TrakEM2: saving each image(RGB) after registration


I have used TrakEM2 to align 4 images. Now I would like to know how to save each image separately

Hi @rsafavi_rsafavi

Are these four images a stack? If so:
(right click) > Export > Make flat image...
is probably what you want.

If its not a stack, and you “stitched” the images into a single layer, then I’ll have some follow up questions for you.


Thanks for the quick response.

So this is what I did:

  1. I have 4 imagas, each with 3 channels. Images are stacked.
  2. For registration, I followed this tutorial :
    He basically uses affine transformation and then click on “apply transform propagation to the last layer”

So I did this for each image, and now I would like to save each image.

  • Great, in that case try: (right click) > Export > Make flat image...
  • Make sure the Start: and End: options cover all 4 of your images.
  • Then for the Export: option, choose Save to file
  • When you click okay, it will ask you for a directory.
  • Once you choose the folder, it will save your images with default file names, and you can rename them if you want.

Hope that helps,

Thanks again, I did what you said, and it seems that each of my images is single channel now instead of being a multi channel. I did my registration my loading multichannel images into TrakEM2


Check what is in the box for the Type option, and make sure its set to RGB Color.

My bad, just saw the box! I’ll try that thank you so so much

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