pathml

pathml is a skill for Claude Code, Codex from halflifezyf2680/Skill-Shelf. It costs 46 tokens per session (2,772 once invoked), scanned B, original, no licence file.

A computational pathology toolkit for analysing whole-slide images, which are high-resolution digital scans of microscope slides. It covers multiplexed fluorescence images, cell-nucleus segmentation, tissue graphs, and machine-learning model training.

In plain words
What is it for?
Use it to analyse stained or fluorescent pathology slides, identify cell nuclei, represent tissue as connected structures, and train models on pathology data.
Why use it?
It brings common pathology-image analysis tasks into one toolkit, reducing the need to assemble separate methods for different slide formats and analyses.

Skill for Claude CodeCodex

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.

agentmods
npx agentmods add skills/halflifezyf2680/skill-shelf/pathml
Any agent
npx skills add halflifezyf2680/Skill-Shelf --skill pathml
Clone the repo
git clone --depth 1 https://github.com/halflifezyf2680/Skill-Shelf

Made for: Claude Code, Codex.

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.

agentmods badge for pathml

README.md
[![agentmods](https://agentmods.dev/badge/skills/halflifezyf2680/skill-shelf/pathml.svg)](https://agentmods.dev/skills/halflifezyf2680/skill-shelf/pathml)
Your own site
<a href="https://agentmods.dev/skills/halflifezyf2680/skill-shelf/pathml"><img src="https://agentmods.dev/badge/skills/halflifezyf2680/skill-shelf/pathml.svg" alt="Measured on agentmods" 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. Scan, not verified.
Origin unknown No closer match found 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.

ModelPer sessionOnce invoked
Fable 5 $0.00046 $0.02772
Opus 5 $0.00023 $0.01386
Sonnet 5 $0.00009 $0.00554
Haiku 4.5 $0.00005 $0.00277

Measured today against content hash 4a8ba6ac2bb8, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, 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 today.

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
data/hub/packages/academic-research/pathml/SKILL.md · 240 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

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.

  1. today Changed · +75 lines · -23 tokens per session scan A → B 4a8ba6ac2bb8
  2. 5d ago First seen · 165 lines · 69 tokens per session scan A 32a723419c31

Subscribe to this mod's changes

pathml is a skill published in the GitHub repository halflifezyf2680/Skill-Shelf (4 stars, last pushed today), with no licence file. It adds 46 tokens to every session and 2,772 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it B with 1 finding (asks for root). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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