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