A high brightness ion source with a gas chamber includes multiple channels, wherein the multiple channels each have a different gas. An electron beam is passed through one of the channels to provide ions of a certain species for processing a sample. The ion species can be rapidly changed by directing the electrons into another channel with a different gas species and processing a sample with ions of a second species. Deflection plates are used to align the electron beam into the gas chamber, thereby allowing the gas species in the focused ion beam to be switched quickly.