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tooluniverse-image-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
Production-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fluorescence quantification, and statistical analysis of imaging-derived measurements. Processes ImageJ/CellProfiler output (area, circularity, intensity, cell counts), performs Dunnett's test, Cohen's d effect size, power analysis, Shapiro-Wilk normality tests, two-way ANOVA, polynomial regression,….
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tooluniverse-image-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Production-ready skill for analyzing microscopy-derived measurement data using pandas, numpy, scipy, statsmodels, and scikit-image. Designed for BixBench imaging questions covering colony morphometry, cell counting, fluorescence quantification, regression modeling, and statistical comparisons.
- IMPORTANT: This skill handles complex multi-workflow analysis. Most implementation details have been moved to references/ for progressive disclosure. This document focuses on high-level decision-making and workflow orchestration.
- import pandas as pd import numpy as np from scipy import stats from scipy.interpolate import BSpline, make_interp_spline import statsmodels.api as sm from statsmodels.formula.api import ols from statsmodels.stats.power import TTestIndPower from patsy import dmatrix, bs, cr.
Source Doc
Excerpt From SKILL.md
When to Use This Skill
Apply when users:
- Have microscopy measurement data (area, circularity, intensity, cell counts) in CSV/TSV
- Ask about colony morphometry (bacterial swarming, biofilm, growth assays)
- Need statistical comparisons of imaging measurements (t-test, ANOVA, Dunnett's, Mann-Whitney)
- Ask about cell counting statistics (NeuN, DAPI, marker counts)
- Need effect size calculations (Cohen's d) and power analysis
- Want regression models (polynomial, spline) fitted to dose-response or ratio data
- Ask about model comparison (R-squared, F-statistic, AIC/BIC)
- Need Shapiro-Wilk normality testing on imaging data
- Want confidence intervals for peak predictions from fitted models
- Questions mention imaging software output (ImageJ, CellProfiler, QuPath)
- Need fluorescence intensity quantification or colocalization analysis
- Ask about image segmentation results (counts, areas, shapes)
BixBench Coverage: 21 questions across 4 projects (bix-18, bix-19, bix-41, bix-54)
NOT for (use other skills instead):
- Phylogenetic analysis → Use
tooluniverse-phylogenetics - RNA-seq differential expression → Use
tooluniverse-rnaseq-deseq2 - Single-cell scRNA-seq → Use
tooluniverse-single-cell - Statistical regression only (no imaging context) → Use
tooluniverse-statistical-modeling
Core Principles
- Data-first approach - Load and inspect all CSV/TSV measurement data before analysis
- Question-driven - Parse the exact statistic, comparison, or model requested
- Statistical rigor - Proper effect sizes, multiple comparison corrections, model selection
- Imaging-aware - Understand ImageJ/CellProfiler measurement columns (Area, Circularity, Round, Intensity)
- Workflow flexibility - Support both pre-quantified data (CSV) and raw image processing
- Precision - Match expected answer format (integer, range, decimal places)
- Reproducible - Use standard Python/scipy equivalents to R functions
Optional (for raw image processing)
import skimage import cv2 import tifffile bash pip install pandas numpy scipy statsmodels patsy scikit-image opencv-python-headless tifffile
---
Use cases
- Have microscopy measurement data (area, circularity, intensity, cell counts) in CSV/TSV.
- Ask about colony morphometry (bacterial swarming, biofilm, growth assays).
- Need statistical comparisons of imaging measurements (t-test, ANOVA, Dunnett's, Mann-Whitney).
- Ask about cell counting statistics (NeuN, DAPI, marker counts).
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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