Mobile microscopy is a newly formed field that emerged from a combination of optical microscopy capabilities and spread, functionality, and ever-increasing computing resources of mobile devices. Despite the idea of creating a system that would successfully merge a microscope, numerous computer vision methods, and a mobile device is regularly examined, the resulting implementations still require the presence of a qualified operator to control specimen digitization. In this paper, we address the task of surpassing this constraint and present a “smart” mobile microscope concept aimed at automatic digitization of the most valuable visual information about the specimen. We perform this through combining automated microscope setup control and classic techniques such as auto-focusing, in-focus filtering, and focus-stacking—adapted and optimized as parts of a mobile cross-platform library.