WORKSHOP: Spatial omics sampler

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: Dr Sarah Williams, Senior Bioinformatician, QCIF Ltd.

Date/Time: 25 February 2026, 2 - 4 pm AEDT / 1 - 3pm AEST / 1:30 - 3:30 pm ACDT / 11 - 1 pm AWST (check in your timezone).

Location: Online

Learning outcomes:

By the end of the workshop you should be able to:

• Undertake basic differential expression analysis of spatial omics data in R
• Outline considerations for spatial analyses
• Use Spatial Sampler to identify worked examples relevant to your work

This workshop will NOT cover:

• QC and filtering of the data for further analysis
• PCA, UMAP and clustering analyses to group and visualise cells

Who the workshop is for:

This workshop is for people using or planning to use spatial transcriptomics in their work. It is suitable for newcomers to spatial analyses.

You must be associated with an Australian organisation for your application to be considered.

Prerequisites

• Recommended: basic knowledge of spatial omics technology and analysis is helpful but not essential. We recommend watching our introductory webinar Getting started with spatial omics.
• Required: R skills. 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, Tuesday 11 February 2026.

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, and QCIF 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