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The plot thickens.
I did some testing this morning and found 2 problems.
Somehow the gain setting had changed in my Sharpcap profile.
It was set at 400 (should have been 200).
That led to a huge increase in noise.
I took some darks at both settings and at gain 400, the image is total crap.
Now this is weird:
I put a red filter on the scope and took a few images.
To see the image correctly (red) in the sharpcap preview, I use the GRBG debayer setting.
I have previously assumed that this same code is used in PI for the debayer process.
Guess what...it's different.
I had to use GRGB code to get a red image.
Someone has got it wrong (either PI or Sharpcap)
So that explains my lack of colour.
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