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Hi Peter,
Yes, my suggestion is to lower your target ADU for flats. If we take the stats from the SX site. Well depth 17k-e with a gain/ADU of .3 then we can quickly derive a target ADU for flats.
(full well/gain)*Z%=target flat ADU
(17,000/0.3)*35%=19,833 ADU
Z is the well capacity you are trying to reach which I typically work on a value between 30% to 50%. 50% gets you close to 28,000 ADU. The above is quick and dirty way given the stats off the SX site may not apply to your camera. The figures are generalised for the model. The camera gain is likely to be correct (.25 rounded to .3) but your well depth could be greater or smaller than whats listed. Testing your camera's capabilities through a proton transfer curve is the only way to get accurate stats unique to your camera. It should also be highlighted that ABG camera go non-linear as they being to reach saturation point. i.e. they being bleeding charge. Many will begin bleeding before they reach the well depth which results in the camera going from linear to non-linear. You want to make sure your target ADU for flats is well away the non-linear stage. I doubt you would be hitting it at 35k ADU anyway but I probably wouldn't go higher.
The above said and done, I don't think flats is your main challenge. The flats could well be working as expected without changing anything. Its the desire to not inject noise into what is an already very quiet ccd. If you are hitting the right flat target ADU and have plenty of subs, noise will not be injected. In fact your stats indicate this;
Raw Frame s/n = 2.61
Flat calibratio only 2.45
Bias only .43
Dark only .38
Bias + Dark .38
Dark + Bias + Flat .39
Bias + Flat .43
The last test indicates that no further noise is being injected by the flat. Please make sure you are measuring the exact same X and Y coordinates in each image to ensure you are obtaining comparable readings. Did the flat successfully apply i.e. can you see the difference and confirm in the fits header that it was applied. What is missing from the tests is Dark + Flat.
With regards to the negative number, was this for the same area you were previously measuring or the image as a whole? If its negative, use pixel math to make it a positive value otherwise you'll have data rejection troubles. The subtraction of a dark shouldn't do this however. Strange behavior. Note that CCDStack does not add a pedestal to the image data by default with exception to 16bit colour FITS and TIFF which are given 100 ADU pedestal. Until you nut out whether the noise from the bias can be reduced, perhaps stay away from the adaptive subtraction pedestal value.
I think I'll need to check how CCDstack measures the S/N in the information window. From memory its mean divided by standard deviation of non rejected pixels within the selected area. A basic approach but is still comparable.
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