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I noticed that the backgrounds of my geotiffs were transparent up until I started added overviews with gdaladdo.

Is there a way to combat this?`

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I'm running into a similar issue. As far as I can tell it's not related to gdal not honoring the nodata but to the fact that the jpeg compression I'm using truncates my 16bit geotiffs to 12bit in the overviews. –  Colin Talbert Jun 4 at 14:11

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You may want to raise a bug on the gdal-dev mailing list, because the page for gdaladdo says that it "will honour properly NODATA_VALUES tuples".

Although I've just thought, is your data using a mask band rather than a nodata value? That might be the issue because the formats that are used for overviews may not support a mask band - although that is mostly speculation.

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