Elastic stack registration



Hello there,

I am new to ImageJ and hope you could help me solving following question:

I have a stack of images that do have an elastic movement in it, which I want to get rid of. So I tried out BunwarpJ, which works really good for the movement that I have- but it just compares two images (source and target) - and I would like to adjust the complete stack (600+ images). Do you have an idea?

Thank you very, very much



Hi @Schamanin,

There’s a list of plugins that do registration on the fiji wiki:

For 3d, nonlinear registration. I’ve liked cmtk quite a bit. It even has a fiji gui.

There’s also ANTs which I think is great, but is runnable by the command line.

Also elastix which I’ve heard good things about buy havn’t tried myself.



I really like elastix, so much that I wrote a Fiji plugin to make it easier to use:


Thank you both very much. I used TrakEM2 for registration, which works quite alright (Elastix sounds really good to me, too).

But now it somehow won’t measure the intensity whithin the ROIs over the whole stack. Sometimes it just gives no values ( or stable 255), sometimes it just works for one image. I think I am missing something?

Thank you very much