Individual skill
pathml
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 multiplex images, or building cell and tissue graphs. Not for clinical diagnosis or patient care decisions.
plugins/KalarisLabs/research-agent-skills/skills/pathml/SKILL.md
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# 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