Welcome to QuPath!

This page hosts the documentation for QuPath 0.3.

Using QuPath v0.1.2?

The original documentation for v0.1.2 is still available on GitHub.

Contents:

• Introduction
  • What is QuPath?
  • Installation
  • Supported image formats
  • Acknowledgements
  • How to cite QuPath
  • QuPath versions
• Getting started
  • First steps
  • Viewing images
  • Annotating images
  • Manual counting
  • Two essential tips
  • Getting help
• Tutorials
  • Projects
  • Separating stains
  • Detecting tissue
  • Measuring areas
  • Cell detection
  • Cell classification
  • Density maps
  • Exporting measurements
  • Multiplexed analysis
  • Pixel classification
  • Superpixels
• Concepts
  • Overview
  • Images
  • Processing & analysis
  • Objects
  • Object hierarchy
  • Classifications
  • Measurements
• Advanced
  • ImageJ
  • Exporting images
  • Exporting annotations
  • StarDist
  • Command line
  • OMERO
• Scripting
  • Workflows
  • Workflows to scripts
  • Custom scripts
• Reference
  • FAQs
  • Shortcuts
  • Commands
  • Configuration
  • Building from source
  • Project structure