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.