pathml
Supports local computational pathology research with PathML: slide loading and tiling, preprocessing and QC, h5path storage, multiplex quantification, spatial graphs, and bounded model inference. Use for whole-slide H&E, CODEX, Vectra, Mesmer, HoVer-Net, and HACTNet workflows.
- Version
- 1.4
- License
- MIT
- Compatibility
- Requires Python 3.10-3.12 for the PathML 3.0.8 dependency stack, native OpenSlide, a JDK/compiler for python-javabridge, and Bio-Formats. Network needed for installation and optional model/dataset downloads. Bundled Python 3.10+ planners and validators need only the standard library; optional metadata/image inspection needs its reader package.
Pinned to revision 68105dd992f1, 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/SKILL_CN.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.