When you talk about the eye, you're realling dealing with (at least) two systems. Theres the "hardware" of the eye, i.e. the actual iris, retina, nerves etc, and the "software" of the eye, which is basically the way your brain interperets the signals from your eye.
Interestingly, the eye itself can detect individual photons. This is fairly remarkable, as it means that there is technically no light so dim that you cannot see it.
This is a problem however, because if your eye could see single photons, there would be large amounts of noise in your vision. This is handled by the "software" side of your vision, which not only processes the signals to turn them into images, it also filters the signals in various ways. Various experiments have concluded that on average (to people accustomed to the dark), 3 photons hitting a rod in close succession looks like a dim light, and anything less than that is not guaranteed to be seen as light by the brain. Remeber also that only a fraction of the light that hits the retina will hit a light detecting cell.
Unfortunately this doesn't mean very much for you. I assume that youre not trying to communicate with people who have been in a dark room for half an hour, and so are asking how long you have to light an LED in a normally lit room for it to be seen. As one of the other people said, this can pretty much only be done by experimentation, as it will depend on which direction the led is facing, ambient light levels, specific LED model, etc. Luckily, you're using a microcontroller, so it really is very easy and quick to test different timings.