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pathml

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A full-featured computational pathology toolkit for advanced WSI analysis, including multiplexed immunofluorescence (CODEX, Vectra), nuclei segmentation, tissue graph construction, and machine learning model training on pathology data. Supports over 160 slide formats. For simp...

scientific-skills/Data Analysis/pathml/SKILL.md

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Sep 17, 2026
License
MIT

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

# PathML

## When to Use

- Use this skill when you need a full-featured computational pathology toolkit for advanced wsi analysis, including multiplexed immunofluorescence (codex, vectra), nuclei segmentation, tissue graph construction, and machine learning model training on pathology data. supports over 160 slide formats. for simple tile extraction from h&e slides, histolab may be simpler in a reproducible workflow.
- Use this skill when a data analytics task needs a packaged method instead of ad-hoc freeform output.
- Use this skill when the user expects a concrete deliverable, validation step, or file-based result.
- Use this skill when `the documented workflow in this package` is the most direct path to complete the request.
- Use this skill when you need the `pathml` package behavior rather than a generic answer.

## Key Features

- Scope-focused workflow aligned to: A full-featured computational pathology toolkit for advanced WSI analysis, including multiplexed immunofluorescence (CODEX, Vectra), nuclei segmentation, tissue graph construction, and machine learning model training on pathology data. Supports over 160 slide formats. For simple tile extraction from H&E slides, histolab may be simpler.
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