Description:

imaris_channel_to_zarr.py correctly writes intermediate channel files as zarr.zip using zarr.ZipStore(path, mode='x'), but imaris_to_ome_zarr.py was reading those same files by passing the path string directly to zarr.open() and da.from_zarr(). Neither call auto-detects a .zarr.zip path as a ZipStore — they default to treating it as a directory store with mode 'a', which causes zarr to attempt writing .zgroup metadata into what is actually a zip file, resulting in a FileExistsError.

This is made worse by the shadow: "minimal" directive on the imaris_to_ome_zarr rule, which symlinks the input .zarr.zip files into the shadow directory — the file-vs-directory conflict happens immediately on open.

Fix:

Explicitly open the input zarr files as ZipStore objects in read mode before passing them to zarr.open and da.from_zarr, consistent with how the writer script already handles them.