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Chemical fixation stabilizes biological samples by cross-linking proteins and preserving cellular structures before exposure to the electron beam and vacuum. Fixatives like glutaraldehyde and formaldehyde cross-link proteins, while osmium tetroxide fixes membrane lipids. Rapid fixation is critical because sample properties begin changing immediately after removal from their natural environment, such as altered mitochondrial appearance due to decreasing oxygen levels.

Dehydration removes water from samples to prevent damage from the vacuum environment inside the electron microscope. Samples are gradually treated with increasing concentrations of ethanol or acetone to avoid shrinkage and structural distortion. Complete desiccation ensures the sample remains stable under low-pressure conditions during imaging.

Transmission electron microscopy (TEM) embeds samples in hard epoxy resin and slices them into ultrathin sections using an ultramicrotome, allowing electrons to pass through. Scanning electron microscopy (SEM) uses critical point drying with liquid carbon dioxide and applies sputter coating with conductive metals like gold. SEM samples are examined on their surface rather than sectioned, providing three-dimensional topographical information.

Heavy metal stains such as uranyl acetate bind to cellular molecules and appear darker in electron microscopy images, creating contrast that reveals ultrastructural details. The differential binding of metals to different sample components produces the contrast needed to distinguish cellular structures. This staining technique enhances image quality by highlighting molecular composition and organization.

Sputter coating deposits a thin conductive metal layer, typically gold, onto sample surfaces using argon ions. This coating prevents thermal damage caused by electron bombardment and improves image quality by enhancing electron conductivity. The process makes non-conductive samples conductive, allowing better electron interaction and clearer visualization of surface features.

Cryofixation rapidly freezes samples using plunge freezing for small cells or high-pressure freezing for larger tissues, preventing water crystallization that damages ultrastructure. Plunge freezing immerses samples in liquid ethane cooled by liquid nitrogen, while high-pressure freezing applies approximately 2000 bar pressure to decelerate ice crystal formation. This technique preserves native cellular structures better than chemical fixation alone.

Negative staining allows small samples like ribosomes, viruses, and proteins to be imaged directly without sectioning by mixing them with electron-opaque compounds such as ammonium molybdate or uranyl acetate. A metal layer forms on the grid except where the sample lies, creating a negative image with contrast from metal distribution patterns. This technique is particularly useful for studying ultrastructural details of bacteria, viruses, and isolated macromolecules.