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Hi Chris,
Thanks for the test subs. I was able to reproduce the problem. It looks like StarAlignment is confusing hot pixels in your data for stars. Increasing the "Hot pixel removal" parameter on the Star Detection tab from 1 to 2 was enough to get a good alignment on the 4 test subs you gave me. Give it a try on the full data set and let us know how it went. You could crank it up a little more if you still have some subs that aren't registering.
I normally use CosmeticCorrection as part of my calibration process so there aren't usually many hot pixels left in the subs that I register. Your subs don't look particularly bad, but apparently there are enough hot pixels there to confuse StarAlignment with the default parameters.
Cheers,
Rick.
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