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Could you please share CR2

Could you please share CR2 samples w/ filters equal to 0 to check them up.

In D60 (and most other old canons) case, margins are not set by manufacturer, but hardcoded in libraw source. For metadata-specified margins there is always a chance that margins will change with firmware update.

So we (again) suggest to consider to use full sensor area for flats, darks, etc.

-- Alex Tutubalin