Individual skill
tooluniverse-image-analysis
Microscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count statistics, dose-response curves, and ANOVA/Dunnett on image-derived measurements. Uses pandas/numpy/scipy/scikit-image. Use for analyzing tabular outputs from CellProfiler/ImageJ, image-derived measurement statistics, and image-based assay quantification.
plugins/tooluniverse/skills/tooluniverse-image-analysis/SKILL.md
Source commit 5598a9fc97e32964fe9b703818e7d0747142f179
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- Network or broad shell
- Last checked
- Nov 9, 2026
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- Repository last updated
- Nov 8, 2026
- License
- Apache-2.0
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SKILL.mdcore · 12,582 bytesSKILL.mdcore · 12,582 bytesSKILL.mdcore · 12,582 bytesSKILL.mdcore · 12,582 bytesSKILL.mdcore · 12,582 bytesreferences/cell_counting.mddoc · 15,226 bytesreferences/fluorescence_analysis.mddoc · 14,692 bytesreferences/image_processing.mddoc · 11,945 bytesreferences/segmentation.mddoc · 17,933 bytesreferences/statistical_analysis.mddoc · 22,795 bytesreferences/troubleshooting.mddoc · 10,053 bytesscripts/batch_process.pyruns · 8,869 bytesscripts/measure_fluorescence.pyruns · 7,217 bytesscripts/segment_cells.pyruns · 7,588 bytes
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# Microscopy Image Analysis and Quantitative Imaging Data
## RULE ZERO — Check for pre-computed results FIRST
Before following any instruction below, scan the data folder for:
- `*_executed.ipynb` → read with `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` and cite its cell outputs as the authoritative answer
- Pre-computed result files (CSV/TSV with names like `*results*`, `*deseq*`, `*enrich*`, `*stats*`, `*_simplified.csv`) → read directly and report the requested value
- Canonical analysis scripts (`analysis.R`, `run_*.py`, `find_*.R`, `*.Rmd`) → execute as-is and read the output
Only follow this skill's re-analysis recipe below if **none** of the above exist. Re-running from raw data produces different numbers than the published answer and is much slower (often 5-10× turn count).
---
## CRITICAL — "Relative proportion of A to B" defaults to PERCENTAGE