a Methylene blue-stained ACF enlarged to show detail. b Surface plot enhanced image of a showing ACF topography with crypt detail. c Surface plot image of a with pseudo color applied to show changes in both topography and density. d High-contrast image of b depicting software selected crypts in red. Small gray/white regions indicate areas lying below the crypt threshold, which were automatically discarded by the software. Larger, elongated gray/white indicate areas that were falsely identified as crypts by the software, but were removed by the user prior to analysis based on information gleaned from topographical views in b and c, i.e., slight invaginations were present on the surface of the ACF, but did not penetrate deep enough to be classified as a true crypt. Bar = 100 μm.