A system, apparatus and method for using modular microscopes is disclosed. Connecting the housings of the individual microscope modules provide the structural framework of the modular microscope. Furthermore, the modular microscope can include specialized software, the distribution and use of which can be controlled using security keys or identifiers stored on one or more of the microscope modules. The security keys and identifiers can be based on calibration data associated with the physical, electrical, or optical properties of one of more of the modules. The illumination modules disclosed provide for selectable wavelengths and controllable levels of output illumination for both bright field and dark field illumination.