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Pass orientation override to vessel segmentation via zarrnii_kwargs#122

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akhanf merged 2 commits intoakhanf/vesselfm-updatesfrom
copilot/sub-pr-119
Mar 8, 2026
Merged

Pass orientation override to vessel segmentation via zarrnii_kwargs#122
akhanf merged 2 commits intoakhanf/vesselfm-updatesfrom
copilot/sub-pr-119

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Copilot AI commented Mar 8, 2026

The run_vesselfm rule was calling ZarrNii.from_ome_zarr without the orientation override that all other rules in the workflow pass via zarrnii_kwargs, causing vessel segmentation to ignore the configured coordinate orientation.

Changes

  • vessels.smk: Added params: zarrnii_kwargs={"orientation": config["orientation"]} to run_vesselfm, matching the pattern used across segmentation.smk, patches.smk, and import.smk
  • vesselfm.py: Unpacked **snakemake.params.zarrnii_kwargs in the ZarrNii.from_ome_zarr call
# Before
znimg = ZarrNii.from_ome_zarr(
    snakemake.input.spim,
    level=int(snakemake.wildcards.level),
    channel_labels=[snakemake.wildcards.stain],
)

# After
znimg = ZarrNii.from_ome_zarr(
    snakemake.input.spim,
    level=int(snakemake.wildcards.level),
    channel_labels=[snakemake.wildcards.stain],
    **snakemake.params.zarrnii_kwargs,
)

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Co-authored-by: akhanf <11492701+akhanf@users.noreply.github.com>
Copilot AI changed the title [WIP] WIP address feedback from review on vessel segmentation PR Pass orientation override to vessel segmentation via zarrnii_kwargs Mar 8, 2026
@akhanf akhanf marked this pull request as ready for review March 8, 2026 01:48
@akhanf akhanf merged commit 18cbdf3 into akhanf/vesselfm-updates Mar 8, 2026
@akhanf akhanf deleted the copilot/sub-pr-119 branch March 8, 2026 01:49
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