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@Volker That is fixed when you use BigStitcher-Spark: https://github.com/PreibischLab/BigStitcher-Spark/blob/main/README.md
It supports affine and non-rigid fusion to N5, ZARR, HDF5 (HDF5 only when running locally on a computer). It can even run in a cluster & cloud environment.
Happy to help with it!
@Volker Actually, I have not tried this on 2D data, only 3D ... there might be a few bugs in there for the 2D case still.