Abstract: A biopsy system includes various features. A tissue sample holder kit of the system comprises a rotatable member with chambers configured to receive tissue receiving features of a tissue sample tray. A biopsy device of the system includes user input features and user feedback features disposed on a body. A user interface of the system includes a graphical representation of a tissues ample holder. A biopsy site marker applier of the system includes markings associated with different biopsy device configurations. The biopsy system may undergo a multi-step initialization process. In operation, the biopsy system may execute pneumatic control algorithms including the use of vacuum, saline, and atmospheric air.