I. Introduction
The Atlas Pixel detector has been installed in its final place into the ATLAS cavern in July 2007. After providing all the necessary connections, the final testing and commissioning has been performed before the first beam was circulated through the LHC in September 2008. The connection between the 1744 detector modules and the readout electronics in the counting room is done via optical links, that have to be commissioned and tuned in order to be able to send commands to and receive data from the modules. Tests for optical and electrical functionality of components during production and assembly sorted out failing parts. The commissioning work on the installed detector showed more than 97% of the system being functional.