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Introduction

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?

Index

By Peter Bankhead, Alan O'Callaghan, Fiona Inglis, Laura Nicolas Saenz, Leo Leplat

© Copyright 2025-2026.