In a scanning microscope, slides are fed automatically from a magazine to the imaging system. Each slide is labeled in some fashion with information for selecting the appropriate modality of operation of the scanner for that slide and the modality is implemented automatically. The information is preferably tied to and defined by a laboratory information system (LIS). For example, the instructions may regard the type of microscopy (i.e., trans- or epi-illumination), multi-spectral imaging with particular spectral bands combined with a particular set of z-positions, alternative filters, settings for the numerical aperture of the condenser, alternative detector operation for different resolutions, and alternative post-scan analyses of the data, as deemed optimal for the scan. The label may also contain the slide's identity, a pathologist's name, desired post-scan handling protocol, etc. The preferred array microscope to carry out the invention is also described.