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1b91a54
feat(virtual-stain): rewrite CLI on cytoland predict_sliding_windows
ieivanov Jun 3, 2026
a7058af
refactor(virtual-stain): reuse VisCy normalization and rotation TTA
ieivanov Jun 3, 2026
36c24c3
chore: bump cytoland pin to VisCy read_norm_meta rename
ieivanov Jun 3, 2026
274919a
chore: bump cytoland pin to lint-fixed VisCy commit
ieivanov Jun 3, 2026
716e999
style: ruff-format virtual_stain.py
ieivanov Jun 3, 2026
fae6f9d
feat(virtual-stain): expose sliding_window_step, device, output_ome_z…
ieivanov Jun 4, 2026
05a4656
feat(virtual-stain): hardcode per-position resources
ieivanov Jun 4, 2026
5e4c8ff
feat(virtual-stain): lower slurm_array_parallelism to 20
ieivanov Jun 4, 2026
c21be5a
feat(virtual-stain): generous TTA-aware slurm_time budget
ieivanov Jun 4, 2026
11153f4
docs(virtual-stain): add batch_size to example config
ieivanov Jun 4, 2026
e3a7d62
test: register virtual-stain example config (jsonargparse-validated)
ieivanov Jun 4, 2026
8c7a03e
feat(virtual-stain): add click.echo progress to per-position worker
ieivanov Jun 4, 2026
1ae3483
Merge remote-tracking branch 'origin/main' into refactor/virtual-stai…
ieivanov Jun 12, 2026
c5d57d3
build(deps): pin cytoland to VisCy PR #465 commit
ieivanov Jun 12, 2026
9c8648c
refactor(virtual-stain): address PR review comments
ieivanov Jun 12, 2026
034e98c
update vs resources for nextflow
ieivanov Jun 12, 2026
18e83a1
refactor(virtual-stain): align CLI pattern with deskew/flat-field
ieivanov Jun 12, 2026
7b6bd08
update vs resource allocation
ieivanov Jun 12, 2026
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4 changes: 2 additions & 2 deletions biahub/flat_field_correction.py
Original file line number Diff line number Diff line change
Expand Up @@ -247,7 +247,7 @@ def flat_field_correction_cli(
monitor: bool = False,
init_only: bool = False,
):
r"""Apply flat field correction across T and selected C axes.
"""Apply flat field correction across T and selected C axes.

\b
SLURM fan-out of positions across a whole plate:
Expand All @@ -260,7 +260,7 @@ def flat_field_correction_cli(
\b
In-process run of a single position (e.g. from a Nextflow worker):
>>> biahub flat-field --cluster debug -i ./input.zarr/A/1/0 -c ./flat_field_params.yml -o ./output.zarr
"""
""" # noqa: D301
flat_field(
input_position_dirpaths=input_position_dirpaths,
config_filepath=config_filepath,
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