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Replace create_empty_hcs_zarr with iohub's create_empty_plate #215

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Replace create_empty_hcs_zarr with iohub's create_empty_plate #215

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5553616
Replace create_empty_hcs_zarr with create_empty_plate from iohub
tayllatheodoro Mar 12, 2026
d60f390
style
tayllatheodoro Mar 12, 2026
4d3ce7f
change to iohub function
tayllatheodoro Mar 12, 2026
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4 changes: 2 additions & 2 deletions biahub/stabilize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import submitit

from iohub.ngff import open_ome_zarr
from iohub.ngff.utils import create_empty_plate
from scipy.linalg import svd
from scipy.spatial.transform import Rotation as R

Expand All @@ -23,7 +24,6 @@
)
from biahub.cli.utils import (
copy_n_paste_czyx,
create_empty_hcs_zarr,
estimate_resources,
process_single_position_v2,
yaml_to_model,
Expand Down Expand Up @@ -214,7 +214,7 @@ def stabilize(
}

# Create the output zarr mirroring input_position_dirpaths
create_empty_hcs_zarr(
create_empty_plate(
store_path=output_dirpath,
position_keys=[p.parts[-3:] for p in input_position_dirpaths],
**output_metadata,
Expand Down
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