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