Light vs electron microscopy

The choice comes down to required resolution and sample type.

Light (optical) microscopy

Resolution limited by the wavelength of visible light (~200 nm). Live cells, stained tissue, routine pathology. Variants: brightfield, phase contrast, fluorescence, confocal.

Electron microscopy

Uses an electron beam for nanometre/sub-nanometre resolution. SEM images surfaces in 3D; TEM images internal ultrastructure of thin sections. Samples must be fixed, dried/sectioned and usually conductive — no live imaging.

Use light microscopy for dynamics and routine cytology, electron microscopy when you need ultrastructure.