But unfortunately there is no linux programm to handle these 48bit tiffs.
What kind of handling do you need? The old version of NETPBM handled 16bps images in text mode just fine (and could be compiled to do some level of binary-mode support, IIRC); I'd be surprised if the new version has lost that capability. Of course, you'd have to handle EXIF stuff separately, and it can take some experimentation to get the right set of commands piped together, but it always seemed to work pretty well for me. Can't say that I've done any 16bps work in recent years, though.
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