1. A method of determining component misalignment in a multi-modality imaging system including a first modality unit and a second modality unit, said method comprising: imaging a plurality of target objects with the second modality unit to generate an emission image data set; determining a location of the target objects in the emission image data set to produce emission target object location coordinates; calculating a positional alignment vector for each target object based on the emission target object location coordinates; and aligning the multi-modality imaging system based on the positional alignment vectors.