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chore: post-rebase refinements and additional diagnostics#111

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FIrgolitsch wants to merge 1 commit intopr-ci-nextflowfrom
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chore: post-rebase refinements and additional diagnostics#111
FIrgolitsch wants to merge 1 commit intopr-ci-nextflowfrom
pr-tail-cleanup

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@FIrgolitsch FIrgolitsch commented Apr 28, 2026

Stacked PR 13/16 — review order: #115#97#98#99#100#101#108#106#107#87#116#110#111#40#112#113

Base: pr-ci-nextflow (#110). Retargets to main as upstream PRs merge.


PR #111 — Post-Rebase Refinements & Additional Diagnostics

Captures post-rebase improvements that were applied after the original chain branches were created.

Diagnostics scripts (new)

linum_aggregate_dilation_analysis, linum_analyze_acquisition_rotation, linum_analyze_registration_transforms, linum_analyze_stitch_affine, linum_analyze_tile_dilation, linum_benchmark_gpu, linum_compare_stitching, linum_diagnose_pipeline, linum_diagnose_reconstruction, linum_stack_motor_only, linum_stitch_motor_only, linum_suggest_params

Other new scripts

linum_resample_nifti, linum_stack_slices_2d, linum_axis_XYZ_to_ZYX

Tests

test_mosaic_motor, test_mosaic_stacking

Refinements

linumpy/intensity/psf_model.py, linumpy/mosaic/grid.py, several scripts, workflows/reconst_2.5d/soct_2.5d_reconst.nf, doc updates across the suite

Build

uv.lock refresh

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