Fixes - #215
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The cellposev4 segmentation component exists but was not listed in any run script, so it never ran. Add it to segmentation_methods alongside cellpose (active in the seqeracloud scripts, commented in the local/test scripts, matching the existing convention). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Promote gene_efficiency_correction from an expression-correction method to its own stage (methods_gene_efficiency_correction) that runs after expression correction, offering two options: no_correction (pass-through) and gene_efficiency_correction. - New API src/api/comp_method_gene_efficiency_correction.yaml (input and output on file_spatial_corrected_counts). - New components under methods_gene_efficiency_correction/; the moved gene_efficiency_correction now reads --input and preserves an upstream normalized_uncorrected layer. - Remove gene_efficiency_correction from methods_expression_correction. - run_benchmark: insert the gene_eff stage between expression correction and aggregate_spatial_data; it overwrites the output_correction state key so aggregate_spatial_data and the similarity metric need no rewiring and controls keep working. Add --gene_efficiency_correction_methods and alias the colliding no_correction dependency (gene_eff_no_correction). - Update run scripts' method lists for the new stage. Verified: viash config view, viash ns build (components + workflow, deps and alias resolve), and viash test on both new components (output spec-conformant). Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
The process_dataset crop fix (transform-agnostic crop_points_by_global_xy) eliminated the out-of-bounds transcripts that motivated segger's in_bounds exclusion + seg_orig_idx row_index remap; a full validation run on re-processed Xenium + MERFISH confirmed n_oob == 0. Replace the exclusion with a plain edge clamp matching basic/baysor/proseg, write all transcripts so segger's row_index indexes tx_pd directly, and keep an n_oob == n_tx coordinate-mismatch guard. Script-only change (deploys via viash ns build + build/main regen, no image rebuild). NOTES.md updated; the separate empty-bd validation-tile crash on MERFISH is documented as still-open. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…MERFISH) Huge whole-section images (e.g. ABCA whole-brain MERFISH, ~83k x 102k px) place the tissue well off-centre, so the image-centred crop window can miss it entirely (mouse1_coronal kept 0 of 42M transcripts). Add a --tissue_centered_crop flag (default false = historical image-centred behaviour) that centres the crop window on the transcript density (median global x/y), clamped inside the image. Forwarded through the process_datasets workflow fromState; enabled in the ABCA combine script. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Proposed changes are described in the CHANGELOG.md
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