cellprofiler

1# CellProfiler quantitative microscopy
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3Use this skill when a user needs a repeatable CellProfiler `.cppipe`, nuclear counts, nuclear
4fluorescence, or batch microscopy measurements. The bundled assay accepts **one 2D grayscale
5TIFF nuclear channel per field**, with black-is-zero (MINISBLACK) pixels and bright nuclei on a
6dark background. Palette and white-is-zero TIFFs need an explicit conversion. For volumetric
7segmentation, multichannel cell painting, or tissue-specific models, design a separate pipeline
8and validate those assumptions rather than silently projecting or splitting the images.
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10The official application and manual remain **4.2.8**. PyPI publishes **4.2.8.1**; its seven
11modules used here and embedded Threshold module match the 4.2.8 source, but this review did
12not execute that native distribution. Keep the helper environment separate from CellProfiler's
13older dependency stack; see the runtime reference for the verification boundary.
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15## Workflow
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171. Establish the acquisition unit: plate, well, site, time point if present, pixel size, nuclear
18   channel identity, camera bit depth, exposure, and biological replicate. Keep original image
19   intensities. Convert proprietary formats explicitly with Bio-Formats before using this helper.
202. Create the CSV manifest below. `image_path` is absolute or relative to the manifest; sample IDs use letters, digits, dots, dashes, or underscores; sample IDs
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