Support nf-core/mcmicro output in the mcmicro reader - #410
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Auto-detect labsyspharm vs nf-core layout (override via `pipeline=`), handle multiple samples and segmenters in WSI and TMA modes, and add a test suite. Fixes a labsyspharm multi-segmenter label-name collision. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Hi @adamjtaylor, thanks for opening this PR and for providing the test dataset. I see that the PR is still marked as draft; please before marking it as ready for review can you please go through the checklist at the end of the ("Contribution Guide – Contributing readers and converters") and confirm which steps applies to this PR? This will greatly simplify the review process for us and future maintainers. Thank you! |
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Auto-detect labsyspharm vs nf-core layout (override via
pipeline=), handle multiple samples and segmenters in WSI and TMA modes, and add a test suite. Fixes a labsyspharm multi-segmenter label-name collision. Closes #409