refactor(virtual-stain): rewrite CLI on cytoland predict_sliding_windows - #267

Merged

ieivanov merged 18 commits into

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refactor/virtual-staining

Jun 12, 2026

Commits on Jun 3, 2026

feat(virtual-stain): rewrite CLI on cytoland predict_sliding_windows

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1b91a54
refactor(virtual-stain): reuse VisCy normalization and rotation TTA

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a7058af
chore: bump cytoland pin to VisCy read_norm_meta rename

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36c24c3
chore: bump cytoland pin to lint-fixed VisCy commit

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style: ruff-format virtual_stain.py

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716e999

Commits on Jun 4, 2026

feat(virtual-stain): expose sliding_window_step, device, output_ome_zarr_version

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feat(virtual-stain): hardcode per-position resources

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05a4656
feat(virtual-stain): lower slurm_array_parallelism to 20

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feat(virtual-stain): generous TTA-aware slurm_time budget

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c21be5a
docs(virtual-stain): add batch_size to example config

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11153f4
test: register virtual-stain example config (jsonargparse-validated)

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feat(virtual-stain): add click.echo progress to per-position worker

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8c7a03e

Commits on Jun 12, 2026

Merge remote-tracking branch 'origin/main' into refactor/virtual-staining
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build(deps): pin cytoland to VisCy PR #465 commit

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c5d57d3
refactor(virtual-stain): address PR review comments

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9c8648c
update vs resources for nextflow
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refactor(virtual-stain): align CLI pattern with deskew/flat-field

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18e83a1
update vs resource allocation
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