Introduction

Welcome to the QuPath workshop book!

Here you’ll find all the content we plan to cover during the workshop (and some sneaky extras we won’t have enough time for).

We hope you’ll follow along during the workshop on your own device.

To help us get started quickly, there are a few things you’ll need to do in advance.

Table of contents

Before the workshop

• Setup
• Install extensions
• Download images

Part 1: Getting started

• How do I open an image?
• How do I change colours?
• How do I create a project?
• How do I find my way around?

Part 2: Annotating images

• How do I draw annotations?
• How do I detect tissue?

Part 3: Detecting & measuring

• How do I handle multi-channel images?
• How do I count positive cells?
• How do I view measurements?

Part 4: Classifying & exporting

• How do I classify cells?
• How do I export results?

Extras

• How do I do batch processing?
• How do I make figures?
• How do I manage images?
• How do I write scripts?