The immune system integrates critical information across multiple scales to develop an effective response against invading pathogens and cancer. Modern approaches, such as imaging mass spectrometry and state-of-the-art microscopy, are key technologies to understand the mechanisms that spatially regulate leukocyte function. Multimodal imaging approaches, such as microscopy and mass spectrometry, is capable to analyse the local regulation of immune responses in infections and cancer. Our interdisciplinary coregistration algorithm combines immunohistochemistry (IHC), matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) and liquid chromatography with tandem mass spectrometry (LC-MS/MS) to unravel the immunological landscapes in diseases to improve diagnosis and therapies.