Biopsies are a diagnostic tool for the diagnosis of histopathological, molecular biological, proteomic, and imaging data, to narrow down disease patterns or identify diseases. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) provides an emerging stateof-the-art technique for molecular imaging of biological tissue. The aim of this study is the registration of MALDI MSI data sets and data acquired from different histological stainings to create a 3D model of biopsies and whole organs.