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Contents:

  • Introduction
  • Getting started
  • Tutorials
  • Concepts
  • Advanced
  • Scripting
  • Reference
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Welcome to QuPath!ΒΆ

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
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