alterlab-pathml
CommunityStreamline computational pathology workflows.
Education & Research#pathml#pathology#graph-analysis#computational-pathology#multiparametric-imaging#tile-based-processing
AuthorAlterLab-IEU
Version1.0.0
Installs0
System Documentation
What problem does it solve?
PathML-based toolkit for end-to-end computational pathology workflows, unifying image loading, preprocessing, segmentation, graph construction, and ML deployment into a modular framework.
Core Features & Use Cases
- End-to-end PathML pipelines for loading, preprocessing, segmentation, graph analysis, and model inference.
- Multiparametric imaging support (CODEX, Vectra, MERFISH) with integrated QC and data management.
- Scalable processing for large whole-slide datasets via tile-based processing, distributed computing, and HDF5/AnnData export.
- Real-world use case: construct cell graphs from tissue sections and run ML models to classify cell types.
Quick Start
Load a pathology slide, apply a predefined PathML pipeline, and export results to disk.
Dependency Matrix
Required Modules
None requiredComponents
references
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: alterlab-pathml Download link: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/archive/main.zip#alterlab-pathml Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 471,000+ vetted skills library on demand.