Pathml Skill for Codex

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:

• Confirm authorization, consent/waiver, data-use terms, and institutional policy.
• De-identify pixels and metadata; keep the re-identification key outside the

analysis workspace.

• Use pseudonymous patient_id, slide_id, and specimen_id values. Do not put

direct identifiers in filenames, logs, .h5path labels, model cards, or reports.

• Keep inputs, intermediates, and outputs on approved local encrypted storage.
• 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:

uv venv --python 3.11
source .venv/bin/activate
uv pip install "pathml==3.0.5"
python -c "import importlib.metadata as m; print(m.version('pathml'))"

PathML 3.0.5 declares no package extras: do not use pathml[all]. Its base

distribution pins a large scientific/ML stack, including Torch 2.8.0, ONNX 1.17.0,

ONNX Runtime 1.17.x, OpenSlide Python 1.3.1, python-bioformats 4.1.0, and

python-javabridge 4.0.4.

Install native prerequisites before the uv command:

# Debian/Ubuntu
sudo apt-get install openslide-tools gcc g++ libblas-dev liblapack-dev openjdk-17-jdk

# macOS
brew install openslide openjdk@17

# Windows OpenSlide option documented upstream
vcpkg install openslide

Java/Bio-Formats is needed for the broad multidimensional format backend.

OpenSlide handles common brightfield WSI formats more efficiently. CUDA is

optional and must match the pinned PyTorch build; follow PyTorch's platform

selector rather than guessing a CUDA wheel. See references/image_loading.md.

Stable minimal workflow

PathML 3.0.5 uses slide convenience classes and SlideData.run(). It does not

provide SlideData.from_slide(), and Pipeline does not have run():

from pathml.core import HESlide
from pathml.preprocessing import BoxBlur, Pipeline, TissueDetectionHE

slide = HESlide("data/pseudonymous_slide.svs", backend="openslide")
pipeline = Pipeline(
    [
        BoxBlur(kernel_size=5),
        TissueDetectionHE(mask_name="tissue", min_region_size=5000),
    ]
)
slide.run(
    pipeline,
    distributed=False,
    tile_size=512,
    tile_stride=512,
    level=0,
    tile_pad=False,
)
slide.write("derived/pseudonymous_slide.h5path")

Start with a bounded manual sample before a full run:

from itertools import islice

for tile in islice(slide.generate_tiles(shape=512, stride=512, level=0), 8):
    pipeline.apply(tile)
    assert tile.masks["tissue"].shape[:2] == tile.image.shape[:2]

Tiles use (i, j) = (row, column) coordinates at the selected pyramid level.

For OpenSlide, PathML maps them to level-0 coordinates internally. Record the

level and downsample; convert to (x, y) or micrometres explicitly downstream.

Research workflow

• Inventory locally. Validate the manifest, reject URLs/symlinks, inspect only

allowlisted technical metadata, and remove identifiers.

• Freeze splits. Assign every patient and all their slides to one split before

generating overlapping tiles, graphs, normalization references, or features.

• Plan bounds. Estimate tile count, RAM, output size, and pipeline stages.
• Pilot preprocessing. Inspect tissue masks, whitespace/artifact labels,

stain behavior, edge padding, and empty-mask cases on representative training

slides. Do not tune from test slides.

• Run and preserve coordinates. Keep tile level, (i, j), downsample, MPP,

mask names, QC decisions, and failed/skipped tiles.

• Build spatial data deliberately. Validate channel order, physical units,

instance labels, node-feature alignment, graph edges, and cell-to-tissue

assignments.

• Infer in bounded batches. Verify model provenance and checksum without

loading unknown pickle checkpoints. Keep predictions linked to slide/tile

coordinates and stitch overlaps with a documented rule.

• Report provenance and limits. Include package lock, source hashes, scanner,

stain, parameters, seeds, split manifest, model card, exclusions, and QC.

No-network default and explicit consent gate

Do not instantiate download-capable classes or set dataset download=True unless

the user explicitly opts in after receiving the endpoint and disclosure:

• SegmentMIFRemote downloads an ONNX file from

https://huggingface.co/pathml/test/resolve/main/mesmer.onnx at construction,

then runs inference locally. Stable source does not upload image pixels.

The request still discloses network metadata such as IP address and headers and

creates temp.onnx; there is no built-in checksum or offline flag.

• Deprecated SegmentMIF imports local DeepCell Mesmer, but DeepCell model

initialization may need separately provisioned weights. It is not a PathML

extra and is not the preferred stable API.

• RemoteTestHoverNet downloads a model from Hugging Face.
• PanNukeDataModule(download=True) contacts Warwick; DeepFocusDataModule

contacts Zenodo. Both default to download=False.

Before any future hosted prediction call, state the exact destination, pixel

channels/regions, metadata, identifiers, retention, legal basis, and safeguards;

obtain explicit consent; and never send PHI by default. Prefer reviewed,

checksummed local model artifacts and local inference.

Model-code security

• PyTorch model.eval() means evaluation mode for modules; it is not Python's

dangerous built-in evaluator. Never use Python dynamic evaluation or execution.

• Do not name local files pathml.py, torch.py, onnx.py, or after standard

libraries; shadow modules can silently change imports.

• PathML's EntityDataset loads .pt objects with weights_only=False. Never

open an untrusted graph/checkpoint. Treat pickle-based pipelines and .pt files

as executable code.

• ONNX is safer than pickle but not inherently trusted. Verify source, SHA-256,

expected input/output schema, file size, and runtime limits; use isolation for

third-party models.

Bundled local CLIs

All helpers reject URLs and symlinks, cap inputs/work, use strict JSON, avoid

network access, and require no PathML import for --help:

python scripts/slide_manifest.py validate --manifest manifest.csv --root .
python scripts/slide_manifest.py inspect --slide data/example.svs --root .
python scripts/plan_pipeline.py --width 100000 --height 80000 --tile-size 512 --stride 512
python scripts/image_qc.py synthetic --width 256 --height 256
python scripts/validate_spatial_schema.py graph --input graph.json --root .
python scripts/validate_spatial_schema.py multiplex --input cells.csv --root .
python scripts/plan_inference.py --tile-count 4000 --batch-size 16 --height 256 --width 256

The inference planner reads numbers or a bounded JSON model card only; it never

imports a model framework or opens a checkpoint.

Detailed references

• references/image_loading.md — slide classes, backends, formats, levels,

coordinates, technical metadata, and privacy.

• references/preprocessing.md — stable transforms, masks/QC, stain processing,

pipeline execution, and leakage prevention.

• references/data_management.md — .h5path, manifests, datasets, provenance,

splits, and safe downloads.

• references/multiparametric.md — multidimensional layout, CODEX/Vectra,

quantification, AnnData, DeepCell/Mesmer, and network disclosure.

• references/graphs.md — instance maps, feature alignment, KNN/RAG/HACT graphs,

spatial units, schemas, and validation.

• references/machine_learning.md — HoVer-Net/HACTNet, local ONNX inference,

batching, checkpoint trust, evaluation, and model provenance.

Primary sources

All checked 2026-07-23:

• PyPI metadata: https://pypi.org/project/pathml/3.0.5/
• Stable source tag: https://github.com/Dana-Farber-AIOS/pathml/tree/v3.0.5
• Releases: https://github.com/Dana-Farber-AIOS/pathml/releases
• Stable documentation: https://pathml.readthedocs.io/en/stable/
• Rosenthal et al. (2022), PathML toolkit:

https://doi.org/10.1158/1541-7786.MCR-21-0665

• Omar et al. (2025), multiplex workflows:

https://doi.org/10.1016/j.labinv.2025.104220