Overlay of two z-stack images

Dear all,

I hope you can help me with the following problem:
I have two z-stack images of immunofluorescent stained brain slices. The slices are consecutive, meaning that the lowest part of the upper z-stack is theoretically followed by the first part of the lower z stack. My aim is to overlay both 3D images that the cells from the upper and lower stack match each other. I already tried this plugin (https://sites.google.com/site/qingzongtseng/template-matching-ij-plugin#downloads) but it does not work on windows 10.
Do you have any ideas?

Additional info: On my slices I have stained neurons and astrocytes that I could or want to use as landmarkers.


Welcome to the forum.

Your images are not aligned, is that correct? And you want to line them up with each other? If that’s correct, you should check out the list of image registration plugins.

I’ll also point out Bigwarp in particular (because I wrote it).

Post back with any more questions,

Thank you for your fast reply.
Yes, that is right, the images are not aligned. They are captured at the same brain area but the cells of the two stacks are not aligned and therefore I have to somehow match those two pieces upon each other.

I will definitely try out those plugins.