This document provides instructions for performing structured illumination using a Zeiss Apotome 2 microscope. It describes what structured illumination is, how it works to optically section images, and its advantages over confocal microscopy. It outlines the calibration steps required before acquisition, including a transmitted light phase calibration and focus calibration that must be done for each objective and wavelength used. Detailed instructions are provided for performing the focus calibration workflow in Zen software. The document concludes by noting the acquisition process once calibrations are complete.