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PathML Computational Pathology Helper

Guides local PathML research on whole-slide images: loading, tiling, preprocessing, QC and planning.

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
13 files

What it does

Once installed, the agent follows a structured PathML workflow for analysing digital pathology slide images on your own machine. It knows the pinned PathML 3.0.8 APIs, warns about installation pitfalls, and uses bundled helper scripts to validate manifests, plan tiling and pipeline runs, and check image QC on synthetic or local data without opening real slides. It also enforces privacy steps such as de-identification, pseudonymous IDs and patient-level data splits.

Great for

  • Researchers doing local computational pathology experiments with PathML
  • Developers setting up a reproducible PathML 3.0.8 environment
  • Students learning whole-slide image tiling and preprocessing concepts

Skip it if

  • Clinical diagnosis, grading, staging or treatment decisions: the skill states PathML is beta research software, not a medical device or pathologist substitute
  • Processing identifiable patient slides without institutional authorization and de-identification, since the skill requires these steps first
  • Projects needing a simple install: the native stack (OpenSlide, JDK, Bio-Formats) is heavy and the skill says test the exact environment

Try asking

  • “Set up a reproducible PathML 3.0.8 environment on Python 3.11 for my H&E slide project”
  • “Plan tiling and pipeline work for my whole-slide images before running a full job”
  • “Validate my slide manifest and check that no URLs or identifiers are included”
  • “Write a bounded pilot preprocessing script that runs on 8 tiles before a full run”
Step-by-step guide: how to use PathML Computational Pathology HelperInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 13 original files, the MIT licence and an attribution note.

    pathml.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip pathml.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip pathml.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Work on de-identified, pseudonymised data only, and split by patient before tiling or fitting any preprocessing step.
  • Use the bundled planners and validators first; they need only the standard library and do not open slides.
  • Do not use pathml[all] (no extras are declared), and do not upgrade pinned NumPy, Torch or ONNX packages independently.

What's inside

  • references/data_management.md
  • references/graphs.md
  • references/image_loading.md
  • references/machine_learning.md
  • references/multiparametric.md
  • references/preprocessing.md
  • scripts/_common.py
  • scripts/image_qc.py
  • scripts/plan_inference.py
  • scripts/plan_pipeline.py
  • scripts/slide_manifest.py
  • scripts/validate_spatial_schema.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.