First check the combination of LED and camera without microscope to see if you get sufficient signal at all. If not, you could first try an IR led with a relatively short wavelength (NIR, e.g. ~850 nm) to see if that is working. At this relatively short wavelength you expect that the transmission of the optical elements is still fine. Then you could move to longer wavelengths and at certain longer wavelengths the transmission will drop (due to absorption by the lens materials and/or due to the optical coating). Hope it helps.