QuPath bioimage analysis workshop

QuPath is an open-source bioimage analysis software. During this interactive workshop, you will learn how to visualize images, annotate objects, create pixel classifiers, and detect and classify objects in order to extract quantitative data.

!Please note that QuPath can open but is not ideally suited for time lapse or 3D data, it is mainly a tool for whole slide image (WSI) and fluorescent images analysis (2D)!

Planned Outline

1. Introduction

2. Hands on exercises on an example dataset

• General usage
• Data and project structure
• Cell segmentation
• Pixel and object classification
• StarDist (+ other segmentation) implementation
• Workflow automation

3. Bring your own images and test the analysis on them

Additional information

• Registration is mandatory as seats are limited and places will be distributed on a first-come first-served basis.
• You need to bring along to bring your laptop.
• The workshop is free but no-show fees of 50CHF will be applied in absence of cancellation 24h prior to the workshop.
• We kindly ask you to be present for all hands-on sessions in case you are registering.
• Using a work-email address (@unibas.ch / @fmi.ch / @iob.ch / @psi.ch / @ethz.ch) for registration is mandatory.
• Further details will be communicated after the registration, before the start of the course.