A Python toolkit for processing medical-slide images in local research workflows. It can load and divide large slides into smaller image tiles, run quality checks, quantify multiplex images, build spatial graphs, and prepare limited model runs.

Preparing whole-slide images, cleaning and checking image data, analyzing multiplex tissue images, representing nearby cells or regions as graphs, and planning model analysis.

It organizes repetitive image-processing steps while keeping sensitive pathology data in an authorized local workspace. Its results are for research, not for diagnosing or treating patients.

pathml — Skill for Claude Code by agentlas-ai/agentlas-desktop

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add agentlas-ai/agentlas-desktop --skill pathml

Clone the repo

git clone --depth 1 https://github.com/agentlas-ai/agentlas-desktop

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/pathml/github.svg)](https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/pathml)

Your own site

<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/pathml"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/pathml/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/pathml"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/pathml.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 46 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 2,772 The whole file, excluding the scripts and references it only reads on demand.

Security scan B 1 finding. A grade says what 26 rules found in the file — not that it is safe.

Origin 100% copy Near-identical to another mod in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00046	$0.02772
Opus 5.5	$0.00018	$0.01109
Sonnet 5.5	$0.00009	$0.00554
Haiku 4.5	$0.00005	$0.00277

Measured 1mo ago against content hash 4a8ba6ac2bb8, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade B, and why

pathml scanned grade B with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.

The scan reads SKILL.md. This mod also ships 6 executable files (scripts/_common.py, scripts/image_qc.py, scripts/plan_inference.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Asks for rootmediumPrivilege escalation

A mod that escalates privileges can change anything on the machine, not only the project.

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

Origin

This is a copy

100% identical to pathml — 69 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

plugins/agentlas-science-skills/skills/pathml/SKILL.md · 240 lines

How it starts

The opening of the file, as written. The whole thing — 240 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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'))"

Read the full file on GitHub · 240 lines

Files

What ships with it

12 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

1mo ago First seen · 240 lines · 46 tokens per session scan B 4a8ba6ac2bb8

Subscribe to this mod's changes

pathml is a skill published in the GitHub repository agentlas-ai/agentlas-desktop (6 stars, last pushed yesterday), licensed Apache-2.0. It adds 46 tokens to every session and 2,772 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it B with 1 finding (asks for root). It is 100% identical to pathml, differing in 69 lines, and is treated as a copy.

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