Combine individual images to stack using distinct z-values for every plane

Hi guys,

I have the following situation:

  • I got image which are taken at individual z-position inside a sample
  • the distance between the planes is not identical (not equidistant planes)

What is the easiest way to combine those images into one stack, where the z-position of every plane has the correct value?


Hi @sebi06,

Check out this plugin for z-spacing correction by @hanslovsky.

It comes with Fiji, and is runnable by: Plugins > Transform > Z-Spacing Correction


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Hi John,

thanks for the hint, but I think I described my problem not correctly. I got the stack in Fiji and now I need to assign every plane a distinct Z-value, which I have in a list inside a text file. Can this plugin do this?

Hi @sebi06 unfortunately, that is not what the plugin does: Instead, the plugin estimates the z-positions (that you have in a text file) and optionally renders the result with BigDataViewer or into an ImagePlus. If programming your own solution is an option, have a look at those links for inspiration. Unfortunately, I am not aware of any plugins that would do exactly that in ImageJ (but my knowledge of Plugins is very limited).

Hello sebi06,
Rename each image (right click within the image) as the number of the z_ value eg, 1,2.3 …etc. When you reassemble the stack ( Image > Stacks > Images to Stacks), each image will be named as the z title.