pathml
Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.
npx skills add LeonChaoX/qinyan-academic-skills --skill pathml --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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. ## When to Use This Skill Apply this skill for: - Loading and processing whole-slide images (WSI) in various proprietary formats - Preprocessing H&E stained tissue images with stain normalization - Nucleus detection, segmentation, and classification workflows - Building cell and tissue graphs for spatial analysis - Training or deploying machine learning models (HoVer-Net, HACTNet) on pathology data - Analyzing multiparametric imaging (CODEX, Vectra, MERFISH) for spatial proteomics - Quantifying marker expression from multiplex immunofluorescence - Managing large-scale pathology datasets with HDF5 storage - Tile-based analysis and stitching operations ## Core Capabilities PathML provides six major capability areas documented
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Image Loading & Formats
- 2. Preprocessing Pipelines
- 3. Graph Construction
- 4. Machine Learning
- 5. Multiparametric Imaging
- 6. Data Management
- Quick Start
- Installation
- Basic Workflow Example
- Common Workflows
- References to Detailed Documentation
Install PathML uv pip install pathml With optional dependencies for all features uv pip install pathml[all]
What does the pathml skill do?
Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill pathml --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.