Course Modules

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1. Introduction
2. Microscopy Image Basics
3. Image Enhancment and Annotation
4. Cell Detection
5. Training a classifier

Module 1: Introduction to QuPath

Learning Objectives

Understand what QuPath is and why it's used for digital pathology.
Explore QuPath’s interface for handling whole-slide images.
Learn about basic image properties and how to view them in QuPath.

Key Concepts

Use the arrows below to learn about QuPath and how it was created.

Downloads

Here are some useful links to get started:

QuPath Download

Obtain the latest QuPath release from GitHub or official website.

Download QuPath

Sample Data

Test files (e.g., Hamamatsu) for digital slide analysis.

Download Samples

Using QuPath Desktop

Practice Exercise

Download and install QuPath (or use a portable release if provided).
Obtain or open a sample whole-slide image from the provided link.
Explore the QuPath interface: create a project or drag-and-drop a single file.
Set your image type (e.g., Brightfield (H-DAB)) in the Image tab and inspect image properties.

Quick Quiz

1. What is QuPath primarily designed for?

General-purpose web development High-throughput bioimage analysis of whole-slide images Basic text editing and note-taking

2. Who created QuPath?

Pete Bankhead MathWorks, Inc. A group of undergraduates as a semester project

3. QuPath can be used to...

View & annotate whole-slide images Play multi-player online games Edit PDF files

4. Which of the following is TRUE about opening images in QuPath?

You cannot open images without creating a project first You can drag & drop a single file, but you might lose some project-based features QuPath only supports BMP images