Add tiling QC metric for tile-boundary segmentation artifacts#1156
Closed
timtreis wants to merge 1 commit into
Closed
Add tiling QC metric for tile-boundary segmentation artifacts#1156timtreis wants to merge 1 commit into
timtreis wants to merge 1 commit into
Conversation
Cells segmented in tiles get cut at tile borders, producing fragments with artificially straight edges. This adds: - `sq.experimental.tl.calculate_tiling_qc`: per-cell scoring via collinearity-based straight-edge detection (max_straight_edge_ratio, cardinal_alignment_score, cut_score). Scores stored in .obs of a QC AnnData table linked to the labels element via spatialdata_attrs. Algorithm parameters recorded in .uns["tiling_qc"]. - `sq.experimental.pl.tiling_qc`: diagnostic plot via spatialdata-plot (renders labels coloured by score; tile grid emerges from the data). - `extract_labels_tile_lazy` in _tiling.py for labels-only tile extraction without materialising an image. - Test fixture with 400x400 dask-backed ellipsoid cells cut by a 3x3 tile grid, with ground-truth cut/intact classification. - 35 tests (unit, integration, visual regression). Co-Authored-By: Claude Opus 4.6 (1M context) <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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
sq.experimental.tl.calculate_tiling_qc— per-cell scoring that detects cells artificially cut by tile boundaries during segmentation, using collinearity-based straight-edge detection on contourssq.experimental.pl.tiling_qc— diagnostic plot via spatialdata-plot where the tile grid emerges from high-scoring cells without requiring tile-border metadata.obsof a QC AnnData table ({labels_key}_qc) with properspatialdata_attrslinking and algorithm params in.uns["tiling_qc"]Metrics
max_straight_edge_ratiocardinal_alignment_scorecut_scoreTest plan
🤖 Generated with Claude Code