A method is proposed for generating a series of sections of a microscopic sample (10), in which the sections are detached from the sample (10) by means of a blade (21), collected, and placed onto a transfer device. A sequence in which the sections are detached from the sample is detected; detachment of the sections from the sample (10) and/or collection of the sections and/or placement of the sections onto the transfer device is monitored by means of one or several observation cameras, accompanied by the acquisition of moving-image data; the sections are tracked in the moving-image data; and positions of the sections on the transfer device are correlated, on the basis of the tracking in the moving-image data, with the sequence in which they were detached from the sample. Also subjects of the present invention are a method for three-dimensional reconstruction of a microscope sample (10), in which sections of the sample (10) are microscopically investigated accompanied by acquisition of section image data and in which the section image data are assembled into a volume image; and a corresponding microtome system (100) having a microtome (110) and a data acquisition and evaluation unit (120), and having one or several observation cameras (30).