Pooling hyperstacks all together from different stacks

Hi,

I am a biologist who is fairly new in ImageJ, and I am working on confocal microscope image stacks.

So, I have a stack (called stack A) consisting of 4 hyperstacks. Meanwhile, I also have another stack (called stack B) consisting of 3 hyperstacks. Both of them are taken from different indivduals (Individual X for stack A, and individual Y for stack B), so the slice number are different between stack A and B. However, these individuals are the same in species, age and sex, so I am expecting that the stacks are comparable despite not identical.

So, the idea is that I would like to pool the stacks alltogether so that it will show 7 hyperstacks in just one stack. My goal is to generate 3D atlas out of them.

Since my method can only map 4 different parts at one time, I need another indivdual to map other 3 different parts.

Is there any way to do so in ImageJ or Fiji? Or is there any other software that can process them?

I will appreciate any answer. Thank you very much in advance. :slight_smile:

Royan