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In vivo flow cytometry(IVFC)has been a powerful technique in biomedical research,especially for tracking specific cells in circulatory system.The reported IVFC is limited to use fluorescent dyes in visible spectrum,while infrared dyes have their own advantages,such as deeper penetration,less absorption and light scattering,etc.Here,we set up an infrared in vivo flow cytometer with a 785 nm laser.A visible channel with the 488 nm laser is added to solve the problem of the invisibility of infrared light and to make this system more flexible.We demonstrate initial testing of infrared IVFC with this system by ex vivo labeling cells with the infrared fluorescent dye IR-780 and injecting them into circulation.Typical peaks corresponding to infrared fluorescent circulating cells can be observed.By comparing infrared fluorescent cell counts with DiD labeled cells and EGFP cells,we find out that the infrared IVFC shows higher sensitivity than the visible IVFC.Thus,we have successfully extended the IVFC to the infrared range and make it the same detection range with conventional flow cytometry.We also discuss the major key points for the design of infrared in vivo flow cytometer and the potential applications of infrared IVFC in biomedical research.