mcpbeat

Alterlab Pathml

alterlab-ieu/alterlab-pathml

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.

27k tokens
context cost
the whole folder, loaded on every use
8
files
instructions only
0
copies elsewhere
how many repositories repackaged it
56
stars on the repo
on the repository, not the skill itself

Install

one command, takes just this skill from the repository 
npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-pathml

How to use it

Copy the folder

Take alterlab-ieu/alterlab-pathml from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.

Install what it needs

The instructions reference pip, uv. Without those the skill loads but fails at the first command.