In MATLAB, you can perform image registration by specifying a region of interest (ROI) in the images, which allows the registration algorithm to focus on a particular part of the images. This can be especially useful when you have images with large regions that should be excluded from the registration process, such as the black-filled margins in your case.
By using ginput, you can focus on specific parts of the image that are important for registration, and the algorithm will ignore the black-filled margins. After estimating the transformation using these points, you can then apply it to the entire image, including the black-filled parts. This allows you to preserve the entire image content while still focusing the registration on the central, content-rich areas.
For further information, refer to the documentation link below:
