Spatial biology is the study of how individual cells fit within the context of a tissue, what their environment says about their behavior, where they are and why they are there. In this course, we provide an introduction to spatial transcriptomics and spatial proteomics methods, introduce you to the existing spatial omics microscopy systems in the facilities in Basel, and go through their basic analysis pipelines.

This workshop is articulated in two parts: A general introduction in the morning and hands-on sessions in the afternoon.

The general introduction (9:15-12:00, at the D-BSSE room D65.2)

General introduction to spatial biology, including spatial transcriptomics and spatial proteomics, commercially available solutions and custom-designed protocols.
Please note that for the morning only, registration is not required.

Hands-on session (13:15-17:00)

In the hands-on sessions, participants will learn how to run basic cell segmentation and data visualization of spatial omics datasets using SOPA and QuPath.
For participation in the hands-on session, registration is required, and the presence in the theory sessions is mandatory.
Prior experience with basic programming is a plus.

Registration with a professional email address is mandatory (e.g., @unibas.ch, @fmi.ch, @iob.ch, @psi.ch, @ethz.ch).

The hands-on session is free of charge; however, a no-show fee of 50 CHF will apply if you do not cancel at least 24 hours in advance.

We kindly ask that you attend the full hands-on session if you register.

Introduction to Spatial Biology