Stitching surface 1D

Hello all,

I’m having troubles when it comes down to stitching images of a material’s surface.
I’m only interested in the actual surface, and I want to reconstruct the way how it was deformed.
Because of this, I was forced to adjust the y-position for each image during the SEM image acquisition to keep the surface in view.

However this complicates the 1D-stitching of the surface, erroneous stitched image:
https://1drv.ms/u/s!AswNyH67eiWVmBCQG052hktye8By (83 MB)
Basically, I want to force Fiji to stitch the surface in a sequence of images regardless of the y-displacement.
The way I went about this is through grid/collection stitching > grid size x = [amountOfPictures], grid size y = 1.

Stitching the problem images pairwise works which tells me that Fiji is able to align the images just fine, but not when the FOV is too broad.
I want to avoid stitching each picture individually as much as possible, since my dataset is quite large.

Hopefully there is a better way to go about this.
Thanks for your input.