A biopsy system may have modes whereby fluid communication varies as a function of an axial position of a cutter. A tissue sample holder may be rotatable to index tissue chambers defined by removable trays, and may include a passage for inserting an instrument. A controller may control a tissue sample holder rotation mechanism based on the sensed position of a rotatable manifold, such as to present a collected biopsy sample to a user before collecting another biopsy sample in another chamber. A biopsy system may have an interface including visual features and user input devices. A vacuum canister may come packaged with tubing, and may include a port configured to mate with a port in a vacuum control module upon engagement of the canister with the module. A biopsy device may include features for sharps reduction, light sources, a motor driven firing mechanism, or a fine pitch drivetrain.