Welcome to QuPath!

This page hosts the documentation for QuPath 0.6.x.

The latest release is QuPath 0.6.0. To read up on the latest changes, check out the release notes

Quick links

Can’t install QuPath?

Check out Installation for instructions & solutions to common problems

Images won’t open?

See Supported image formats to find out which formats should work - and ways to increase this.

Not sure where to begin?

See First steps for a quick guide, before heading to Tutorials for more details & videos

Got more questions?

The Scientific Community Image Forum is the best place to discuss QuPath with users & developers

Full contents

• Introduction
  • What is QuPath?
  • Installation
  • Supported image formats
  • License & Acknowledgements
  • How to cite QuPath
  • Extensions
  • 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
• Scripting
  • Workflows
  • Workflows to scripts
  • Custom scripts
  • Scripting setups
• Deep learning
  • Deep Java Library
  • Bioimage Model Zoo
  • InstanSeg
  • StarDist
  • WSInfer
  • GPU support
• Advanced
  • ImageJ
  • Exporting images
  • Exporting annotations
  • Command line
  • OMERO
  • View tracker
• Reference
  • FAQs
  • Shortcuts
  • Commands
  • Configuration
  • Building from source
  • Styling QuPath
  • Project structure