WORKSHOP: Spatial omics sampler

This record includes training materials associated with the Australian BioCommons workshop ‘Spatial omics sampler’. This workshop took place on 25 February 2025.

Event description

This workshop provides a practical introduction to comparative analysis of spatial omics data. Starting with a pre-processed in situ spatial dataset, we will undertake some basic differential expression, look at differences of proportions of cell types, and exploratory plotting. We will work in R, using mostly Bioconductor tools. We will use a cosMx dataset, but these approaches are applicable to other technologies like Xenium or vizgen.

Along the way we will discuss considerations specific to spatial analyses, how to scale it up to a full analysis, and how to assess our results. We will also introduce the Spatial Sampler collection of worked examples and code snippets for analyses on spatial datasets.

Lead trainer and content developer: 

Dr Sarah Williams, QCIF

Facilitators: 

Fred Jaya, Sydney Informatics Hub, University of Sydney

James Sinclair, Griffith University

Infrastructure provision: 

Dr Giorgia Mori, Australian BioCommons

Dr Mitchell O'Brien, Sydney Informatics Hub, University of Sydney

Uwe Winter, Australian BioCommons

Coordination and host:

Dr Melissa Burke, Australian 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.

• 2026-02-25 Spatial_Sampler_slides (PDF): The slides presented during this workshop

Materials shared elsewhere:

Training materials including detailed notes, exercises and code: https://swbioinf.github.io/spatial-taster-workshop/

Rmd files of R code used during the workshop via GitHub: https://github.com/swbioinf/spatial-taster-workshop