The latter. The tissue block is sliced first in the ATUM which collects the sections on tape. These are then mounted on silicon wafers, and imaged with the MultiSEM.

Our preprint at https://www.biorxiv.org/content/10.1101/2021.05.29.446289v1 has some more details about the process, including figures illustrating the ATUM and the tissue block.

(I'm one of the authors of the paper)