The invention provides for medical instrument (800, 1000) comprising a magnetic resonance imaging system. Execution of the instruction cause a processor controlling the instrument to: execute (900) a magnetic resonance data processing application (42, 852) thereby providing a plug-in framework, execute (902) a protocol definition interface to load a first selection (858) of the plug-ins into the plug-in framework, acquire (904) the magnetic resonance data by using the pulse sequence data to control the magnetic resonance imaging system； and reconstruct (906) a magnetic resonance image from the magnetic resonance data using the first selection of the plug-ins.
