Microscopy and stains: H&E, PAS, trichrome, silver, immunohistochemistry !

Technique

Tissue is almost transparent; stains give it colour so nuclei, cytoplasm, fibres, mucus and specific proteins can be told apart.

Updated 2026-11-01

See it in 3D: Liver · Skin · Stomach

What it is

An unstained section has hardly any contrast, so it is coloured with dyes that bind particular chemical groups. Haematoxylin and eosin (H&E) is the routine stain; special stains and immunohistochemistry answer questions H&E cannot, such as whether there is fibrosis, glycogen, amyloid or an organism, or which protein a tumour expresses.

Key facts

Haematoxylin is a basic (cationic) dye: it colours acidic structures blue-purple, such as nuclear DNA and ribosomal RNA.
Eosin is an acidic (anionic) dye: it colours cytoplasmic proteins, collagen and mitochondria pink.
Basophilic = takes up haematoxylin; acidophilic or eosinophilic = takes up eosin.
Histochemical stains (PAS, trichrome, silver, Perls) rely on a chemical reaction; immunohistochemistry uses antibodies against one antigen.
Metachromasia: toluidine blue stains heparin-rich mast-cell granules magenta instead of blue.

The stains to recognise

Stain	What it colours	Colour	Classic use
Haematoxylin and eosin (H&E)	Nucleus and RER / cytoplasm, collagen	Blue-purple / pink	Routine for every biopsy
PAS (periodic acid-Schiff)	Glycogen, neutral mucin, basement membranes, glycocalyx	Magenta	Liver glycogen, glomerular basement membrane, Whipple disease
Masson trichrome	Collagen versus muscle and cytoplasm	Collagen blue or green; cytoplasm red	Grading fibrosis in liver (cirrhosis) and kidney
Silver impregnation (reticulin)	Reticular fibres (type III collagen), neurons, some organisms	Black	Framework of liver, lymph node and spleen
Verhoeff-van Gieson	Elastic fibres	Black	Elastic laminae of arteries
Congo red	Amyloid	Red; apple-green under polarised light	Amyloidosis
Prussian blue (Perls)	Iron (haemosiderin)	Blue	Haemochromatosis, iron overload
Ziehl-Neelsen	Acid-fast bacilli	Red on a blue background	Tuberculosis
Immunohistochemistry	One antigen (cytokeratin, oestrogen receptor, HER2, Ki-67)	Brown in the usual method	Origin and typing of tumours

Markers

H&E
PAS
Trichrome
Silver
Congo red
Prussian blue
Ziehl-Neelsen
IHC

In the lab

Under the microscope with H&E: blue-purple nuclei, pink cytoplasm, bright red erythrocytes, and pale pink fibrous collagen.
What does not stain is also informative: fat cells and mucin-filled cells look empty because lipids dissolve during processing.
A plasma cell shows very basophilic cytoplasm (lots of RER) and a pale halo beside the nucleus (the Golgi).

Test yourself

Think of the answer, then tap the question to see it.

Why does the nucleus stain blue-purple with haematoxylin?

Haematoxylin is a basic dye that binds acidic structures such as the nucleic acids of the nucleus and ribosomal RNA.

Which stain shows glycogen and basement membranes?

PAS (periodic acid-Schiff), which colours carbohydrates magenta.

Which stain is used to grade fibrosis in a liver biopsy?

Masson trichrome, which separates collagen (blue or green) from parenchyma (red).

What Congo red finding confirms amyloid?

Red deposits that show apple-green birefringence under polarised light.

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See it in 3D

The structures of Durgical's 3D anatomy where it is found.

Microorganisms

Mycobacterium tuberculosis

← All of histology

Educational content on normal microscopic structure and its clinical relevance; no substitute for studying slides or for a health professional's advice.

Sources: Stains 02 (Digital Histology, 2024); Stains 6 (Digital Histology, 2024); Stains 8 (Digital Histology, 2024); Stains 11 (Digital Histology, 2024).

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Representative model, for educational purposes only.