Individual skill
pathml
Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.
bundled/skills/pathml/SKILL.md
Source commit 8af6e230d3db0f3022236e67632be6d8b9323bf0
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Network or broad shell
- Last checked
- Nov 11, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
Install this skill
Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.
An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.
Repository context
- Repository stars (not skill ratings)
- 3,817
- Repository last updated
- Nov 9, 2026
- License
- Apache-2.0
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- ai-agents Repository topic
- ai-workflow Repository topic
- automation Repository topic
- codex Repository topic
- developer-tools Repository topic
- skills Repository topic
- ai-skills Repository topic
- claude-code Repository topic
- llm Repository topic
- vibe-coding Repository topic
- data Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Browse files
SKILL.mdcore · 7,866 bytesSKILL.mdcore · 7,866 bytesSKILL.mdcore · 7,866 bytesreferences/data_management.mddoc · 19,018 bytesreferences/graphs.mddoc · 16,726 bytesreferences/image_loading.mddoc · 12,146 bytesreferences/machine_learning.mddoc · 19,946 bytesreferences/multiparametric.mddoc · 18,199 bytesreferences/preprocessing.mddoc · 18,209 bytes
Read excerpt
# PathML
## Overview
PathML is a comprehensive Python toolkit for computational pathology workflows, designed to facilitate machine learning and image analysis for whole-slide pathology images. The framework provides modular, composable tools for loading diverse slide formats, preprocessing images, constructing spatial graphs, training deep learning models, and analyzing multiparametric imaging data from technologies like CODEX and multiplex immunofluorescence.
## Routing Boundary
Use this skill for full computational pathology workflows, PathML pipelines, WSI analysis, nucleus segmentation, tissue or cell graphs, spatial pathology, multiplex pathology, and multiparametric imaging. Basic WSI tile extraction should stay with histolab, DICOM tag/anonymization work with pydicom, IDC/TCIA/DICOMWeb retrieval with imaging-data-commons, and OMERO server or ROI management with omero-integration.
## When to Use This Skill
Apply this skill for:
- Loading and processing whole-slide images (WSI) in various proprietary formats