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.
- 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 70a605012eee, 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.
- Read
- Write
- Edit
- Bash
- Glob
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.