Is there anyway to apply the overlay option in ImageJ to an entire stack? For example - I have 2 stacks of 100 images each. The result I’m looking for is slice 1 from stack 1 overlayed on to slice 1 from stack 2, slice 2 from stack 1 overlayed onto slice 2 from stack 2 etc. I have tried using merge channels, which did create a composite stack. However when trying to save this as an image sequence, ImageJ saved it as 200 images (i.e both stacks) as opposed to the composite stack.
Any help would be greatly appreciated. Thank you.