WORKSHOP: Spatial omics

This record includes training materials associated with the Australian BioCommons workshop ‘Spatial omics. This workshop took place over two sessions on 28 - 29 October 2025.

Event description

Spatial omics provides unprecedented opportunities for the understanding of cells, tissues and systems by combining omics and imaging technologies.

This hands-on workshop will show you how to analyse data from in situ spatial (e.g. CosMx, Xenium) experiments with Seurat in R to visualise gene expression within tissue samples. Using real-life experimental data we step through the process of reading in data, quality control, filtering, dimensionality reduction, visualisation and differential expression analysis. We will discuss the ‘why’ behind each step and essential best practices for designing and running spatial omics experiments.

Lead trainers: 

Dr Sarah Williams, QCIF.

Fred Jaya, Sydney Informatics Hub, University of Sydney and Australian BioCommons

Facilitators:

Dr Nicholas Matigian, QCIF

Dr Ciccy Wang, Garvan Institute of Medical Research

Dr Mitchell O’Brien, Sydney Informatics Hub, University of Sydney and Australian BioCommons

Dr Amarinder Singh Thind, Sydney Informatics Hub, University of Sydney and Australian BioCommons

Infrastructure provision: 

Dr Mitchell O’Brien, Sydney Informatics Hub, University of Sydney and Australian BioCommons

Dr Giorgia Mori, Australian BioCommons

Host:

Dr Melissa Burke, Austrlaian BioCommons

Training materials

Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.

Files and materials included in this record:

• Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.

Materials shared elsewhere:

• Training materials including detailed notes, exercises and code:  https://swbioinf.github.io/intro-spatial-transcriptomics-workshop/index.html
• Rmd files of R code used during the workshop via GitHub: https://github.com/swbioinf/intro-spatial-transcriptomics-workshop