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cellprofiler

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Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/channel manifests, headless batch execution, segmentation overlays, and measurement QC for 2D fluorescence assays.

skills/cellprofiler/SKILL.md

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Nov 9, 2026
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# CellProfiler quantitative microscopy

Use this skill when a user needs a repeatable CellProfiler `.cppipe`, nuclear counts, nuclear
fluorescence, or batch microscopy measurements. The bundled assay accepts **one 2D grayscale
TIFF nuclear channel per field**, with black-is-zero (MINISBLACK) pixels and bright nuclei on a
dark background. Palette and white-is-zero TIFFs need an explicit conversion. For volumetric
segmentation, multichannel cell painting, or tissue-specific models, design a separate pipeline
and validate those assumptions rather than silently projecting or splitting the images.

The official application and manual remain **4.2.8**. PyPI publishes **4.2.8.1**; its seven
modules used here and embedded Threshold module match the 4.2.8 source, but this review did
not execute that native distribution. Keep the helper environment separate from CellProfiler's
older dependency stack; see the runtime reference for the verification boundary.
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