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(covers information from several alternate timelines)
In 2152, Doctor Phlox conducted a microcellular scan of Lieutenant Malcolm Reed's left leg, which had been injured by a Romulan mine. Phlox examined the scan while an alien medical device was healing the leg. The scan showed him the device was using a cytokinetic enzyme to stimulate the cell devision in Reed's limb. (ENT: "Dead Stop")
Later that year, in an alternate timeline, after Captain Jonathan Archer was struck by a spatial anomaly, a microcellular scan performed by Doctor Phlox revealed that Archer's hippocampus had been infected by parasites, which were preventing the formation of long-term memories. Many years later, when one cluster of parasites were eradicated from Archer's brain, that same cluster also disappeared from microcellular scans taken in the past. Theorizing that eradicating the parasites in the present also removed them in the past, Archer, Phlox, and T'Pol successfully destroyed the remaining parasites, creating another timeline in which the parasites did not infect Archer. (ENT: "Twilight")
In 2371, Doctor Julian Bashir performed a microcellular scan on Chief Miles O'Brien when the latter was experiencing shifts in time. The scan revealed that the temporal shifts were causing damage to the chief's cerebrospinal nerve cells, which would worsen and lead to death if the shifts continued. (DS9: "Visionary")
In 2372, while trapped in an alternate timeline in which he was not aboard the USS Voyager when it was stranded in the Delta Quadrant, Harry Kim suggested that Lasca and Admiral Strickler run a microcellular scan on his cerebral cortex to prove that his memories were not altered and that he really was Harry Kim. (VOY: "Non Sequitur")
The transporter buffer of an Intrepid-class starship performed its own version of a microcellular scan every time a person was transported. The Doctor used these scan logs to determine when Harry Kim's DNA had been altered by the Taresian retrovirus. (VOY: "Favorite Son")
The Doctor also ran a microcellular scan on Dammar to search for residual energy traces, after the Nyrian claimed that his mysterious appearance on Voyager involved a number of physical discomforts. (VOY: "Displaced")