A neutron microscope was a scientific instrument developed by the Denobulans. Using a stream of neutrons, it was capable of imaging objects on the atomic level.

It was considered an advanced piece of equipment in 2152, when Enterprise acquired one while attending an Interspecies Medical Exchange conference on Dekendi III. Feezal, one of Phlox's wives, accompanied the microscope and instructed Charles "Trip" Tucker in its installation and use. The microscope's parts included an aperture ring, condenser lens, an imaging filament, quantum filters, and a reflectometer. (ENT: "Stigma")

A year later, Phlox was working at the neutron microscope while infected by Borg nanoprobes. He stopped working the device just before Captain Jonathan Archer entered sickbay. After they had a discussion, Phlox returned to the microscope, pausing briefly to tell Archer, "I have no intention of turning into one of those cybernetic creatures." (ENT: "Regeneration")

Shortly after Enterprise entered the Delphic Expanse later the same year, Phlox again used the neutron microscope, this time to analyze Xindi-Reptilian epithelial cells from an incinerated corpse. Phlox showed the screen of the neutron microscope to Sub-Commander T'Pol. She was able to see that, as Phlox had thought to himself beforehand, the epithelial cells looked more like scales, suggesting that the Xindi species being examined had reptilian characteristics. The microscope's screen continued to show the Xindi epithelial cells while Phlox demonstrated a computer-generated rendering of what was intended to be a typical Xindi-Reptilian to Captain Archer, displaying the figure on an overhead screen in sickbay, and while Phlox subsequently spoke with Tucker. (ENT: "The Xindi")

In December 2153, Phlox was at his neutron microscope when the Sphere-Builder test subject, who was a patient in Phlox's sickbay, suddenly approached him from behind and grappled him in a chokehold that then resulted in the Sphere-Builder's right arm passing through Phlox's body, causing Phlox to lose consciousness. (ENT: "Harbinger")

In the final draft script of "Stigma", this type of microscope was described as "an intricate, high-tech microscope." In ultimately unused dialogue from the same script, Tucker stated to Feezal, about his first time of trying to operate the neutron microscope, "I'm supposed to calibrate the imaging filter before I focus, right?" [1]
In the final draft script of "Regeneration", the neutron microscope was introduced with a bracketed statement clarifying the device should be "as introduced in 'Stigma'".
As evidenced by the final draft script of "Similitude", the neutron microscope – though not used in the final version of that episode – was at one point intended to be operated by Phlox at the start of the final scene in the episode's third act, in which Phlox advises Archer that, if Sim's brain is used for extraction of neural tissue, Sim will die.