One aspect of the invention concerns a method for characterizing the internal three-dimensional organization of a
biological tissue sample comprising a plurality of types of biological elements (201, 202), said method having the following steps:For at least one type of biological elements (201, 202, 203, 204) of interest among the plurality of types of biological elements (201, 202, 203, 204), automatic or semi-
automatic segmentation in each image (IZ) from a stack of images (I3D), of at least one region containing at least one biological element (201, 202, 203, 204) having as type, the type of biological elements (201, 202,203, 204) of interest, the stack of images (I3D) having been acquired by Z-series imaging by automated ultramicrotomy under scanning
electron microscopy and including a plurality of images (IZ) each acquired in a plane perpendicular to a depth axis (Z) and each associated with a position on the depth axis (Z), the plurality of images (IZ) being ordered by increasing position in the stack of images (I3D, 102);Characterization of a set of biological elements (201, 202, 203, 204) having as type the type of biological elements (201, 202, 203, 204) of interest, by calculation, for each biological element (201, 202, 203, 204) from the set of biological elements (201, 202, 203, 204), of at least one indicator (301, 302) relating to the structure, the morphology, the size, the polarity, the texture, the constitution, the orientation, a surface area, the alignment, the convergence, the density, the convexity or the concavity of the biological element (201, 202, 203,204), from each corresponding segmented region (104);Comparison between the indicators (301, 302) calculated for the set of biological elements (201, 202, 203, 204).