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AES10 specifies 62.5/125, or OM1, fiber for use with MADI. However, 50/125 fibers has advantages in bandwidth and distance and is now much more standard than the "old" OM1 standard. I'm not too well versed in fiber, so I'm reticent to use any other cable than what's recommended in the standard, but it would be good to be able to run other things down a fiber installation in the future, such as video.

Will MADI run on 50/125 - OM3 - fiber? Or equivalently, is fiber "backwards-compatible" so to speak?

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what is MADI? You mention video at the end of your question, but it isn't clear how (or if) this is relevant to audio or video production. –  ObscureRobot Nov 24 '12 at 6:07
    
MADI is short for "Multichannel Audio Digital Interface", and is one of the most standard digital audio interfaces on the market, typically run over coaxial or fiber. It is ubiquitous in the industry, in studios, theaters, broadcast, etc. –  jodles Nov 26 '12 at 12:08
    
If you want to know more about MADI then check out the AES10 standard. –  jodles Nov 26 '12 at 12:13

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I have done some more research and come to a conclusion of my own:

Fiber is not necessarily "backwards-compatible" as it depends on the optical transducers (laser and receiver) within each piece of MADI-supported equipment. There seem to be a trend in the industry towards 50/125, because a smaller glass core (50um vs 62.5um) reduces modal dispersion and thus allows for longer reach (see more here, pdf).

The situation is a bit of a two-egged sword, as most new, non-MADI equipment run on OM2 or OM3 (50/125) and some include backwards compatibility with OM1 (62.5/125). However, MADI equipment is guaranteed to run on OM1 (because of the standard), but might not support OM2 or 3. E.g. Avid has published information about their XLogic IO products claiming that their transducers are optimised for both OM1 and OM2 (see here, HTML). (Note that Avid claims that OM1 allows for longer distances, which must be a typo.)

So all-in-all, it doesn't seem necessarily straightforward. The bottom line is that it really depends on what equipment you eventually will put in, and what kind of fiber that that equipment has been designed to work with.

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