cellprofiler
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.
- Version
- 1.1
- License
- MIT
- Compatibility
- Python 3.12+ with numpy and tifffile for current helper-only dependencies; a separate CellProfiler 4.2.8 application/container for segmentation. Full CellProfiler has older native dependencies. Network access is needed for installation only. No credentials required.
Pinned to revision 92ace75ac21e, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/cellprofiler/SKILL.md
- skills/cellprofiler/assets/nuclei.cppipe
- skills/cellprofiler/references/runtime-and-qc.md
- skills/cellprofiler/scripts/nuclei_assay.py
Every link opens the file at its source, pinned to the revision this page describes.