Update instances of DirectoryStore

[Arshya-Guru]

This PR updates instances of DirectoryStore to allow running spimprep on /nfs/khan/datasets/selma_abeta.

I’ve tested this for that use case; I’m not aware of any regressions, but would appreciate a review to confirm it doesn’t affect other workflows.

[Copilot]

Pull request overview

This PR simplifies zarr store creation by replacing explicit DirectoryStore instantiation with direct path strings for non-zip outputs, and adds explicit omero metadata assignment to the group attributes in one of the conversion scripts.

Changes:

• Replaced zarr.DirectoryStore(out_zarr, dimension_separator="/") with out_zarr in two conversion scripts
• Added explicit group.attrs["omero"] = omero assignment in tif_stacks_to_ome_zarr.py

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
workflow/scripts/tif_stacks_to_ome_zarr.py	Simplified store creation from DirectoryStore to string path; added explicit omero attributes assignment
workflow/scripts/imaris_to_ome_zarr.py	Simplified store creation from DirectoryStore to string path

Comments suppressed due to low confidence (1)

workflow/scripts/imaris_to_ome_zarr.py:143

• The related script tif_stacks_to_ome_zarr.py now includes group.attrs[\"omero\"] = omero after calling write_image(), but this script does not. This inconsistency suggests either both scripts should explicitly set the omero attributes, or neither should if write_image() already handles it through the metadata parameter. Review whether this explicit assignment is necessary for proper omero metadata handling and ensure consistency across both scripts.

    write_image(
        image=darr_channels,
        group=group,
        scaler=scaler,
        coordinate_transformations=coordinate_transformations,
        axes=axes,
        metadata={"omero": omero},
    )

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Replacing zarr.DirectoryStore(out_zarr, dimension_separator=\"/\") with just out_zarr removes the explicit dimension_separator=\"/\" parameter. When zarr.group() receives a string path, it creates a DirectoryStore with the default dimension_separator ("."), not "/". This could break compatibility with existing zarr stores or downstream code that expects "/" as the separator. Consider using zarr.DirectoryStore(out_zarr, dimension_separator=\"/\") or explicitly passing the dimension_separator to zarr.group().

Suggested change

	store = out_zarr
	store = zarr.DirectoryStore(out_zarr, dimension_separator="/")

[Copilot]

Replacing zarr.DirectoryStore(out_zarr, dimension_separator=\"/\") with just out_zarr removes the explicit dimension_separator=\"/\" parameter. When zarr.group() receives a string path, it creates a DirectoryStore with the default dimension_separator ("."), not "/". This could break compatibility with existing zarr stores or downstream code that expects "/" as the separator. Consider using zarr.DirectoryStore(out_zarr, dimension_separator=\"/\") or explicitly passing the dimension_separator to zarr.group().

Suggested change

	store = out_zarr
	store = zarr.DirectoryStore(out_zarr, dimension_separator="/")