Bruker has introduced the automated setup of MALDI imaging with SCiLS™ autopilot and IntelliSlides™. SCiLS autopilot automatically conducts six key performance optimisations to quickly move from a prepared slide to acquisition of data. The scanned sample image is registered with the barcode on the IntelliSlide, tissue margins are automatically detected, followed by automated multi-step optimisation to decrease the time and expertise needed for MALDI imaging, and to ensure reproducibility and image quality. Through SCiLS autopilot automation, MALDI imaging can be easily integrated by non-expert users to add physiological tissue context to their 4D-Omics studies.