Automate Image Alignment Via Reference Points

Hello all,

I am currently working with images of varying stains and performing some analysis via the interactive image alignment/affine transform.

I was wondering if there was any way to automate this process in such a way to get the affine transform matrix without physically aligning the images yourself.

I was thinking a way possibly by placing reference points on the image and using some script to align those reference points and then get the affine matrix?

I may be a little in over my head with this idea but if anyone has any advice/suggestions/starter code and is willing to help I would be very grateful.

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The interactive image alignment should have an alignment function (edit* “estimate transform”), have you tried that, or did it fail? There are various circumstances that can cause it not to work, but it would be hard to tell what is happening without more information or an error message.

There is some description of the alignment interface within the subsections of the post here:

Check this

https://imagej.net/Fijiyama

The manual registration function in this plugin might work for you