A microtome system for cutting sections from a specimen includes a knife including a knife edge configured to cut a section from the specimen, a knife holder, a specimen holder, an illumination, a first actor, a detector, and a controller. The knife holder and specimen holder are configured to be relatively moveable in a cutting direction. The first actor is configured to cause a rotation of the knife holder or specimen holder about an axis. The illumination is configured to illuminate a gap between a front face of the specimen and the knife edge to generate a light gap. The detector is configured to detect a geometric feature of the light gap. The controller is configured to automatically align, or provide indications to manually align, the knife edge with the front face, by controlling the first actor depending on the detected geometric feature.