pathml
Use PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and QC pipelines, manage h5path data, quantify multiplex images, construct spatial graphs, and plan bounded model inference.
npx skills add K-Dense-AI/scientific-agent-skills --skill pathml --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# PathML ## Scope and safety boundary Use PathML for **local computational pathology research**. It is beta research software, not a validated medical device, diagnostic system, clinical decision support tool, or substitute for a pathologist. Do not use outputs to diagnose, grade, stage, or treat a patient. Pathology files may contain faces, labels, accession numbers, patient identifiers, DICOM tags, filenames, or linked clinical data. Before processing: 1. Confirm authorization, consent/waiver, data-use terms, and institutional policy. 2. De-identify pixels and metadata; keep the re-identification key outside the analysis workspace. 3. Use pseudonymous `patient_id`, `slide_id`, and `specimen_id` values. Do not put direct identifiers in filenames, logs, `.h5path` labels, model cards, or reports. 4. Keep inputs, intermediates, and outputs on approved local encrypted storage. 5. Split by patient (then slide) before tiling or fitting any preprocessing step. ## Version baseline, verified 2026-07-23 - **Installable stable release:** PyPI `pathml==3.0.5`, published 2026-03-24. - The v3.0.5 release notes state Python **3.10-3.12** and sunset 3.9. PyPI does not declare `Requires-Python` an
- Scope and safety boundary
- Version baseline, verified 2026-07-23
- Reproducible installation
- Stable minimal workflow
- Research workflow
- No-network default and explicit consent gate
- Model-code security
- Bundled local CLIs
- Detailed references
- Primary sources
uv venv --python 3.11
source .venv/bin/activate
uv pip install "pathml==3.0.5"
python -c "import importlib.metadata as m; print(m.version('pathml'))"
Debian/Ubuntu
sudo apt-get install openslide-tools gcc g++ libblas-dev liblapack-dev openjdk-17-jdk
macOS
brew install openslide openjdk@17
Windows OpenSlide option documented upstream
vcpkg install openslideWhat does the pathml skill do?
Use PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and QC pipelines, manage h5path data, quantify multiplex images, construct spatial graphs, and plan bounded model inference.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill pathml --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.