A system for providing the timing alignment for a scanner. The system includes a removable source and detector assembly which is placed near the center of the scanner when in use. The source includes a long-lived positron emitting radioactive source. The radioactive source is in close contact with a fast plastic scintillator or other mechanism of detecting the ionization due to positron decay. A method for reading out the precise time at which the surrounding medium detects the ionization due to positron decay. A mechanism for using this time as a reference clock unto which the detectors in the scanner can be aligned.