A medical imaging system for illuminating tissue samples using three-dimensional structured illumination microscopy is port-based surgery is provided. The system comprises: an image sensor; a mirror device; zoom optics; a light modulator; a processor; and collimating optics configured to convey one or more images from the modulator to the mirror, the mirror configured to convey the images to the zoom optics, the zoom optics configured: to convey the image(s) from the mirror to a tissue sample; and convey one or more resulting images, formed by the image(s) illuminating the sample, back to the mirror, which conveys the resulting image(s) from the zoom optics to the image sensor, and, the processor configured to control the modulator to form the image(s), the image(s) including at least one pattern selected to interact with the sample to generate different depth information in each of resulting image(s).