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pathml

80 / 100 · Low risk

Fine to try.

By KalarisLabs/research-agent-skills (GitHub) · research · 126 stars · scanned at commit 802bbea

Covers local, research-only computational pathology with PathML 3.0.5: loading and tiling whole-slide images (OpenSlide, Bio-Formats), preprocessing and QC pipelines run via SlideData.run(), .h5path data management, multiplex image quantification, spatial graph construction (KNN, RAG, HACT), and bounded local ONNX model inference planning. Use when loading or tiling slides, building tissue-mask or stain pipelines, managing .h5path files and patient-level splits, quantifying CODEX or Vectra mult…

Works with any agent that supports SKILL.md skills.

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What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'pathml' ] || [ -L ~/.agents/skills/'pathml' ]; then echo 'A skill folder named pathml already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/KalarisLabs/research-agent-skills' "$d" && git -C "$d" checkout --quiet '802bbea44e551abac24d6856f83fc55149bbdba3' -- 'skills/pathml' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/pathml' ~/.agents/skills/'pathml' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'pathml' ~/.claude/skills/'pathml' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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