UPDATE FROM MABULA
I have had a very rough 2 months unfortunately health wise. I was struck 3x in a row with bacterial infections. The second infection occurred  after a routine hospital checkup and I became very sick. I had to rest and take a lot of antibiotics. Once I was recovering and restarting work 1 month ago, I again became sick. The infection was not yet gone, so even more antibiotics and rest was needed. Needless to say, it took a lot of my energy and I needed a lot of rest.
Finally, the infection is really gone and my energy is coming back step-by-step now and I have started work again. I am terribly sorry to have kept you waiting for support. I will address all outstanding questions and e-mails step-by step and will be on the forum daily from today.
APP 2.0.0-beta47 will come soon as well, a lot of work was already completed before I became very ill, so the release is also nearly ready for you. Beta47 will be much faster actually. Many workflows will be more than 2x faster, mosaics can even be 10x faster than before because registration really received a major boost... all compared to beta46. Â Before I release it, I will make sure that everything is working properly and then I will release it.
I was creating some new master flats and chose "Automatic" as the integration method. I loaded 30 subs, yet APP still used median as the integration method when I read the output from the console as it was working. This is in contrast to what I've always read that if you have more than 20 subs you should choose average.
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Is this correct behavior?
Yes indeed, that is correct behaviour.
For masterflat creation, the automatic integration will always use median integration. Reason being that it prevents a lot of issues with flatpanels 😉 and/or short exposed flats. Simply said, to get a proper masterflat, in most cases, median integration of your flats is much more robust for good flat-field calibration.
And yes, for bias, darks/darkflats, lights you definitely want to use average over median with more than 20 frames. Reason being that average integration is superior to median integration when it comes to noise reduction, and that fact... is almost never a problem with MasterFlats. The Signal to Noise Ratio is already very good of single flats, let alone of a MasterFlat.
So the rule does not apply really for flats. If you have good stable flats, then by all means integrate with average if you wish, but it will very likely not affect the noise levels in your final light frame integrations significantly.
Kind regards,
Mabula
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Excellent. Thank you so much for that quick reply.