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I think I may have found my solution, although I will need to wait until I get home tonight to try it. Anthony Wesleys (bird on IIS) ninox program has the following option which I may be able to utilise:
-debayer=N (8bpp monochrome data only) Assumes the input frames are 8bpp RAW data from a colour CCD (ie encoded bayer colour data) and converts the RAW format to 24bpp colour. N selects the correct debayer pattern as follows:
1 = GBG
2 = RGR
3 = BGB
4 = GRG
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