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CellProfiler Nuclei Assay

Runs repeatable CellProfiler nuclear counting and fluorescence measurements on microscopy images

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
3 files

What it does

Lets the agent set up and run a standardized CellProfiler pipeline that finds and counts cell nuclei in 2D grayscale fluorescence microscopy images and measures each nucleus's DNA stain intensity, area and shape. It checks the image manifest and input files, runs CellProfiler in batch mode, records checksums and run status in a QC file, and summarizes the resulting tables. It does not replace visual inspection of the segmentation overlays, which the skill itself says are required.

Great for

  • Researchers running nuclear counts or nuclear fluorescence measurements on single-channel 2D TIFF images
  • Lab staff who need a reproducible, documented CellProfiler batch run with saved pipeline and checksums
  • Users who already have CellProfiler 4.2.8 installed or available as a container

Skip it if

  • Volumetric (z-stack), multichannel cell painting, or tissue-specific segmentation, which the skill says needs a separate validated pipeline (wrong results if forced)
  • Clinical or diagnostic decisions, since the skill only checks counts and overlays and does not prove correct segmentation
  • Users without CellProfiler or microscopy experience, because the inputs must be correctly formatted and calibrated to give valid numbers

Try asking

  • “Count nuclei in my DAPI TIFF images for these 40 wells and export per-nucleus intensity tables”
  • “Build a CSV manifest for my plate images and prepare a CellProfiler LoadData file”
  • “Run the nuclei assay with my tuned .cppipe pipeline into a fresh results folder and summarize the outputs”
  • “Check my intensity measurements for saturation and bit-depth problems before comparing conditions”
Step-by-step guide: how to use CellProfiler Nuclei AssayInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 3 original files, the MIT licence and an attribution note.

    cellprofiler.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip cellprofiler.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip cellprofiler.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Calibrate the 8–80 pixel nuclear diameter range and threshold on a pilot set with overlays before running the full batch, and keep one tuned pipeline for all conditions.
  • Use a fresh, empty output folder for each run and treat the run as valid only when assay_qc.json shows success and the Complete marker is present.
  • Convert proprietary microscope formats with Bio-Formats first and do not compare intensities across different bit depths, exposures or staining batches without calibration.

What's inside

  • references/runtime-and-qc.md
  • scripts/nuclei_assay.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.