Fixes - #216
Merged
Merged
Conversation
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>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Describe your changes
Checklist before requesting a review
I have performed a self-review of my code
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI Tests succeed and look good!