/pathml
Computational pathology toolkit for whole-slide images (WSIs): load slides, extract tiles, stain normalization, nuclear segmentation, feature extraction, and ML training. Supports H&E and multiplex. For end-to-end pipelines from raw WSIs to quantitative outputs.
$ npx -y skills add jaechang-hits/SciAgent-Skills --skill pathml --agent claude-codeHow it fires
How this skill gets triggered: by you, by Claude, or both.
- Fires itselfAuto-invocation. Claude auto-loads it when your prompt matches the work.
- You can call itInvoke it directly when you want it.
- Slash command
/pathml
Context preview
The summary Claude sees to decide when to auto-load this skill.
Computational pathology toolkit for whole-slide images (WSIs): load slides, extract tiles, stain normalization, nuclear segmentation, feature extraction, and ML training. Supports H&E and multiplex. For end-to-end pipelines from raw WSIs to quantitative outputs.
Turn your AI coding agent into a life sciences expert — 199 bioinformatics skills for Claude Code covering RNA-seq, single-cell analysis, genomics, proteomics, drug discovery, and more. Boosted BixBench from 65% to 92%. Open source.
Other skills on sciagent-skills.
- /sciagent-skill-creator
Scaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates skills/{category}/{name}/SKILL.md with valid frontmatter, appends the registry.yaml entry, runs validation. Enforces name uniqueness, kebab-case, description keyword rules, schema rules
Open skill - /pymc-bayesian-modeling
Bayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction. Hierarchical, logistic, GP variants; predictive checks.
Open skill - /scikit-survival-analysis
Time-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data. C-index, Brier, time-dependent AUC; Kaplan-Meier, Nelson-Aalen, competing risks. Pipeline/GridSearchCV compatible. Use statsmodels for frequentist, pymc
Open skill - /statistical-analysis
Guided statistical analysis: test choice, assumption checks, effect sizes, power, APA reporting. Pick tests, verify assumptions, or format results for publication. Covers frequentist (t-test, ANOVA, chi-square, regression, correlation, survival, count, reliability) and Bayesian.
Open skill - /statsmodels-statistical-modeling
Python statistical modeling: regression (OLS, WLS, GLM), discrete (Logit, Poisson, NegBin), time series (ARIMA, SARIMAX, VAR), with rigorous inference, diagnostics, and hypothesis tests. Use scikit-learn for ML; statistical-analysis for test choice.
Open skill - /cellpose-cell-segmentation
DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image watershed for
Open skill