Landmark Correspondences and multichannel images

I have multichannel images that I would like to align (center and rotate). The plugin “Landmark Correspondences” does the job admirably well, however it seem to only preserve one channel of my images. Both my template and moving images have 4 channels. Is there a way to obtain a registered images while preserving all the channels?

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Hi @MarinManuel,

Welcome to the forum.

Check out BigWarp, I think it will likely suit your needs. (disclaimer - I wrote and maintain Bigwarp).



Hi John,

Thank you for your reply. I did like the simplicity of Landmark Correspondences, but BigWarp does the job in multichannel images, so thanks for that.

Couple questions though:

  • I have a lot of images to align to the same target image (but not with the same “wrap field”). Is there a way to keep the target images with its landmark loaded and just open a new moving image and only reclick the landmarks in the moving image?

  • Is there any way to preserve the lookup tables when saving as ImagePlus? If I save after having aligned my images, they appear in grey levels, which means I have to redo the lookup tables for all the channels and for all the images that I “BigWarp’d”. I guess this could be scripted if that’s not an option.


Hi @MarinManuel,

Yes. If you click only the target landmarks and save, you can reload those target landmarks when opening a different image.

This would take some work to get into bigwarp, I made an issue to keep track of it.

Making a script that sets the LUTs for the exported ImagePlus such that they’re the same as the original
should be straightfoward though.