A cassette for holding a tissue sample includes a body having a bottom wall and a plurality of side walls extending upwardly with respect to the bottom wall to define an interior space for receiving the tissue sample. A lid is configured to be received in the interior space, and the cassette is sectionable in a microtome. Sensing elements are associated with the body or lid and configured to allow an automated sensing system to determine at least one characteristic of the cassette. A flange extends along upper portions of at least two of the side walls and includes a plurality of holes. Other features are included to more effectively and efficiently manufacture and use the cassette.