alterlab-pathml
From the author
Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, multiplexed immunofluorescence (CODEX, Vectra, MERFISH), nucleus segmentation/classification (HoVer-Net, HACTNet), tissue- and cell-graph construction, HDF5 dataset management, and deep-learning model training on pathology data. Use when the user builds end-to-end deep-learning pathology pipelines, analyzes multiplexed or spatial-proteomics slides, or segments nuclei. For lightweight H&E slide preprocessing, tissue masking, or plain Random/Grid/Score tile extraction prefer alterlab-histolab instead. Part of the AlterLab Academic Skills suite.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-pathml -a claude-code
Installs to .claude/skills/alterlab-pathml/ · Each command fetches the skill straight from GitHub with the open skills CLI.
No download: this skill’s licence (GPL-2.0) does not let us redistribute its files. The install commands fetch them from GitHub instead.
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