I am part of a university CubeSat team looking to use an S-Band radio at 2.4GHz to communicate between the ground station and the satellite. We already have approvial by the NTIA and IARU to do so. Does anybody know how I would go about creating or customizing a protocol to handle such long distances and still work with the RouterOS and Metal 2SHPn radio? Thanks so much.

I think you must contract sales@mikrotik.com for this personalization.....

Will the metal even work in this problematic temperature environment?

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Sounds like a job for nstreme. Use dual radio one for transmit and second for receive.