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Debug: imaris_to_ome_zarr tweaks + add KI3 batch2 samples #70

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Merged
akhanf merged 2 commits into from
Feb 19, 2026
Merged

Debug: imaris_to_ome_zarr tweaks + add KI3 batch2 samples #70

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Debug: imaris_to_ome_zarr tweaks + add KI3 batch2 samples
Feb 19, 2026
cdfa8bc
Delete config/samples_ki3_batch2.tsv
akhanf Feb 19, 2026
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5 changes: 3 additions & 2 deletions workflow/scripts/imaris_to_ome_zarr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -92,8 +92,9 @@
darr_list = []
for zarr_i, in_zarr in enumerate(snakemake.input.zarr):
# open zarr to get group name
zi = zarr.open(in_zarr)
darr_list.append(da.from_zarr(in_zarr, component="Data").rechunk(rechunk_size))
in_store = zarr.ZipStore(in_zarr, mode="r")
zi = zarr.open(in_store, mode="r")
darr_list.append(da.from_zarr(in_store, component="Data").rechunk(rechunk_size))

# append to omero metadata
channel_metadata = {
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