A technique in which cells or thin sections of biological tissue that are normally transparent are immersed in one or more coloured dyes (stains) to make them more clearly visible through a microscope. Staining heightens the contrast between the various cell or tissue components. Stains are usually organic salts with a positive and negative ion. If the colour comes from the negative ion (organic anion), the stain is described as acidic, e.g. eosin. If the colour comes from the positive ion (organic cation), the stain is described as basic, e.g. haematoxylin. Neutral stains have a coloured cation and a coloured anion; an example is Leishman’s stain. Cell constituents are described as being acidophilic if they are stained with acidic dyes, basophilic if receptive to basic dyes, and neutrophilic if receptive to neutral dyes. Vital stains are used to colour the constituents of living cells without harming them (see vital staining); nonvital stains are used for dead tissue.

Counterstaining involves the use of two or more stains in succession, each of which colours different cell or tissue constituents. Temporary staining is used for immediate microscopical observation of material, but the colour soon fades and the tissue is subsequently damaged. Permanent staining does not distort the cells and is used for tissue that is to be preserved for a considerable period of time.

Electron stains, used in the preparation of material for electron microscopy, are described as electron-dense as they interfere with the transmission of electrons. Examples are salts of heavy metals, such as lead hydroxide, phosphotungstic acid (PTA), uranyl acetate (UA), and osmic acid.