[Durgical](https://durgical.com/en/) › [DurgiPedia](https://durgical.com/en/durgipedia/) › [Histology](https://durgical.com/en/histology/) › [Methods and stains](https://durgical.com/en/histology/#a-methods) › Microscopy and stains: H&E, PAS, trichrome, silver, immunohistochemistry

[Histology](https://durgical.com/en/histology/) · [Methods and stains](https://durgical.com/en/histology/#a-methods)

# 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](https://durgical.com/en/anatomy/liver/) · [Skin](https://durgical.com/en/anatomy/skin/) · [Stomach](https://durgical.com/en/anatomy/stomach/)

## Key points

- Basic haematoxylin stains acidic things (nucleus, RER); acidic eosin stains basic things (cytoplasm, collagen).
- PAS = carbohydrates: glycogen, mucin, basement membranes; magenta.
- Trichrome measures fibrosis; silver shows reticulin; Verhoeff shows elastin.
- Congo red with apple-green birefringence = amyloid.
- Immunohistochemistry identifies specific proteins and points to a tumour's origin.

## 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).

## Memory aid

Opposites attract: the basic dye (haematoxylin) heads for the acidic nucleus, the acidic dye (eosin) for the basic cytoplasm.

## 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.

[Add to my cards (4)](https://durgical.app/estudiar/?add=/en/histology/microscopy-and-stains-h-y-e-pas-trichrome-silver-immunohistochemistry/)

## See it in 3D

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

- [Liver](https://durgical.com/en/anatomy/liver/)
- [Skin](https://durgical.com/en/anatomy/skin/)
- [Stomach](https://durgical.com/en/anatomy/stomach/)

## Related

- [From biopsy to slide: fixation, sectioning, frozen section](https://durgical.com/en/histology/from-biopsy-to-slide-fixation-sectioning-frozen-section/)
- [Electron microscopy: what it shows that light can't](https://durgical.com/en/histology/electron-microscopy-what-it-shows-that-light-can-t/)
- [Extracellular matrix: collagen types, elastin, ground substance](https://durgical.com/en/histology/extracellular-matrix-collagen-types-elastin-ground-substance/)
- [Liver: lobule, acinus, hepatocytes, sinusoids, Kupffer cells](https://durgical.com/en/histology/liver-lobule-acinus-hepatocytes-sinusoids-kupffer-cells/)

## Related conditions

- [Pulmonary tuberculosis](https://durgical.com/en/conditions/pulmonary-tuberculosis/)
- [Breast cancer](https://durgical.com/en/conditions/breast-cancer/)

## Microorganisms

- [Mycobacterium tuberculosis](https://durgical.com/en/microbiology/mycobacterium-tuberculosis/)

[← All of histology](https://durgical.com/en/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](https://digitalhistology.org/histology-basics/stains/stains-02/) (Digital Histology, 2024); [Stains 6](https://digitalhistology.org/histology-basics/stains/stains-6/) (Digital Histology, 2024); [Stains 8](https://digitalhistology.org/histology-basics/stains/stains-8/) (Digital Histology, 2024); [Stains 11](https://digitalhistology.org/histology-basics/stains/stains-11/) (Digital Histology, 2024).

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Representative model, for educational purposes only.

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Source: https://durgical.com/en/histology/microscopy-and-stains-h-y-e-pas-trichrome-silver-immunohistochemistry/
License: CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). Cite as: DurgiPedia (durgical.com), https://durgical.com/en/histology/microscopy-and-stains-h-y-e-pas-trichrome-silver-immunohistochemistry/