The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN. Approximately 80 M electronic channels of the detector, made of silicon, allow to detect particle tracks and secondary vertices with very high precision. After connection of cooling and services and verification of their operation the ATLAS Pixel Detector is now in the final stage of its commissioning phase. Prior to the first beams expected in Summer 2009, a full characterization of the detector is performed. Calibrations of optical connections, verification of the analog performance and special DAQ runs for noise studies are ongoing. Combined operation with other subdetectors in ATLAS allows to qualify the detector with physics data from cosmic muons. The talk will show all aspects of detector operation, including the monitoring and safety system, the DAQ system and calibration procedures. The summary of calibration tests on the whole detector as well as analysis of physics runs with cosmics data will be presented.