Purple
Cytoplasm: Green

Methyl Green – Pyronin
DNA: Green-Blue
RNA: Red

Amyloid
The classical, histopathological definition of amyloid is an extracellular, proteinaceous deposit exhibiting beta sheet structure. Common to most cross-beta type structures they are generally identified by apple-green birefringence when stained with Congo Redand seen under polarized light. These deposits often recruit various sugars and other components such as Serum Amyloid P component, resulting in complex, and sometimes inhomogeneous structures.

Congo Red
Amyloid: Red
Nuclei: Blue
Eosinophils, Elastin and Keratin: Red

Glycogen, Carbohydrates and Mucins

Periodic Acid Schiff (PAS)
Glycogen and other periodate-reactive carbohydrates : Mangenta
Nuclei: Blue
*glycogen can be digested out with pre-treating slide with diastase*

Alcian Blue for Acid Mucins
Acid Mucopolysaccharides: Blue
Nuclei: Red
*The pH of the solution can be changed according to the type of mucins you wish to demonstrate*
pH0.2: Strongly sulphated mucins.
pH1.0: Weakly and strongly sulphated mucins.
pH2.5: Most acid mucins except some strongly sulphated mucins.

Lipids
These stains must be carried out on  unfixed frozen sections as processing the speciems will dissolve out any lipids                   

Oil Red O
Unsaturated hydrophobic lipids: Red
Phospholipids: Pink
Nuclei: Blue

Nile Blue
Neutral Lipids: Red-Pink
Acidic Lipids: Blue

Pigments & Minerals

Perls’ Prussian Blue
Ferric Iron: Blue
Nuclei: Red

Fouchet
Bile: Green
Other Elements: As counterstain

Masson Fontana
Melanin, Argentaffin, Chromaffin, Some Lipofuscins: Black
Nuclei: Red

Von Kossa
Calcium Deposits: Black
Other Elements: As counterstain

Rhodanine
Copper: Red
Nuclei: Light Blue

Grimelius
Agryrophil Granules: Black
Pancreatic α2 Cells: Black
Background: Yellow

Hexamine Silver
Basement Membrane: Black
Other Elements: As counterstain

Luxol Fast Blue Cresyl Fast Violet
Myelin: Deep Bright Blue
Red Blood Cells: Turquoise
Lipofuscin: Bright Blue
Nissl Granules: Purple
Background: Colourless

Micro Organisms and Fungi

Gram Stain
Gram Positive Organisms: Blue
Gram Negative Organisms: Red
*some fungi, keratohyalin and keratin may also stain blue*

Ziehl-Nelson
Tubercle Bacilli: Red
Background: Pale Blue

Wade-Fite
Leprosy and Other Mycobacteria: Red
Background: Light Blue

Alcian Yellow Toluene Blue
Mucin: Yellow
Helicobacter Pylori: Blue
Background: Pale Blue

Grocott
Fungi: Black
Pneumocystis: Black
Other Elements: As counterstain
*Cellulose, chitin, amoeboe, some mucins, melanin, glycogen and starch may also be black*

PAS
Fungi: Mangenta
Nuclei: Light blue