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, Senior Bioinformatician, QCIF Ltd.
Fred Jaya, Senior Bioinformatician (Australian BioCommons), Sydney Informatics Hub, University of Sydney.
Date/Time: 28 -29 October 2025, 1 - 4 pm AEDT /12- 3pm AEST / 12:30 - 3:30 pm ACDT / 10 - 1 pm AWST
Format:
This online workshop will take place over two sessions. You must attend both sessions in order to get the most out of the workshop. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action.
Learning outcomes:
By the end of the workshop you should be able to:
Load CosMx data into a Seurat object and annotate it
Perform QC and filter the data for further analysis
Visualise tissues and gene expression
Perform PCA, UMAP and clustering analyses to group and visualise cells
Perform differential expression analysis
Who the workshop is for:
This workshop is for Australian researchers who have or will work on spatial transcriptomics data as part of their projects. You must be associated with an Australian organisation for your application to be considered.
Prerequisites
You should have basic knowledge of spatial omics technology - we recommend watching our introductory webinar Getting started with spatial omics.
You should also have some familiarity with R. While you don’t need to be an expert, being able to work with tables of data, load an R library and make basic plots (ideally with ggplot2) will help you get the most out of the workshop.
How to apply:
This workshop is free but participation is subject to application with selection.
Applications close at 11:59 pm AEDT, Friday 10 October 2025.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. More information on the selection process is provided in our Advice on applying for Australian BioCommons workshops.
This workshop is presented by Australian BioCommons, QCIF Ltd. and the Sydney Informatics Hub with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to the Australian BioCommons newsletter