I am quite new to image processing as well, so please do correct me if I am wrong. In case of affine transformations, aren’t the matrices for rotation/scaling/etc 3 * 3? Where each row corresponds to a dot product operation on the x-coordinate, y-coordinate and the intensity respectively. If my image were say 1000 * 1000 * 1 (and mind you, these are just the intensities, excluding the x, y coordinates), how would I go about multiplying a 3*3 matrix with it? Fairly basic from what you say, but I am probably missing something very obvious here…
Also about the use case, I think this is a fairly common problem in medical image registration. You have multiple snapshots of the patient at different times, across different modalities. So the patient could have moved a bit, the camera setup could be different, but essentially, it’s an image of the same patient part.