Internal LVDS for between-board communicatino

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Thanks for the tips. My motivation to go for LVDS stems from electrical requirements, and not particularly speed. The two cards' digital grounds are not shorted together, and differential is the best way I can see to transfer data between them.

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Just how disconnected are your ground domains? If they are not connected at all, you will want to AC couple the LVDS signal lines, at least with capacitors, if not a transformer. An encoding scheme such as 8b10b will then be required to prevent DC drift on the AC coupling components.