TrakEM2:Export two aligned image respectively

Hello!! everyone!!
I have a confusing question.

I have aligned these two photos.I don’t know how to export them respectively and maintain the size of the images but mask the unaligned portions with black pixels as “align” module of cellprofiler do:

Hope somebody can give me suggestions!!!

Hi @CristinaKaka,

I’m a bit confused about what you’re trying to do, but have you tried:
<right click> > Display > Autoresize canvas / LayerSet
<right click> > Display > Resize canvas / LayerSet

Those are often helpful.

By “unaligned,” do you mean the parts of the images that don’t overlap?
It would help if you describe in more detail what it is about the output that you want to change.


Sorry for confusing you…
I have stainded two marker and hematoxylin three times respectively on the same slide.So I have three photos captured once I stained a marker.(Photos I posted are something that I stain a marker and hematoxylin respectively.)
What I wanna to do is aligning three photos(Location Registration) so that I can analyze colocalization or segementaion.
I have tried the module “photoMerge” on Photoshop.But the result is not that acceptable.
I am a newbie on ImageJ.Could you give some advice?Thankyou so much!Really looking forward to your replying!!!

I have tried using Cellprofiler to do coregistration,but it is not that accurate and time-consuming.Is there any solution to this by ImageJ? Looking forward to your advice!!!