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I've noticed that when I deal with GeoTIFF files exported from FME that I need to specify whether the raster is filled with elevation data or colour data when loading into other programs. I believe other software's specify in the TIFF header/metadata that the raster is elevation data but I dont think there's an option in FME to do so. Is anyone aware of a way to set this parameter?

I don't think there is such a parameter actually. Elevation data in GeoTiff is "just" numeric values in the raster, it's up to the software that uses it to interpret what it is (or check with the user)

It is possible though that when values over e.g. 255 are encountered many GIS softwares will assume it's going to be elevation data.

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