pathml

Load, preprocess, and analyze whole-slide images with modular pipelines.

15|2|Updated Dec 17, 2025
One-click install
npx skills add https://github.com/rubensliv/k-dense-ai --skill pathml-rubensliv
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: pathml
Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/pathml
Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill pathml-rubensliv

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

PathML streamlines computational pathology workflows by providing an end-to-end toolkit for WSIs and multiparametric imaging.

Core Features & Use Cases

  • Modular preprocessing pipelines to load, normalize, and segment pathology images.
  • Graph construction and spatial analysis for tissue and cell architectures.
  • Prebuilt ML models (HoVer-Net, HACTNet) and end-to-end ML workflows.
  • Data management and reproducibility with HDF5 and dataset versioning.

Quick Start

Install PathML and run a basic preprocessing pipeline on a sample whole-slide image to see PathML in action.

Frequently Asked Questions about pathml

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I build machine learning pipelines for whole-slide imaging data?

You can build machine learning pipelines for whole-slide imaging by using a toolkit that loads diverse slide formats, applies modular preprocessing, and trains prebuilt models like HoVer-Net for end-to-end pathology workflows.

What is computational pathology graph construction and when is it needed?

Computational pathology graph construction maps spatial relationships between tissue and cell architectures. It is needed when analyzing multiparametric imaging data to extract structural insights beyond standard pixel-based segmentation.

Can I use HDF5 for managing whole-slide imaging datasets?

Yes, you can use HDF5 for managing whole-slide imaging datasets. It enables data storage and dataset versioning to ensure reproducible, scalable pathology research across large multiparametric imaging cohorts.

Does this approach support multiparametric imaging analysis across biology and medicine?

Yes, this approach supports multiparametric imaging analysis across biology and medicine. It provides modular preprocessing pipelines and prebuilt ML models to analyze diverse spatial and cellular architectures.

What's the best way to normalize and segment whole-slide pathology images?

The best way to normalize and segment whole-slide pathology images is through modular preprocessing pipelines that systematically load, normalize, and segment slides before constructing spatial graphs for analysis.

Are there limitations when training custom ML models on whole-slide images?

While prebuilt ML models like HoVer-Net and HACTNet are available for whole-slide images, custom model training relies on the toolkit's modular pipeline architecture, meaning scalability depends on your HDF5 data management setup.