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The development of confocal microscopy and its application to studies of plant–pathogen interactions have revolutionised research into the role of selected molecules and cell components in pathogen infection strategies and plant defence responses. Confocal microscopy allows high-resolution visualisation of a variety of fluorescent and fluorescently tagged molecules in both fixed and living cells, not only in single cells but also in intact tissues. Confocal microscopes greatly improve image quality by reducing interference by out-of-focus light and can capture high-resolution serial optical sections through samples in the z-axis. In combination with a range of computational image analysis techniques, confocal microscopy provides a powerful tool by which molecules, molecular interactions, and cell components can be localised and studied.