Abstract Image registration is a fundamental task in today’s medical imaging. In particular for histological serial sectioning, where a three-dimensional object is cut into thin sections for a further microscopic analysis, registration leads to a three dimensional reconstruction of the sections. This reconstruction enables an exploration of the digitized data in any direction, not only in the cutting direction. In this paper, we describe cutting and reconstruction procedures. For the reconstruction, we use linear as well as non-linear registration schemes. Moreover, we present some results for a whole brain of a Sprague Dawley rat.