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I want to stack 50 different galaxies on top of each other, each having different central coordinates and in very different parts of the sky.
I'm trying to calculate the cumulative light from all of them, and stacking is a nice way to do this.

Is there any way with imstack (or another package) where I can list the center coordinate of each galaxy for every .fits file, and then stack all the images based on these different coordinates?

Thanks!

I think the task you're looking for is IMCOMBINE, it has several options for specifying how the images align depending on whether you want to use WCS or pixel coordinates. Otherwise, have a look at the IMALIGN task as a way to align the frames before stacking, or if you simply stack image cutouts centered on the galaxies in question you should be able to sum the images directly.