A neutron microscope is a scientific instrument developed by the Denobulans. Using a stream of neutrons, it is 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' wives, accompanied the microscope and instructed Charles Tucker in its installation and use. The microscope's parts include an aperture ring, condenser lens, an imaging filament, quantum filters, and a reflectometer. (ENT: "Stigma")