We present here an integrated SoC platform, called APEX-SoC, that is aimed at speeding-up the design of next-generation space flight instruments avionics by providing a convenient infrastructure for hardware and software based science data processing. We use a case-study drawn from the JPL Compositional Infrared Imaging Spectrometer (CIRIS) to illustrate the process of integrating instrument-dependent data acquisition and processing stages in this platform. In order to enable the use of APEX-SoC-based instruments in deep space missions, the platform implements Radiation Hardening By Design (RHBD) techniques and offers support for instantiating multiple processing stages that can be used at runtime to increase reliability or performance, based on the requirements of the mission at each particular stage. Finally, in the specific case of CIRIS, the data processing includes a stage to cope with radiation affecting the instrument photo-detector.