• Clinical science

Pathology techniques


The primary objective of pathological techniques is the diagnostic classification of pathologically altered tissue (histology) and the assessment of cell morphology (cytology). In addition to post-mortem examination, histological and cytological evaluation of tissue is the main task in pathology. Evaluating tissues and cells with light microscopy requires comprehensive skills in specimen assessment, processing, and preservation. However, an alternative to more traditional macroscopic and microscopic investigation may be found in new procedures that focus on the cellular level.

This article provides an overview of the most common methods of examination and staining in pathology.

Specimen types

Macroscopic examination

Processing of every specimen includes:

  • Measuring and weighing (e.g., enlarged heartcardiomegaly, enlarged liverhepatomegaly)
  • Photography
  • A description including:
    • Shape (e.g., malignant changes in organ shape)
    • Color (e.g., atypical color in malignancies or necrosis )
    • Structure and consistency (e.g., hard and knotty surfaces in the case of liver cirrhosis)
    • Smell (e.g., discharge of foul-smelling pus is a sign of bacterial infection after the opening of cysts or abscess cavities)

In addition, the degree of penetration, the resection edges, lymph node involvement, and visible metastasis are assessed in the case of tumors!

Microscopic examination

In cytology, cells are analyzed and sampling is easy and minimally invasive. In histology, tissue is obtained with invasive techniques, but it allows for the assessment of the local spreading of tumor (T stage of TNM score).References:[1][2]


Every microscopic examination is preceded by the processing and preservation of cells and tissues (embedding and cutting procedures).

  • Histopathology
    • Paraffin sections: Used for routine diagnostic testing and to prepare histopathological sections for long-term storage
      • Procedure: formaldehyde fixationdehydration by exposing the specimens to solutions of increasing alcohol concentration → alcohol removal (“clearing”) by immersing specimens in xylene or toluene → embedding of specimen in molten paraffin → paraffin solidification and section cutting → section transfer to glass slide → staining (see below)
    • Frozen sections: Used for intraoperative sections and special examinations, e.g., (immuno)histochemistry.
  • Cytopathology
    • Smears: cells are smeared onto a glass slide → alcohol fixation (or fixation spray) → staining


Staining methods

Routine stainings

Special stainings

Staining Blue Red Black Yellow Green Application
Routine staining Hematoxylin-eosin staining (H&E staining)
  • Routine histopathological staining
Papanicolaou staining (PAP staining)
  • Nucleus
  • Bacteria
  • Mucus in acidic environment
Giemsa staining
  • Intracellular: nucleus
  • Bacteria
  • Other basophilic substrates

Routine cytopathological staining:

  • Differentiation between blood components
  • Parasites (Trypanosoma cruzi), protozoa (malaria, leishmaniasis)
Special staining Pappenheim staining (MGG staining)
  • Nucleus (blue-violet)
  • Other basophilic substrates
  • Basophilic granules
  • Differentiation between blood and bone marrow components
Van Gieson's stain
Masson-Goldner staining

Periodic acid–Schiff reaction (PAS reaction)


Prussian blue reaction Iron in mitochondria
  • Nucleus

Iron detection

Congo red Nucleus
  • Amyloid (β-fibrils, green after polarization)
Von Kossa staining
  • Nucleus
Calcium phosphate
  • Calcification
Ziehl-Neelsen stain (acid-fast stain)
  • Acid-fast rods (Mycobacteria, Nocardia)
  • High mycolic acid content


H&E staining

Giemsa staining

Pappenheim staining

Van Gieson's staining

PAS reaction

Prussian blue reaction

Congo red


Special methods in pathology and molecular biology

See the article on laboratory methods for more information on blotting techniques, enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), and chromosome testing.


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last updated 09/24/2020
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