Agent skill · research science · k-dense-ai
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.
Why this skill is useful
Provides specific commands and workflows for using PathML in computational pathology that are not commonly known.
What it needs
Requires g++, gcc, libblas-dev, liblapack-dev, openjdk-17-jdk, openslide-tools, python installed locally. About 5k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
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 patientid, slideid, and specimenid 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 and still has a stale 3.8 classifier, so use the release statement and test the exact environment. GitHub releases v3.0.6 (2026-04-14) and v3.0.7 (2026-07-09) exist, but PyPI has no artifacts for them as of this review. v3.0.7 updates Torch/TorchVision/ torch-geometric and ONNX export code. Do not mix those source dependencies with the 3.0.5 wheel. ReadTheDocs /latest identifies itself as 3.0.5. Examples here were checked against the v3.0.5 tag and PyPI wheel metadata, not unversioned snippets. This skill is MIT-licensed. PathML itself is GPL-2.0 with upstream commercial licensing options; review upstream terms before redistribution. Reproducible installation Use Python 3.11 unless the project has tested another supported interpreter: PathML 3.0.5 declares no package extras: do not use pathml[all]. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/pathml