Merge channels: more than 7!



Dear all,
I’m doing spectral confocal Imaging with more than 8-10 colors.
In ImageJ, I didn’t find the possibility to merge more than 7 channels.
Could you help me please?
Best regards.

Help! Cannot merge more than 3 channels

Welcome to the ImageJ forum, @Seb!

You can always use

  • Image > Stacks > Images to Stack to fuse single images into a stack (or Image > Stacks > Tools > Concatenate… to fuse several stacks), and then:
  • Image > Hyperstacks > Stack to Hyperstack to define the number of channels and slices

Note that the Composite display mode (e.g. from Image > Color > Channels Tool…) won’t work when working with more than seven channels, but Color mode works, and you can define custom LUTs per channel.


I should add that once you have a multi-channel hyperstack with custom LUT, then “Image > Color > Stack to RGB” will flatten the HS to make a single merged image.


Dear all,

thanks for your help.

I foolwed our advices. Now, I have a stack with 10 channels and each of them has its own LUT.
Now, how can I make a composite image please?

Best regards.


I think Image > Color > Stack to RGB only works when you can use Composite display mode (≤ 7 channels, as @imagejan mentioned). I can’t get it to merge 10 channels.


You’re right I forgot a detail. I use the “Stack to RGB” command to convert a multi-channel (>30 channels) hyperstack into a regular RGB stack, then Stack > Z project with the “Sum Slices” option to get a flattened image.


Hi I just joined, I am new to imageJ I have about 10 Channels, I followed these steps but how do I give 10 different colors to each channels? I got up to 7 and rest of my images are still grayscale.


As I mentioned in my post above, you can use look-up tables (LUTs) for each channel:


Thank you, it works.