Thanks to John Lapage the Fiji Stitching is now able to stitch images sequentially.
John Lapage wrote in his GIT commit: “It is useful if you are working with images that you know you took in an overlapping order (e.g. video from a microscope) but you don’t have any kind of positional or grid information. Simply works by allowing the user to specify the range of images to be compared and then pairing images up,in the same way that the ‘Unknown Positions’ option pairs all images and the grid option pairs up images expected to overlap.