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A physical or checkup was a full examination that assessed an individual's general health and wellbeing.
In 2375, The Doctor added deep-body scanning with his holographic imager as part of annual physicals on-board USS Voyager, allowing him to create images of his patients down to the subatomic level. Captain Kathryn Janeway, however, did not report for her physical, "as usual," forcing him to track her down in her ready room to administer her physical, with a request to drop by Sickbay at her earliest convenience to undergo the deep-body scan. (VOY: "Latent Image")