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histolab — Claude Code skill: what it does, how to install

Prepares whole-slide histology images by segmenting tissue masks, extracting tiles, and normalizing H&E staining.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill histolab -a claude-code
Open on GitHub

What histolab does

This skill guides preprocessing of whole-slide histology images (WSI) using histolab 0.7.0. It inspects metadata across pyramid levels, generates TissueMask or BiggestTissueBoxMask outlines, and extracts image tiles for downstream datasets.

Tile extraction relies on RandomTiler, GridTiler, and ScoreTiler. The mask must be passed directly into locate_tiles() and extract(), with preview methods returning Pillow images. Nuclei and cellularity scores are heuristic area measurements rather than calibrated cancer probabilities.

Histolab requires Linux or macOS, native OpenSlide, and Python 3.8 to 3.11. Windows is not supported. The 0.7.0 release depends on tightly pinned legacy packages like NumPy 1.24.4 and SciPy 1.10.1, so attempting to run it inside a modern Python 3.12 environment will fail.

What it helps with

  • segment tissue boundaries on whole-slide images
  • extract image tiles using random or grid layouts
  • rank tissue sections by cellularity using ScoreTiler
  • standardize H&E slide staining before training models

Example prompts for the agent

  • Generate a TissueMask for slide.svs and extract 100 random tiles at level 0
  • Configure GridTiler with overlap to process tissue sections without gaps
  • Score candidate tiles and save the highest ranked images to a directory

How to install histolab

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill histolab -a claude-code

2Manually: put the files in place

~/.claude/skills/histolab/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/histolab/

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Questions about histolab

How do I install histolab in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill histolab -a claude-code. The skill specification will be installed to ~/.claude/skills/histolab/SKILL.md.

What does the histolab skill do?

It orchestrates WSI inspection, tissue mask creation, tile extraction workflows, and H&E stain normalization. For multiplexed imaging or neural network inference, upstream documentation recommends pathml instead.

What dependencies does histolab require?

You need Linux or macOS, native OpenSlide libraries, and Python between 3.8 and 3.11. The 0.7.0 release does not support Windows.

See also

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