The Nanoimager contains a Microscope Module and Light Engine, which are permanently connected by the Light Link which houses the optical filters, coolant tubings, and electronic cables.

It is supplied with a laptop or a desktop computer to control the instrument and operate the Nanoimager via the ONI software NimOS, and certain consumables for normal operation as agreed by ONI. The cables include a thunderbolt cable to connect the Light Engine and the laptop, the power cord for the Light Engine, and the power supply for the laptop. Two bead slides are included for the initial inspection and calibration. All the necessary parts are carefully packed in a Pelicase and a checklist is provided to help review the shipment.