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On Qu'Vat colony in November 2154, Klingon Doctor Antaak gave a Petri dish, containing a sample of the Klingon augment virus, to Denobulan Doctor Phlox, shortly after Phlox was forcibly taken there in a desperate Klingon attempt to find a cure for the virus. (ENT: "Affliction")
When the USS Enterprise discovered Aurelan and Peter Kirk incapacitated by the yet unknown neural parasites on Deneva in 2267, Captain Kirk demanded to find answers for the cause. However, Doctor McCoy informed Kirk that he would not be able to get the exact cause until he got the plates back from the lab. (TOS: "Operation -- Annihilate!")
When infected with an alien virus forcing Kathryn Janeway and Chakotay to live on New Earth, Janeway collected several supplies, including Petri dishes, a protein analyzer, and DNA sequencers to continue her research in finding a cure. (VOY: "Resolutions")
Upon discovering that the Srivani had infiltrated the USS Voyager in 2374 to conduct their medical experiments, The Doctor remarked that it was as if the ship were "one big Petri dish." (VOY: "Scientific Method")
In 2375, Captain Kathryn Janeway told Seven of Nine to make more nanoprobes with which to counter Species 8472 by whatever means necessary, whether they were extracted from her bloodsteam or grown in a Petri dish. (VOY: "In the Flesh")
To punish his son's misbehavior in 2378, Q transformed him into an Oprelian amoeba and confined him to a Petri dish. Later, upon being assigned his own quarters on the USS Voyager, Junior quipped that the Petri dish was less cramped. (VOY: "Q2")