Fusing irregularly spaced 2D tiles into 3D

We are working on a intelligent acquisition plugin for laser scanning microscopy which deletes positions from a regular 3D grid to save time and storage space. The new results are saved into 2D image tiles for each XYZ location, but the two tools we currently use for stitching (Grid/Collection Stitching and BigStitcher) can’t fuse these properly yet; they output a 2D plane from one of the Z locations.

Does anyone know of other tools that can fuse a set of irregularly spaced 2D tiles into 3D?