The invention relates to a method that includes the following steps: carrying out a treatment of a sample, the treatment being carried out for differentiating diseased cells from healthy cells in the sample (4); carrying out at least one first image acquisition of the sample (4) provided on an analysis plate (8) so as to obtain a plurality of images, each representing an area (18) of the analysis plate, said images being arranged side by side so as to form an image of the entirety of the sample in order to create a virtual analysis plate (2), locating a reference plane of the analysis plate including a slide and a lamella provided above the slide for image acquisition, said reference plane being defined by the surface of the slide or the lamella; and carrying out at least one second image acquisition, said second acquisition being carried out at a different thickness of the sample relative to the first acquisition so as to obtain a plurality of images corresponding to a section of the sample with a different thickness.