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WEHI-SODA-Hub
sp_segment
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AVITI24 cytoprofiling support
- #46
#46
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mcmero
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AVITI24 cytoprofiling support
#46
mcmero
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WEHI-SODA-Hub/sp_segment:dev
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Commits on Jun 29, 2026
fix: combine all membrane markers for cellSAM segmentation
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Commits on Jul 13, 2026
Update snapshots
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Commits on Jul 19, 2026
Merge branch 'WEHI-SODA-Hub:main' into fix/cellsam-combine-membrane-channels
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Merge pull request #32 from mikemcka/fix/cellsam-combine-membrane-channels
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Commits on Sep 2, 2026
feat: add AVITI cytoprofiling segmentation workflow
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Commits on Sep 3, 2026
fix: correct AVITI well stitching layout and add tile gap control
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Update output dirs for segmentation
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fix: write AVITI Nuclear.tif as Elembio's binary 0/1 convention
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Commits on Sep 7, 2026
feat: emit instance-labeled nuclear mask for stitching/CELLMEASUREMENT
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docs: clarify AVITI binary vs instance-labeled nuclear mask split
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Commits on Sep 10, 2026
feat: add per-row Cellpose 3.x membrane model selection for AVITI
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Commits on Sep 13, 2026
feat: assemble AVITI wells into a plate-level pyramidal OME-TIFF + GeoJSON
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Commits on Sep 14, 2026
refactor(aviti): drop cellpaint batch param, remove aviti_defaults.config
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feat(aviti): only assemble a plate when a sample has more than one well
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docs: update readme and add separate AVITI flowchart
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fix(aviti): override SEGMENTATIONREPORT cellpose_ args with aviti_ params
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Merge branch 'main' into aviti
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Remove feature plan
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Apply batched suggestions from Copilot code review
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Merge branch 'dev' into aviti
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Commits on Sep 15, 2026
fix(aviti): name plate outputs from meta.sample, not meta.id
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fix(aviti): report the diameter/model actually used, not the global default
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fix(aviti): promote plate_meta_of/to_report_input to top-level functions
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Commits on Oct 9, 2026
docs(aviti): clarify pixel_size_microns fallback is COMET's 0.28, not AVITI's
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Linting fix
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