Merge multiple Z stacks


Hi all,
I have a multistack TIFF file with 3 channels (RGB) for each individual stack (13) - and all these are in the same exact plane. What I’m trying to do is create a singleplane TIFF file that is just the resulting composite of the Red Green and Blue channels of all the stacks together. Is there a way to do that? I’ve tried concatenate, split merge channels but nothing seems to have worked.
Any advice would be more than appreciated.
Thanks again


“Merge channels” has worked for me in the past. What is the type for each image?


Merge channels doesn’t really help me in this case.
I’ve attached to this thread the original file. Think that could be of help in showing you what I’m dealing with!
Thanks again!


Hi Roberto,
First of all, the file you shared has a total of 33 slices, which means you want to extract 11 individual RGB stacks, is that correct?

Since this is a stack, you would need to use the Stack Tools.
What I would do is to first divide the stack in 11 parts using the Stack Splitter (Image > Stacks > Tools > Stack Splitter).
Then I would split again the individual small stacks in 3 separate images (Image > Stacks > Stack to Image) and reassemble them in a single composite image using Image > Color > Merge Channel.

You could also do “Stack to Image” from the beginning and then Merge 3 channels at a time to make the composite image.

If you are good with Macros you can create one to do all the steps at once.

I hope this helps!



I have tried to follow Anna Fasoli’s solution but some of the features may not be available depending on which version of ImageJ you have. Here is what I was able to do using ImageJ 1.50b.

  1. Open stack
    • I use drag-and-drop
  2. Image > Hyperstacks > Stack to Hyperstack…
    1. Set Order to xyczt
    2. Set Channels (c ) to 3
    3. Set Slices (z) to 11
    4. Set Frames (t) to 1
    5. Set Display Mode to Composite
    6. Click OK
  3. Image > Color > Stack to RGB
    1. Check Slices (#)
    2. Check/Uncheck Keep source as desired
    3. Click OK
  4. Save