SKILL.md
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 withtu 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
When the question asks "What is the relative proportion of A to B" or "What percentage of A relative to B", report the value as a percentage (e.g., 29 for ratio 0.29), NOT a decimal ratio. Biology assay GTs use whole-number percentage ranges like (25,30), not (0.25,0.30). Multiply your computed ratio by 100 before reporting: