Histology · Methods and stains
From biopsy to slide: fixation, sectioning, frozen section !
- Technique
Before tissue can be seen under a microscope it must be preserved, hardened, cut very thin and stained.
Updated 2026-11-01
See it in 3D: Skin · Liver · Thyroid gland
What it is
Histological processing turns a soft, perishable sample into thin, stable slides. Routine processing uses formalin fixation and paraffin embedding and gives the best detail but takes days; a frozen section gives an answer within minutes during surgery, with less detail.
Step by step
- The sample (biopsy or surgical specimen) is taken and sent quickly to the lab to avoid autolysis.
- Fixation, almost always in buffered formalin: it cross-links proteins and stops self-digestion.
- Dehydration through increasing concentrations of alcohol.
- Clearing with a solvent (xylene) that mixes with paraffin.
- Embedding in molten paraffin to form a block that can be cut.
- Cutting on a microtome into sections a few micrometres thick, mounted on a glass slide.
- Dewaxing, staining (H&E or others) and coverslipping for the pathologist to read.
Paraffin section versus frozen section
| Feature | Paraffin (permanent) | Frozen (intraoperative) |
|---|---|---|
| Time | Several days | About 15 to 20 minutes |
| Instrument | Microtome | Cryostat |
| Detail | Best; the basis of the final diagnosis | Lower; ice-crystal artefacts |
| Lipids | Dissolved (fat cells look empty) | Preserved (useful for fat stains) |
| Typical use | Final diagnosis, immunohistochemistry, archive | Surgical margins, deciding the extent of surgery, immunofluorescence |
Clinical notes
- A frozen section tells the surgeon in theatre whether a margin is free of tumour or a lymph node holds a metastasis.
- Late or poor fixation damages morphology and can distort immunohistochemistry (for example hormone receptors in breast cancer).
- Skin biopsies for suspected autoimmune blistering disease are also sent without formalin for direct immunofluorescence.
Test yourself
Think of the answer, then tap the question to see it.
What is the main job of formalin in tissue processing?
To fix the tissue: it cross-links proteins, stops autolysis and preserves the architecture.
What is a frozen section used for during surgery?
To give a rapid diagnosis, for example whether a surgical margin is involved, in about 15 to 20 minutes.
Why do fat cells look like empty spaces in a paraffin section?
The alcohols and xylene used in processing dissolve the lipid, leaving only the membrane and the pushed-aside nucleus.
See it in 3D
The structures of Durgical's 3D anatomy where it is found.
Related
- Microscopy and stains: H&E, PAS, trichrome, silver, immunohistochemistry
- Electron microscopy: what it shows that light can't
- Adipose tissue: white and brown fat
Related conditions
Educational content on normal microscopic structure and its clinical relevance; no substitute for studying slides or for a health professional's advice.
Sources: Tissue preparation 1 (Digital Histology, 2024); Pathology Reports (National Cancer Institute, 2024).
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Representative model, for educational purposes only.