Hi both Shane and Ben,

Thank Shane for your clear description of the problem, and thank Ben for recommending so many stitching techniques that are very useful. And there is another stitching technique (TeraStitcher) both as plugin of the free software Vaa3D and standalone application. Use “Vaa3D -> Plug-In -> image_stitching -> terastitcher -> TeraStitcher” to get the TeraStitcher window.

TeraStitcher a free and fully automated 3D Stitching tool designed to match the special requirements coming out of teravoxel-sized tiled microscopy images that can stitch them in a reasonable time even on workstations with limited resources. The stitching process performs the following main steps: (i) find the relative position between each pair of adjacent stacks; (ii) find a globally optimal placement of stacks in the final image space; (iii) combine all stacks into a single 3D image and substitute overlapping regions with a blended version of them. In addition, the users can intervene manually by easily detecting and possibly correcting the abnormalities before the final image is produced to avoid some wrong computed alignments.

The input is two-level hierarchy of folder as the attachment that can solve your problem very well. For your problem, you can rename the 3 different stacks according to the naming rule.


If you want to know TeraStitcher more, you can refer to this link:
https://abria.github.io/TeraStitcher/

Good luck!