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chore: bump cellmeasurement-py to 0.2.1 - #34
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cellSAM previously received only the first matching membrane channel (first-match-and-break in extract_channels), silently discarding any additional markers. Wire COMBINECHANNELS into the CELLSAM_SEGMENT subworkflow (mirroring the SOPA/Cellpose path) so all listed membrane markers are max-combined into a single 'combined_membrane' channel before segmentation. The background-subtraction variant inherits the fix via its call to CELLSAM_SEGMENT. Because cellSAM now only sees the single combined channel, log which channels were combined in combine_channels.py so that information stays visible in the process log. Add multi-membrane nf-test cases to the combinechannels module and the cellsam_segment subworkflow (reusing synthetic_multichannel.tif with CD45:TRITC). Snapshots still need blessing on a GPU node; the existing cellsam_segment / cellsam_segment_wbacksub snapshots also change because COMBINECHANNELS now runs within those workflows. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…nnels Fix/cellsam combine membrane channels
Update the CELLMEASUREMENT module pins to cellmeasurement-py 0.2.1: - container: ghcr.io/wehi-soda-hub/cellmeasurement-py 0.1.4 -> 0.2.1 - environment.yml: git pin 0.1.2 -> 0.2.1 Snapshots are intentionally not re-blessed in this commit; see the PR description for the sequencing with the cellmeasurement-py release. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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mcmero
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Jul 27, 2026
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Summary
Bumps the
CELLMEASUREMENTmodule to cellmeasurement-py 0.2.1:main.nfcontainer:ghcr.io/wehi-soda-hub/cellmeasurement-py0.1.4->0.2.1environment.ymlgit pin:0.1.2->0.2.1(was stale, and out of sync with the container)Note on the base branch
This branch is cut from
main, so relative todevit also carries the 4 commitsmainalready has thatdevdoes not (#32 multi-membrane cellSAM fix and its snapshot update).devcurrently pins the container to0.2.0withenvironment.ymlstill at0.1.2; this PR brings both to0.2.1.Test status
Run locally with
nf-test ... --profile test,apptainer. Failures split into two groups.Expected, caused by this bump - all show the same signature (
test*.geojson.gz+versions.yml), i.e. cellmeasurement-py 0.2.0's rewritten polygon extraction plus the version string:cellmeasurement(basic functionality, stub)cellsam_segment(tiff, multi-membrane combine)cellsam_segment_wbacksub,mesmer_segmentPre-existing, unrelated to this bump - none of these touch a cellmeasurement output and they fail the same way without this change:
sopa_convertx2,sopa_patchifyimagex2,sopa_resolvecellpose,sopa_segmentationcellpose- sopaversions.ymland zarr.zattrs/zmetadatadriftbackgroundsubtract-test.ome.tifonly (itstest.csvmatches)segmentationreport-test.htmlKRONOSEMBEDDINGS - stub- references a fixture that is not committedSnapshots are deliberately not re-blessed here. The
0.2.1tag of cellmeasurement-py was cut from a commit wherepyproject.tomlstill read0.2.0, so the container reportscellmeasurement-py 0.2.0inversions.yml. Blessing now would bake that wrong version into the snapshots and they would break again as soon as the release is re-cut. Suggested order: land thepyproject.tomlbump in cellmeasurement-py -> re-cut0.2.1-> rebuild the image -> re-bless here in a follow-up commit.Needs a look
cellsam_segment - multi-membrane combinealso drifts intest_multimem_whole-cell.tiff, a segmentation mask rather than a cellmeasurement output, so this bump does not explain it. The standalonecellsamsegmenttests pass with exactly matching mask hashes, so it is specific to the multi-membrane path. I would not bless that snapshot without understanding the cause.🤖 Generated with Claude Code