When doing data analysis where multiple images are compared, ImageAlign is often a great troublesome fixer of any slight misadjustments in the microscope, which I've come to use without even thinking much about it. However I've run into some trouble when dealing with data where a subset of the imagedata is non-existant. Now since you can't generate an image using for instance Missing pixel values, this means that I've resorted to just keeping a seperate mask image which keeps tracks of the pixel values which should not be considered for analysis, and then make due with interpolated data in the image I'm passing along. Now the problem is that since ImageAlign works pretty much like a little black box which just returns the aligned image, I suddenly don't know how to treat my Masking data. Anyways, that's just a short explanation of what I'm dealing with here.
So the question is, is there a simple way of getting the image transformation that ImageAlign[imageA,imageB] applies to imageB, rather than just getting the resulting aligned image? If this was possible It would be quite simple to just reapply the transformtion to the additional mask image that I'm passing along.