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Hi Martin,
Just logged in, busy day today.
Q1. ST only lets you save images as 16-bit TIFF or JPG. So definitely use TIFF, JPG will "kill the image quality" as it uses lossy compression.
Q2. I am following the ST recommendations, just like you said.
Basically the main thing is to crop images the same and to use the same binning. Then the sizes will be identical.
(Also take care if you do any rotations or mirroring)
I have tried doing full image processing for one image and then moving onto the next but it did not work too well for me. Often I would accidentally close ST after the first image and lose the cropping parameters (have to dig through the log files then). Or I would forget to do binning for one of the images. In the end I found that cropping/binning and the saving each of the images before processing worked the best for me. But it may not necessarily be the best way.
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