I work at a particle accelerator. We use White Rabbit (https://white-rabbit.web.cern.ch/) to synchronize some very sensitive devices, mostly the RF power systems and related data acquisition systems, down to nanosecond accuracy.
As far as I'm aware they just timestamp the sample streams based on a local gps backed atomic reference. Then when they get the data/tapes in one computing center they can just run a more sophisticated correlation entirely in software to smooth things out.