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.
- Version
- 1.2
- License
- MIT
- Compatibility
- PathML 3.0.5 is the latest PyPI release and targets Python 3.10-3.12; installation needs uv plus platform libraries for OpenSlide, BLAS/LAPACK, and Java/Bio-Formats. Bundled Python 3.10+ CLIs are local, bounded, dependency-free, and network-free.
Pinned to revision df088027ff23, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
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Files
- skills/pathml/SKILL.md
- skills/pathml/references/data_management.md
- skills/pathml/references/graphs.md
- skills/pathml/references/image_loading.md
- skills/pathml/references/machine_learning.md
- skills/pathml/references/multiparametric.md
- skills/pathml/references/preprocessing.md
- skills/pathml/scripts/_common.py
- skills/pathml/scripts/image_qc.py
- skills/pathml/scripts/plan_inference.py
- skills/pathml/scripts/plan_pipeline.py
- skills/pathml/scripts/slide_manifest.py
- skills/pathml/scripts/validate_spatial_schema.py
Every link opens the file at its source, pinned to the revision this page describes.