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When stacking in Maxim you do each channel individually 

Consequentially when you put the three stacked images together in Photoshop layers any rotational and lateral  differences between the channels have to be manually adjusted to align them.

 

There is a way you can automate the whole process in Maxim but it is so long and convoluted to set up I don't use it 

Edited by Graham
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I see, but that seems like a bit of a faff. I use DSS and just chose 1 image (from any channel) to act as the reference and then stack the images for each channel individually. They are then all aligned with each other.

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it is but it is only needed when I take different channels at different times.

I normally take all the channels in a single session.

I can do as many sessions as I like so long as I am doing all the channels in each session the resulting stacks will be identical.

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