How to save warped image in same format as original (in ImageJ)?


I am trying to align images using BigWarp in ImageJ, and have an issue with saving the files. It seems the only way to save the warped image (moving image) is File --> Export as ImagePlus.

The images I’m aligning are saved tiff images with two merged channels, blue and red. When I export the warped image, it gives a black and white split-channel image. Is there any way to save the warped image in the same color and channel-format as the original images? Does it e.g. have anything to do with the file format of the original images (tiff), or the fact that it’s two channels?
Or is there another tool in ImageJ you can suggest for the purpose of aligning images like this?
I need both channels and colors for the further analysis.

I have tried to search everywhere for answers, but I always end up on the tutorial page for BigWarp (, which doesn’t seem to answer this question.

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Hi @OdaBH,

Welcome to the forum.

Something to try

Could you try the following, and let us know if it accomplishes what you’d like?

  1. Export the multichannel image with bigwarp like before
  2. Convert the image to an color composite.
    • Image > Color > Channels Tool (or Ctrl+Shift+Z), then switch from “Composite” to “Color”.
    • Press OK if a dialog box shows up asking if you want to convert.
    • Choose “Composite” for the display mode.
  3. You may need to adjust brightness and contrast after conversion.

Does that get you what you’d like?

I’ll explain more about what may be going on shortly,

Hi @bogovicj

Thank you so much, that worked!
Now I got exactly what I needed.


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