2025 QuPath Training Course: From Samples to Knowledge

Hands-on training in QuPath

Join us for 2 days of practice with QuPath on February 24-25. We’ll provide example datasets and step-by-step tutorials to take you from the first steps in QuPath through advanced work with the latest segmentation algorithms. Along the way, we’ll discuss histological sample preparation and avoiding artifacts to ensure that the images you are analyzing are as good as can be!

This year, the focus will be on multiplex immunofluorescence analysis. mIF presents unique challenges in image analysis- higher sample heterogeneity and staining noise, overwhelming numbers of phenotype combinations, and volumes of data that challenge even high-end computers. Dr. Sara McArdle, Mr. Mike Nelson, and Dr. Zbigniew Mikulski will discuss our experiences with mIF and the best practices we’ve found to:

• Segment and classify cells
• Manage large project files
• Combine information from multiple rounds of staining or IF + H&E
• Analyze spatial patterns

Bring your laptop and a mouse! Lunch and coffee will be provided, as well as a networking dinner on Monday, Feb 24.

For more information about what this workshop will be like, you can find the 2023 workshop on YouTube.

Following the training course, there will be an Advanced Users Meeting on Wed, Feb 26. In a smaller group to facilitate deep discussion, we’ll each present our ongoing projects, the image analysis challenges we are facing, or any useful tools/scripts we’ve created. We can help each other do better and faster science while promoting our work and growing the QuPath community!

Space is limited, so we ask everyone interested in joining to submit a very short abstract about what they would like to talk about at the meeting- only 100-200 words. There is no additional fee for this meeting. We will review applications on a rolling basis; the deadline to apply is Jan 30.

Host or Publisher La Jolla Institute