What image formats does the Histolab skill support?

Histolab supports various pyramidal whole slide image formats common in digital pathology, including SVS, TIFF, and NDPI.

How does Histolab handle artifacts and background noise?

It uses automated tissue masks and morphological filters to identify informative tissue regions and exclude slide background, pen marks, or artifacts.

What tiling strategies are available?

You can use RandomTiler for diverse sampling, GridTiler for full coverage, or ScoreTiler to select tiles based on specific metrics like nuclei density.

Can I use this skill to prepare data for neural network training?

Yes, the skill is specifically designed to extract small tiles from large slides, filtering for tissue content to create clean datasets for deep learning.

Histolab WSI Processing

Name: Histolab WSI Processing
Author: Sologa

bySologa

0•

데이터 과학 및 ML

Automates tissue detection and tile extraction from whole slide images for digital pathology and machine learning workflows.

Histolab provides a specialized interface for handling gigapixel whole slide images (WSI) in digital pathology pipelines. It simplifies the complex task of identifying tissue regions, filtering out background artifacts, and extracting informative tiles for deep learning model training. By providing multiple tiling strategies—including random, grid, and score-based—and integrated preprocessing filters, it serves as an essential tool for researchers and pathologists building automated analysis systems and preparing high-quality datasets.

주요 기능

01Advanced tile scoring based on nuclei density and cellularity

02Multi-strategy tile extraction (Random, Grid, and Score-based)

03Automated tissue detection and binary masking

04Support for multiple WSI formats including SVS, TIFF, and NDPI

05Integrated image processing and morphological filters

060 GitHub stars

사용 사례

01Large-scale spatial analysis and tile-based feature extraction

02Automated tissue segmentation and artifact removal in slide images

03Preparing image datasets for deep learning pathology models

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sologa/codex-pipeline histolab

For use in Claude.ai and ChatGPT

Download Skill