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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