histolab

Automate whole-slide image processing for tissue detection, tiling, and dataset preparation.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Histolab provides end-to-end tooling for digital pathology workflows, automating tissue detection, tile extraction, and dataset curation from whole-slide images (WSIs) to scale analysis and model training.

Core Features & Use Cases

  • End-to-end WSI processing with tissue masking, tiling strategies (RandomTiler, GridTiler, ScoreTiler), quality control, and visualization.
  • Use cases include creating balanced training datasets, conducting whole-slide analysis, and tissue characterization across H&E or IHC slides.

Quick Start

Load a sample slide and run a tiler to generate training tiles.

Frequently Asked Questions about histolab

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

FAQPage Schema
How do I extract tiles from whole-slide images for deep learning training?▼

You can extract training tiles by loading a whole-slide image into a Slide object and applying a tiling strategy like RandomTiler, GridTiler, or ScoreTiler to automatically detect tissue and extract actionable tiles for deep learning datasets.

What tiling strategies are available for digital pathology dataset preparation?▼

Digital pathology dataset preparation supports RandomTiler for exploratory sampling, GridTiler for systematic coverage, and ScoreTiler for quality-ranked extraction, allowing flexible training data curation from whole-slide images.

How does tissue mask detection work in whole-slide image processing?▼

Tissue mask detection in whole-slide image processing filters out non-tissue regions using pluggable mask pipelines, ensuring that only relevant tissue areas are processed during tile extraction and dataset curation.

Can I use histolab for both H&E and IHC slide analysis?▼

Yes, whole-slide image processing supports tissue characterization and analysis across both H&E and IHC slides, enabling balanced training dataset creation and exploratory tile sampling for various histology workflows.

What is the best way to automate end-to-end whole-slide image processing?▼

End-to-end whole-slide image processing is automated through pluggable architecture classes like Slide, TissueMask, and tiling strategies, handling tissue detection, tile extraction, and dataset curation without manual intervention.

Do I need any specific dependencies to run whole-slide image tiling?▼

No external dependencies are required to run whole-slide image tiling, as the processing architecture operates independently with its own Slide, TissueMask, and tiling classes to generate actionable tiles.