How to combine two stacks together (manually or automatically)?

I have two stacks, each stack has sequence of about 100 images. The first image of the second stack technically should be the next image following the last image of the first stack. The task is to make one stack out of two stacks (to combine or to glue these structures together). I cannot simply concatenate these two stacks (by using Image-Stacks-Tools-Concatenate) because dimensions of two stacks are not the same (but importantly - scale is the same). How is it possible to combine these two stacks together (manually or automatically) to adjust (to move close to each other) structures in last image of the first stack and structures in the first image of the second stack?

Do you mean the two stacks have the same real size (in physical units) but different pixel size? If that’s the case, why don’t you rescale the second one and then concatenate?

X-Y sizes for both stacks are not the same. First stack is 2619x3228 microns, and second stack is 2621x4017 microns (both stacks built of many stacks of confocal tiles automatically stitched together in XY, because object is relatively big). However, dimensions of object (the scale) are the same for both stacks. Both stacks have same object of interest acquired from both sides of the glass (because object was relatively thick). Later second stack was mirrored and reversed numerically (see my previous topic) and adjusted (some top slices were removed) to be a continuation of the first stack. Now the task is to arrange (to glue) them together the way that objects will match each other. How can I arrange these two stacks together and to move in X-Y for the more or less perfect match?

In that case, I believe the easiest options is to register the stacks, or at least the last section of the first stack and the first one of second one (and then apply the found transform to all slices in the second stack). You might want to give a try to Register Virtual Stack Slices, with a translation transform as registration model.

Was trying this. Somehow does not work. Can you please send a macro for any sample (like flybrain where stack can be split into two and one resulting stack can be cropped a bit to have different dimension)?

Have you tried creating a new canvas (File -> New -> Image…) of the same XY dimensions as the largest stack (2621x4017) and pasting in the other stack? Then you can concatenate and use StackReg or similar plugin to register the concatenated stacks properly. This can be written in to a macro very easily (I don’t have time right now).

I also did a quick search to find this canvas resizer plugin that could be even more useful, editing one stack to change the canvas size to the other stack and then repeat above suggested to save making a new blank stack and copy-pasting each slice in to the new stack.

Do you fine a good way to deal with it? I have the same question. Thanks