RobertOToole wrote:I believe, if my memory is correct, that the collage setting [in Photoshop] doesn't scale the layers.
I believe that's correct. Nonetheless, I'm pretty sure the collage setting will still do fractional pixel shifts if that's what gives the best match for the image contents. That implies subpixel interpolation, still not a good idea for precision comparisons.
ray_parkhurst wrote: Is there an option in Zerene to eliminate sub-pixel alignment, ie align to the nearest pixel?
There is not.
If one got added, it might take the form of an interpolator named "nearest neighbor", since that's the mathematical equivalent when just shifting. But for most applications, nearest neighbor interpolation is generally considered to be the worst possible thing you can do, so I would need a pretty compelling use case to explain its presence. Automatic alignment of lens test images to make animations might qualify.
Or maybe just go a different route and include a single checkbox that would disable rotation, disable scale, and force nearest-pixel shifts. That would be less general but also easier to explain & use.
Anyway, for focus stacking, if you need alignment at all then asking for nearest-pixel alignment basically says that you prefer to have most of the pixels completely unmodified, at the cost of up to almost one full pixel misalignment at the transitions between focus planes. That might be a sellable argument also, certainly for lens testing and possibly for natural subjects with random texture -- no long linear features where jogs would grab attention.
But no, there's no such feature now.