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Fix/cellsam combine membrane channels - #32
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mikemcka merged 3 commits intoJul 19, 2026
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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>
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nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).