The MErcury Radiometer and Thermal Infrared Imaging Spectrometer (MERTIS) is an instrument to study mineralogy and temperature distribution of Mercury surface in unprecedented quality. MERTIS was proposed in 2003 as payload of the Mercury Planetary Orbiter spacecraft of ESA-JAXA BepiColombo mission and will reach Mercury in 2026. MERTIS will map the whole surface at 500m resolution combining a push-broom IR grating spectrometer (TIS) with a radiometer (TIR) sharing the same optics, instrument electronics and in-flight calibration components for the whole wavelength range of 7-14μm (TIS) and 7-40μm (TIR). Currently we are developing and testing an ingestion, calibration and transformation pipeline for MERTIS data, from raw telemetry level data to calibrated product and high level derived product. Bepicolombo Science Ground Segment (BC-SGS or SGS) is embracing new technologies for the BepiColombo mission and follows the latest NASA/PDS format, the xml based PDS4. We adopt open source languages and well optimized libraries for the underlying processing. The data processing pipeline is fully containerized via Docker to be independent from transition between server/OSs/environment, drastically reducing the integration and testing time. Due to strict infrastructural constrains like spacecraft downlink bandwidth and onboard mass memory, the already complex observation scenario is subject to further optimizations. This complicates the reconstruction process for higher-level products like global maps of emissivity and thermal inertia.